This article isThis article by protected copyright. All rights reserved. 10.1111/mec.14486 doi: thisarticle as differences to lead between the of this version cite and Version Record.Please copyediting, paginationbeen throughthe andproofreadingtypesetting, process,may which This article acceptedhas been for publication andundergone fullpeer review buthasnot ‘species’ the in fields research shift many paradigm affects species any of and delimitation science biodiversity of cornerstone the is concept species The Abstract science biodiversity in Cryptic species head: Running 390 +386 12573 , fax: 3203371 +386 1 phone: Slovenia; Ljubljana, 101, Jamnikarjeva Ljubljana; Cene Fišer, correspondence: Author for speciation niche conservatism, phylogenetic words Key Villeurbanne, France. 69622, Dubois, Raphaêl 6Rue Lyon, Université de 4 3 2 Slovenia. Ljubljana, Cene concept awindow intoCryptic as species paradigm species the shift ofthe Syntheses and Reviews :Invited Article type 0000 ID: (Orcid FIŠER DR. CENE 1 UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, 1,ENTPE, Université Lyon et Anthropisés, Naturels Hydrosystèmes Ecologie des UMR5023 SubBio Lab, Dept. of Biology, Biotechnical Faculty, University of Ljubljana; Jamnikarjeva 101 Jamnikarjeva ofLjubljana; University Faculty, Biotechnical Biology, Dept. of Lab, SubBio Accepted Article Switzerland. 8092Zürich, ETH Zürich, Biology, Integrative of Institute Switzerland Dübendorf, 8600 133, Überlandstrasse Ecology, Aquatic Dept. Eawag, Fišer paradigm as separately evolving populations using different delimitation criteria delimitation different using populations evolving separately as paradigm 1 , : Amphipoda, biodiversity patterns, convergent evolution, integrative taxonomy, taxonomy, integrative evolution, convergent patterns, biodiversity Amphipoda, : [email protected] ; SubBio Lab, Dept. of Biology, Biotechnical Faculty, University of University Faculty, Biotechnical ofBiology, Lab,Dept. SubBio ; [email protected] Christopher Christopher T. Robinson 8724) -0003-1982- 2,3 , Florian Malard Florian

. 4

Many biologists now are embracing a new new a embracing are now biologists Many . Individual Individual , This article isThis article by protected copyright. All rights reserved. what i.e. issues, Accepted 2004). et al., (Agapow and macroevolution conservation ecology, biogeography, taxonomy, including fields, research important many affects directly concept a because 1997) Mayden, 2005b; 1998, Queiroz, (de 1997) science biodiversity (Mayden, definitions species 24 than less no yielded to challenging most the proven has them Among biodiversity. of components major three are ecosystems and species Genes, INTRODUCTION 1. uncertainty. species for accommodating while conservation biodiversity into integration allowing thus taxa, and space incorporat for time coexistence. species and distribution, species in variation geographic assessments, biodiversity process and patterns biodiversity regarding insights novel to leads species Articleinto distance-based towards biased formal of importance heavily the stress also We methods. is species cryptic of delimitation molecular that show we taxonomy, regarding section next the In diversification. morphological of mechanisms studied a phenomenon, evolutionary an is diversification morphological of species cryptic integrate to is review this of aim The theory. evolutionary and ecological of tests current in considered poorly are but phyla animal diverse from reported being continuously are they shift: paradigm this within fall category species and process speciation the in heterogeneity inherent evolve this to relates concept species the in shift paradigm never may some speciation; of periods different during emerge can criteria research fields that use species as units of analysis of units as species use that fields research An important step forward was made with with made was forward step important An a species is and how they should be delimited (Bock, 2004; Hey, Waples, Arnold, Arnold, Waples, Hey, 2004; (Bock, delimited be should they how and is species ing – which is fundamentally overlooked in biodiversity research. Cryptic species species Cryptic research. biodiversity in overlooked fundamentally is which multi-criteria species approaches aiming to understand speciation across across speciation understand to aiming approaches species multi-criteria biodiversity science. In the first section, we address that the absence absence the that address we section, first the In science. biodiversity in co nceptualize . ly a Decade-lasting disputes over the species concept concept species the over disputes Decade-lasting naming of cryptic species for better integration integration better for species cryptic of naming distinction between conceptual and operational operational and conceptual between distinction . Finally, we show that incorporating cryptic cryptic incorporating that show we Finally,

. Defining a species is central to to central is species a Defining ‘ process ny ’ counterpart to the long- the to counterpart es change in the species species the in change , including large-scale large-scale including , . As such, a a such, As , species species It is is This article isThis article by protected copyright. All rights reserved. heterogeneity in Accepted integrate speciation we can hypotheses, species among heterogeneity to leads process speciation the in heterogeneity If hypotheses. species and process speciation the between links speciation of nature heterogeneous with the contingent properties are whose hypotheses of set heterogeneous a represent taxa species that recognition is development methodological and conceptual this of outcome The 2011). al., et Yeates 2010; Vences, & Riva, la De tested iteratively are which 2003), al., et Hey 2007; Queiroz, (de entities evolving separately of hypotheses 2015). merely considered be Flot, should methods & these with delimited (Dellicour taxa species Furthermore, speciation of context the on depended accuracy whose 2004), 2003, Marshall, & Sites 2007; Pearson, & Rabibisoa, Ingram, Raxworthy, 2015; Tang, & Flot, (Fontaneto, premises different on based methods delimitation species of proliferation prompted delimitation species a delimit universally would that property 2007) 2005a, Queiroz, (de all at if order, sequential and Articlethe of evolution the However, evidence monophyly and isolation reproductive distinguishability, express are that properties different on depends 2016) al., et Roux 2004; (Bock, extinction) or speciation (further species this to end an putting event by and process, this of origin the at event, speciation a by framed is species a view, of point temporal a From challenge. a remains Glossary), (see research biodiversity in used units elementary i.e. taxa, species and concept species the between correspondence the Establishing lineages metapopulation of segments evolving separately as process speciation the from emerging entities are species that 2003) Harrison, & Butlin, using new methods and data in the procedure called called procedure the in data and methods new using A central question raised by this paradigm shift is whether we can make use make can we whether is shift paradigm this by raised question central A to identify lineage divergence and thus delimit species taxa (de Queiroz, 2005 Queiroz, (de taxa species delimit thus and divergence lineage identify to evolutionary, biogeographic and ecological research? This issue has been partly partly been has issue This research? ecological and biogeographic evolutionary, . (B Most authors authors Most ock, 2004; de Queiroz, 1998; Hey, 2006; Hey et al., 2003; Mayden, 1997). 1997). Mayden, 2003; al., et Hey 2006; Hey, 1998; Queiroz, de 2004; ock, se properties is context dependent and can emerge at different times times different at emerge can and dependent context is properties to day agree conceptually (species concept, see Glossary), i.e. i.e. Glossary), see concept, (species conceptually agree day ed . during separate evolution, such as morphological asmorphological such evolution, separate during Not surprisingly, difficulties inherent to species species to inherent difficulties surprisingly, Not . These properties remain the best lines of of lines best the remain properties These “integrative taxonomy” taxonomy” “integrative .

Consequently, there is no particular particular no is there Consequently, .

. Inference of speciation speciation of Inference (Padial, Miralles, (Padial, of the explicit explicit the as a,b scientific scientific , 2007) , in . This article isThis article by protected copyright. All rights reserved. the of understanding better a fostering Accepted speciation role of thereby heterogeneous science, biodiversity into species integrating cryptic fully for agenda research a propose to is review this of aim The science. biodiversity into species cryptic from learn can we what incorporate and exploration of level phenomenological 2007) Caccone, & (Beheregaray theories evolutionary 2016) al., 2008) al., et (Derycke species nematode and 2010) Nadler, & León de (Pérez-Ponce parasite overlooked found been have even They 2007). Schwenk, & Pfenninger 2016; Poulin, & León de Ponce (Pérez- phyla animal most across widespread and 2014) Georges, & Burridge, Raadik, Adams, (M. 2007; al., et (Bickford arenas 2014) Nygren, research 1993; Knowlton, many in forefront the to species cryptic brought now morpholog similar mechanis different Article heterogeneity. al environment between understanding global and opportunity better require generalizations Further ecological 2016). Schluter, 2016; Wiens, & between (Kozak patterns biodiversity explanation mechanistic a provides speciation ecological Hence, 2016). (Schluter, importance time and space in relative vary that opportunities ecological its on depends but radiation, adaptive as such events evolutionary major underlie can 2016) Losos, & Stroud 2000b; (Schluter, evolutionar be can resources accessible ecologically when place takes It 2005). Nosil, & Rundle 2012; (Nosil, differentiation phenotypic with associated is and 2016) Losos, partitioning & resource to due Stroud diverge populations ancestral where 2016; process a is 2000a, speciation Ecological (Schluter, speciation ecological of case the in explored , but also among the largest and heavily studied mammalian species like giraffes (Fennessy et et (Fennessy giraffes like species mammalian studied heavily and largest the among also but , Over the last two decades, increased evidence emerged for speciation governed by entirely by governed speciation for emerged evidence increased decades, two last the Over . In spite of being common, they are still poorly considered in testing ecological and and ecological testing in considered poorly still are they common, being of spite In ies ms is historical (Mayr, 1942), but the use of molecular delimitation methods has methods delimitation molecular of use the but 1942), (Mayr, historical is , leading to to leading , . Indeed, we are now aware that cryptic species are quite common common quite are species cryptic that aware now are we Indeed, so in biodiversity pattern and process. process. and pattern biodiversity -called sibling or cryptic species cryptic or sibling -called and speciation relationships, especially regarding speciation speciation regarding especially relationships, speciation and . Ecological speciation can contribute to speciation rates and and rates speciation to contribute can speciation Ecological . It . is timely to intensify research beyond the the beyond research intensify to timely is

y exploited (ecological opportunity) opportunity) (ecological exploited ily . The idea that species can evolve evolve can species that idea The in mostly mostly . This article isThis article by protected copyright. All rights reserved. Accepted 2). 1, Fig. (Box studies eco-evolutionary in well-studied comprise relatively are they thus and types, Importantly, ecological different indicators. within species cryptic biological numerous as used often are and function, ecosystem in role crucial a play environments, aquatic most in thrive diverse, ecologically rich, species are They morphological Amphipoda the to search literature our limit) not (but focus we diversity, cryptic on status research current the regarding evaluation science. biodiversity enhancing towards directions research promising and research biodiversity in gaps major identify to facets these use we Lastly, science. biodiversity gain into speciation of properties) be (or hypotheses different can incorporating what specifically, more and, research biodiversity into integrated been have understanding improve Article2010) al., et Padial 2015; al., DNA et Fontaneto of 2013; Sites, & fields (Camargo taxonomy burgeoning integrative and taxonomy the into look we Here, distinguishability. morphological of absence the in boundaries species identify to used currently species of properties contingent other explore from them reconsider and species cryptic delimiting in practices the review we Second, mechanism. each elucidate better to tests novel suggest and evidence empirical w recent Here, convergence. i.e., morphological lineages; and conservatism, divergent niche divergence, among distinguishability morphological of lack the explaining mechanisms exclusive non-mutually three explore We perspective. evolutionary an from similarity First, 1). (Fig. science biodiversity , highlighting the recurrent need for naming species. We show how integrative taxonomy can can taxonomy integrative how show We species. naming for need recurrent the highlighting , data-driven provide To phyla. animal all to apply review this in discussed ideas The goal this Towards ly cryptic species, underlying speciation and its relationship to biodiversity science. science. biodiversity to relationship its and speciation underlying species, cryptic of , morphological cryptic evolution. Third, we discuss how cryptic species species cryptic how discuss we Third, evolution. cryptic morphological we examine three inter-related facets of cryptic species in respect to to respect in species cryptic of facets inter-related three examine we . we Amphipods are an excellent invertebrate model for studying studying for model invertebrate excellent an are Amphipods reconsider and define the phenomenon of phenotypic phenotypic of phenomenon the define and reconsider

a taxonomic perspective. W perspective. taxonomic e evaluate the existing existing the evaluate ed by by e This article isThis article by protected copyright. All rights reserved. Accepted to29. papers relevant of thenumber whichreduced Miocene), trees phylogenetic in age node of w Here, 2016). al., et (Egea evident not is presently differentiation morphological and recently diverged have species namely conservatism distinguishability, morphological of lack the explaining hypotheses related three regarding information for searched we articles, 120 these From 2.1. Information). Supporting also (see below topics three the to relevant were that for information of categories searched several were articles Individual time. first the for discovered species cryptic total) 439 the the remaining contain Article collectively morphospecies These subspecies. no contained morphospecies of list The distinctness. morphological their of basis a on delimited were that species i.e., morphospecies, or amphipods of total a yielding removed, duplicates and checked were titles All 2015). September on made was (search 2015 and 2000 between period the analyzed we hence results, no yielded 2000 year the before search The and species) taxonomy). keywords molecular sibling * (Amphipoda/Amphipods using and * phylogeography) Science * (Amphipoda/Amphipods of (Amphipoda/Amphipods Web species), ISI cryptic the in * articles (Amphipoda/Amphipods relevant for searched we reason, this a as detected often were species Cryptic DATA OFLITERATURE 2. COMPILATION Mechanisms causing cryptic diversity cryptic diversity causing Mechanisms ed a total of of total a and 109 morphological convergence. convergence. morphological e morphospecies represent 304 (295-315, depending on the delimitation method of of method delimitation the on depending (295-315, 304 represent morphospecies articles. From this search, our review covers covers review our search, this From articles. 120 analyzed the distribution of age of the cryptic species using reported estimations estimations reported using species cryptic the of age of distribution the analyzed cryptic species. Of species. cryptic 439 . Descriptive estimations of age were discarded (e.g., early early (e.g., discarded were age of estimations Descriptive by 2 nominal species, species, nominal 122 -product in phylogeographic studies of amphipods. For For amphipods. of studies phylogeographic in -product The The recent divergence divergence recent eet divergence recent

13 were found to be synonyms, but synonyms, be to found were 2 morphological species of of species morphological 122 hypothesis posits that cryptic cryptic that posits hypothesis , phylogenetic niche niche phylogenetic This article isThis article by protected copyright. All rights reserved. considered be not may ago decade a used delimitation species for Accepted methods molecular that genes, such nuclear and mitochondrial allozymes, field evolving rapidly a is taxonomy DNA (SNPs). polymorphisms nucleotide single and microsatellites included markers Molecular species. cryptic delimit to used methods the as well as markers molecular of type and number the reviewed We isolation genetic of criteria the using bedelimited can taxa that species and entities, evolving separately are species that premise the on based is research past of analysis as considered they what evaluation the reason, this rarely Authors cryptic species in delimiting practices 2.2 Taxonomic each other. that species cryptic of proportion the quantified we reason, this For evolution. convergent through independently evolved species cryptic of similarity morphological whether explored we Here, 2009). al., et Trontelj 2014; al., et (Bravo pressures selection similar Article to response in species distantly-related among independently evolve may similarity morphological The origins. independent parsimonious ancestor We level. micro-niche the at specialized ecologically were that species sister of complexes among species cryptic of reports for searched we hypothesis, this matching potentially species cryptic of cases identify To 2011). Melville, & Shoo, Harmon, Smith, 2016; al., et Egea 2014; Brumfield, & Remsen, (Bravo, stasis morphological as known phenomenon a selection, by constrained is species descendant across differentiation morphological The conservatism niche phylogenetic morphological a priori a

convergence convergence referred to a well-defined species concept while delimiting species taxa. For For taxa. species delimiting while concept species well-defined a to referred ly

expla ins specialization specialization ins hypothesis also is based on selection and assumes that that assumes and selection on based is also hypothesis hypothesis ass umed

that a single origin of narrow specialization specialization narrow of origin single a that (PNC) postulates that niche evolution and hence hence and evolution niche that postulates (PNC) sister descendants more than multiple and and multiple than more descendants sister in a species was not possible. The following following The possible. not was species

we re not in sister relationships with with relationships sister in not re .

in an

(Padial et al., 2010); both help link taxonomy with evolutionary biology (Sites & Marshall, 2003, 2003, 2004) Marshall, & (Sites biology evolutionary with taxonomy link help both 2010); al., et (Padial data among contradictions detect or 2010) al., et (Schlick-Steiner hypothesis species a for support additional provide either can It 2002). Penkrot, & Wiens 2010; al., et (Padial taxonomy integrative species delimit to types data different Compositing behavior. or ecology physiology, morphology, in differences for analyzed were species cryptic when cases quantified we addition, In This article isThis article by protected copyright. All rights reserved. Accepteddeli often used been have but species, delimit solely to intended not that are differentiation) recognize genetic of We indices analysis, clade exclusivity. nested (e.g. methods allelic genetic population mutual evolved therefore and flow gene by connected longer no are that populations discern to attempt 2010) al., et (Flot methods based Allele-sharing 2014) Bouckaert, & Minin, Fujita, (Leache, data genomic-scale and 2014) 2010, Rannala, & Yang O’Meara 2007; Carstens, & Knowles 2014; Reeder, & Bryson, Grummer, 2011; Carstens, & (Ence loci multiple 2013), Stamatakis, & Pavlidis, Kapli, Zhang, J. 2012; Carstens, & Reid 2006; al., et Pons 2009; al., et (Monaghan locus single using processes coalescent and species-level between point transition likely most the for Article search methods Tree-based 2012). Achaz, & Brouillet, Lambert, (Puillandre, hand at dataset the for calculated threshold best-fitting the or 2006) Gibert, & Gouy, Douady, (Lefébure, threshold fixed a using either delimited are Species species. between than within for distances genetic smaller in result categories should speciation that assume methods Distance-based 1). (Table four used we methods genetics review, population and allele-sharing this tree-based, distance-based, For namely, classification: exercise. difficult a methods different using classification any makes methodology in progress The Glossary). (see taxa species corresponding of delimitation for serves and 2007), Queiroz, (de entities evolving independently of emergence and 2004) (Bock, speciation ongoing of pointer primary a is isolation genetic Such populations. between 2015) al., et Fontaneto 2015; Flot, and 2003 2004, Marshall, & Sites of classifications the example, for (compare, today valid mi Fnly w eaie wehr rpi seis ae bnma nm ad i so if and, name binomial a have species cryptic whether examined we Finally, . tation . In fact, many authors considered genetically distinct populations as putative species. species. putative as populations distinct genetically considered authors many In fact, . All methods, albeit on different premises different on albeit methods, All

, in search for cessation of gene flow flow gene of cessation for search the past past the in respect to species species to respect is , known as as known it , 2010; Z. Z. 2010; , is based based is . This article isThis article by protected copyright. All rights reserved. above. mentioned predictions theoretical to contrast Accepted stark in is Myr 1 than younger were species cryptic 43 the of out five only but left, skewed typically was distribution age The 3). (Fig. amphipods of species cryptic 43 for estimates age obtained We 2000). &Servedio, 2016;Wiens et al., (Egea high is polymorphism ancestral is largeand 2015) Benítez, & (Zúñiga-Reinoso size population effective neutral, selectively are they young if slowly evolve traits morphological Diagnostic relatively be to expected are species cryptic hence divergence, since time on only depends distinctness morphological of evolution The time). through morphology in changes for (2003) al. et Harmon and (2009) al. et Adams e.g., (see alone processes stochastic to due increases disparity morphological that predicts model evolutionary simplest The divergence 3.1 Recent DIVERSITY CRYPTIC CAUSING 3. MECHANISMS analysis. unitsof as species cryptic using inherently thereby species, delimiting criteria for correspond second The Article efforts. conservation misled thus and patterns biodiversity of understanding our biased have might species cryptic whether explore correspond first The research. biodiversity in species cryptic incorporating of ways science. biodiversity in fields across ways different quite in integrated are they rate, ever-increasing an at documented being are species cryptic Although research biodiversity in species 2.3 Cryptic 2015). Puillandre, & Schoelinck, (Pante, biology, of other fields 2016) Renner, 2013; Schrödl, & Jörger 2010; Hardy, & Crisp, Edwards, (Cook, criteria molecular on solely . Although naming is not always done, the naming of new species integrates taxonomy with with taxonomy integrates species new of naming the done, always not is naming Although ed Here, to studies that only retain DNA-based DNA-based retain only that studies to

we distinguish between two major major two between distinguish we One explanation may be that this this that be may explanation ed to studies that that studies to . This result result This . This article isThis article by protected copyright. All rights reserved. 2015). Merceron, & Escarguel, (Clavel, regimes selective changing and evolution neutral of models between discrimination for allows that software developed recently using solved be can issue this Fortunately, evolution. trait of estimation erroneous to lead thus and evolution neutral to similar pattern a produce can also regime selection Lastly level pair species the than rather level clade the at analysis requires ones non-cryptic than younger specificity clade for account to needs hypothesis specific clade is it therefore size, population and polymorphism 2015) al., et Reis (dos papers specialized more consult should readers review; this of scope the beyond estimations age accurate First, requires research. testing future for guidelines as aspects three consider should predictions the of testing under evolve traits morphological second, and, young are species cryptic first, predictions: central two explicit studies examined the of none note, To only similarity of morphological 3 Section (see species old of biased even times at and unavoidable is studies these among estimation age in variation Some datasets. 2015) Yang, & Donoghue, Reis, (dos parameters understood poorly time of number a to over sensitive are ages estimated changed ongoing) still are (and have estimation age for used methods bias methodological invokes explanation alternative The distinctness. morphological their attain quickly species evolving thus 2008), al., et Herrel 2007; Fox, & Reznick, Hendry, (Carroll, rapid is selection environmental to response evolutionary The unlikely. is explanation mechanistic

Accepted Article relatively only delineate accurately that methods delimitation coarse used studies reviewed the , . Second, the distinction between between distinction the Second, . the neutral model of evolution (Brownian motion (Brownian evolution of model neutral the . models of evolution can be estimated from extant morphology and phylogeny, but a changing changing a but phylogeny, and morphology extant from estimated be can evolution of models Second, many evolutionar many Second, . Different authors estimated node ages using different methods, optimized for their their for optimized methods, different using ages node estimated authors Different ). Consequently a small fraction fraction small y young cryptic species might have been simply overlooked. M overlooked. simply been have might species cryptic young ily , . e ocue that conclude we This task is not easy and methodological details are are details methodological and easy not is task This “ young of ly . tested for for tested For instance, assess instance, For known cryptic species. species. cryptic known ” and , see “ divergence recent ” old Glossary eet divergence recent species depends on ancestral ancestral on depends species . Appropriate evaluation of the the of evaluation Appropriate whether cryptic species are species cryptic whether ing ) (Felsenstein 1985). Rigorous Rigorous 1985). (Felsenstein ) . Th presently explains explains presently is hypothesis has has hypothesis , es and current current and . First, the the First, . ost . This article isThis article by protected copyright. All rights reserved. selection stabilizing Acceptedconstrained is morphology of evolution First, 2010). al., et Wiens 2015; al., et (Pyron diversity cryptic causing the of predictions three discuss now We testing. ofexplicit theabsence in problematic is specialization ecological unclear to crypsis morphological attributing Regardless, amphipods. subterranean and Th 2016). Lorion, & Reimer, White, 2012; Shivji, & of species sponge-dwelling and 2010), Li, & (Hou streams mountain 2009) al., et Trontelj 2015; Fišer, & Rađa, Delić, Švara, rock in fissures body whale’s a of parts distinct on living the support might and specialized, highly ecologically were that species amphipod sister of complexes among species cryptic of cases several The 2005). &Graham, Wiens 2010; 2008;Wienset al., 2004, 2008;Wiens, (Losos, variation genetic Article of lack and adaptation, constraining effects pleiotropic adaptation, local swamping flow intention original 2015) Burbrink, & Patten, Costa, (Pyron, further elaborated was concept the recently, More time. evolutionary over niches ecological their retain to lineages some for tendency ( conservatism niche phylogenetic of concept broader the Schluter, 2009, Losos, (e.g., niche ecological its to related 2007) al., et (Bickford mechanisms biological by constrained stasis” “morphological divergence Recent (PNC) conservatism niche 3.2 Phylogenetic PNC PNC hypothesis was n was hypothesis . Morphological disparity remains constant through time, as if being constrained by by constrained being if as time, through constant remains disparity Morphological (C. Fišer & Zagmajster, 2009; Meleg, Zakšek, Fišer, Kelemen, & Moldovan, 2013; 2013; Moldovan, & Kelemen, Fišer, Zakšek, Meleg, 2009; Zagmajster, & Fišer (C. . cannot explain relatively old cryptic species. An alternative hypothesis, so called called so hypothesis, alternative An species. cryptic old relatively explain cannot The biological mechanisms underlying underlying mechanisms biological The . The model of morphological evolution inferred from extant morphology and and morphology extant from inferred evolution morphological of model The , assumes that morphological differentiation of descendant species is is species descendant of differentiation morphological that assumes , ot explicitly tested in the reviewed studies here. Nevertheless, we found found we Nevertheless, here. studies reviewed the in tested explicitly PNC PNC Klsesa t l, 2005) al., et (Kaliszewska hypothesis. These include include These hypothesis.

to stimulate future research regarding mechanisms mechanisms regarding research future stimulate is list is likely longer, especially among deep sea sea deep among especially longer, likely is list 2000a) PNC PNC , some species of of species some ,

. Since a species’ morphology is partly is morphology species’ a Since . ). Initially, Initially, ). encompass stabilizing selection, gene selection, stabilizing encompass , this hypothesis is closely related to to related closely is hypothesis this , Leucothoe , Niphargus PNC Cyamus , was used to explain the the explain to used was but here we refer to its its to refer we here but Gammarus Gammarus (Richards, Stanhope, Stanhope, (Richards, PNC species (whale lice) (whale species species colonizing colonizing species for species with with species for inhabiting inhabiting This article isThis article by protected copyright. All rights reserved. or 2013) Li, & Hou, Yang, (L. freshwater-semiterrestrial colonized independently complex cryptic Accepted same the from species where genera, amphipod several in documented were species cryptic among convergence morphological of Cases sampling. of taxon detection of because completeness estimate on depends low convergence a probably is proportion This groups. sister not were that data reviewed our 2013). Mahler, & (Ingram regimes selective similar to response in species distantly-related among evolved similarity morphological that infers hypothesis third The convergence 3.3 Morphological & Fišer,2017) temperature or pH salinity, e.g. axes, niche along in sympatry evolve supporting arguments strengthen may prediction third the note, To 2008). Smith, & Ree 2013; (Matzke, ranges geographic of evolution the of analysis requires 2005) Graham, & Wiens 2004; Wiens, 2015; al., et Pyron 2006; Wiens, & (Kozak Article2010) Porter, & Wintle, (Kearney, data experimental from or 2008) Turelli, & Glor, Warren, 2007; al., et Raxworthy 2006; Wiens, & (Kozak data distributional niches ecological share to expected are species cryptic sister Second, 2010). al., et Wiens 2006; Wainwright, & Sanderson, Ané, lower be should evolution trait of rates The clades. across evolution trait of rates different for allows that motion Brownian of model using test alternative an proposed authors Some values. likelihood on based selected Glossary see model, Losos, see (but evolution non-neutral simulating models to but motion Brownian neutral to corresponds longer no phylogeny ) (Pyron et al., 2015; Smith et al., 2011; Wiens et al., 2010). The preferred models are are models preferred The 2010). al., et Wiens 2011; al., et Smith 2015; al., et (Pyron Glossary that are not related to morphology. morphology. relatedto not are that wa ) ) s or common: 26% of the nominal amphipods examined contained cryptic species species cryptic contained examined amphipods nominal the of 26% common: , arguably, constantly moving adaptive optima (white noise model, see see model, noise (white optima adaptive moving constantly arguably, , . E qu 2008) ival . These models include stabilizing selection (Orstein-Uhlenbeck (Orstein-Uhlenbeck selection stabilizing include models These . ency among ecological niches can be tested either implicitly from from implicitly either tested be can niches ecological among ency niche-conserved than in niche non-conserved clades clades non-conserved niche in than niche-conserved in . Third, Third, PNC

Mo , but it is not mandatory. Species can can Species mandatory. not is it but , PNC rphological convergence based on on based convergence rphological (Delić, Švara, Coleman, Trontelj, Trontelj, Coleman, Švara, (Delić, promotes allopatric speciation speciation allopatric promotes . This prediction prediction (O’Meara, (O’Meara, a special special This article isThis article by protected copyright. All rights reserved. Accepted related closely hence is similarity morphological on Research 2013). Losos, & Stuart 2000a; (Schluter, displacement character as such diversification morphological of mechanisms long-studied the to counterpart a phenomenon, evolutionary an is diversification morphological of lack The 2012). Nosil, have and species distinguishable 2011; Losos, 2010; al., et Harmon 2011; Losos, & Schulte, morphologically (Collar, centuries for naturalists fascinated of diversity the generated that principles mechanisms ecological and evolutionary same the follow likely They diverse. are clearly species cryptic generating The diversity. cryptic of studies mechanism-oriented to diversity pattern-oriented cryptic from of shift studies a for need a is there pattern), same the generate can mechanisms different (i.e. mechanism infer to enough not are alone patterns science, in usual as Since, species. cryptic generating mechanisms different of importance relative the about knowledge well less much relatively been have comparatively is there Yet, species general. in literature the in and literature amphipod cryptic the in documented distantly-related / closely-related of occurrence the as well as taxa and space across species cryptic of distribution the i.e. species, cryptic of Patterns diversification species invisible of summary 3.4 General Article nullmodel. agiven under thanexpected numerous more shiftsare these whether regimes convergent towards characters phenotypic continuous 1997) Hansen, 2004; King, ( model selection stabilizing Ornstein-Uhlenbeck the to morphology correspond should of evolution The environment. the and morphology between evolution correlated a show must testing Appropriate regimes. selective in shifts from result should evolution convergent descriptive is studies above the from Evidence the within microhabitats or 2008) realm subterranean Juan, & Oromí, Jaume, (Villacorta, habitats subterranean (Trontelj et al., 2009; Trontelj, Blejec, & Fišer, 2012) &Fišer, Trontelj,Blejec, etal.,2009; (Trontelj . Further, Ingram & Mahler (2013) developed a method to map shifts in in shifts map to method a developed (2013) Mahler & Ingram Further, . A central prediction of this hypothesis states that that states hypothesis this of prediction central

on a phylogenetic tree and to test test to and tree phylogenetic a . . e Glossary see ) (Butler & & (Butler ) This article isThis article by protected copyright. All rights reserved. reviewed the of 83% in used was gene (COI) I subunit oxidase cytochrome mitochondrial The 4A). (Fig. genes two or one either using delimited were amphipods of species cryptic most now, to Up methods delimitation 4.1 Species SPECIES CRYPTIC INDELIMITING PRACTICES 4. TAXONOMIC are 5). (section and evolution intoecology process speciation the integrate that better can and hypothesis 3), (section speciation species of properties heterogeneous delivering the in grounded towards theoretically practices taxonomic lead can mechanisms progress impede even and Importantly 2015) Alekseev, & Sukhikh, Lajus, 2016; as 2005) Lozano, & Sáez 1993; Knowlton, 2015; Erséus, identical “completely have authors some Noteworthy, 2015) Benítez, & Zúñiga-Reinoso 1993; Knowlton, 2016; Eberhard, & Djurakic, Karanovic, Sket,2012; species cryptic of concept the consider researchers some Hence, distinctness. morphological yield often delimitation species molecular on based analyses morphological that and exist not does similarity morphological perfect that stated authors Many cryptic. morphologically treated as might be predictionsabove the satisfying pair species any different, morphologically slightly if even Thus mechanisms. causal for test not did attention little received have 2013) Losos, & Stuart 2000a; (Schluter, fitness to relates variation trait how on as well and as traits function of the heritability on information gathering requires It diversification. morphological on that to

Accepted“When Article are species similar enough to be considered morphologically cryptic? morphologically considered be to enough similar species are , . it could hinder exploration of a rather broadly widespread evolutionary phenomen evolutionary widespread broadly rather a of exploration hinder could it Contrary to morphological diversification, mechanisms causing morphological similarity similarity morphological causing mechanisms diversification, morphological to Contrary species . ” idvriy science biodiversity in Most of the reviewed studies focused on revealing cryptic species but but species cryptic revealing on focused studies reviewed the of Most from from led cie a em “ term a coined already “morphologically diagnosable diagnosable “morphologically . hs usin s t ik o ean ihu epilogue without remain to risk at is question This . . This classification may lead to questions such such questions to lead may classification This As discussed further below, the quest for for quest the below, further discussed As as pseudo-cryptic overrated overrated

species” (Jugovic, Jalžić, Prevorčnik, & & Prevorčnik, Jalžić, (Jugovic, ” in order to distinguish distinguish to order in (Achurra, Rodriguez, & & Rodriguez, (Achurra, ” (Karanovic et al., al., et (Karanovic on . .

This article isThis article by protected copyright. All rights reserved. typically methods distance splitting; of degree the in differed but other, each with conflict in not species of number the about Us onl used in methods based Allele-sharing 1). information despite occurred methods based tree- of use the in lag This 2013). al., et Yang L. 2014; Florian, & Anna, Niklas, Weiss, 2015; Delean, 201 Fišer, & Moškrič, Delić, Sari, Rineh, studies seven only in used were 2013) al., et Zhang (J. models process tree Poisson and 2010) Rannala, & al Yang Z. 2003; et Yang, & (Rannala (Pons coalescent Yule-coalescent mixed generalized The methods. tree-based 4 (Fig. methods genetics population and based distance- of combination a using or methods distance-based using delimited were species studies, two combined of studies examined category the single of 30% a only on methods; relied often most species amphipod cryptic of delimitation Molecular here. considered not are and purposes taxonomic for used never were but 2016), Leese, & Weiss 2009; Juan, & Oromi, Canovas, Villacorta, 2015; Grabowski, & Bacela-Spychalska, Rigaud, Wattier, Rewicz, 2012; Stark, & Miller, (Baird, amphipods numerous for developed were Microsatellites amphipods. caprellidean of species two in differentiation genetic interspecific and intra- explore to RAPDs used rDNA). 18S and II ND EF1α, H3, ITS, rDNA, (28S markers nuclear and CytB) and (16S markers mitochondrial additional allozymes, included markers genetic Other 2007). Hebert, species animal of identification and storage for system “barcoding” developed (H phyla animal most across marker this of applicability and use general the reflecting possibly studies, ebert, Cywinska, Ball, & DeWaard, 2003; Hebert, Ratnasingham, & Waard, 2003) and as a well- a as and 2003) Waard, & Ratnasingham, Hebert, 2003; DeWaard, & Ball, Cywinska, ebert, Accepted results conflicting revealed methods delineation species and markers molecular different of e Article y two studies two

(Brad, Fišer, Flot, & Sarbu, 2015; Flot et al., 2014) Flotet al., 2015; & Sarbu, Fišer,Flot, (Brad, . Alternative species delimitations suggested by different methods were were methods different by suggested delimitations species Alternative 78% 5; Katouzian et al., 2016; King & Leys, 2011; Murphy, King, & & King, Murphy, 2011; Leys, & King 2016; al., et Katouzian 5; f h suis inferr studies the of , e.g., haplowebs (Flot, Couloux, & Tillier, 2010), were were 2010), Tillier, & Couloux, (Flot, haplowebs e.g., B) . There was a substantial lag in the application of of application the in lag substantial a was There . (Copilaş molecular phylogenies (supporting (supporting phylogenies molecular ing

Coin ersk 05 Esmaeili- 2015; Petrusek, & -Ciocianu or three methods (Fig. 4B). In most most In 4B). (Fig. methods three . Guerra-García et al. (2006) (2006) al. et Guerra-García

. , , 2006) (Ratnasingham & & (Ratnasingham , multilocus multilocus This article isThis article by protected copyright. All rights reserved. 2010) al., et Padial 2012; Claude, Accepted & Michaux, Ledevin, Renaud, Guillot, 2014; Knowles, & (Edwards geography and behavior ecology, morphology, genetics, including approach integrative an using delimited be should species Ideally, criteria species 4.2 Confronting section. next the discussed in as characters with non-molecular confrontation also 2014) al., et Leache 2012; Moritz, & McGuire, Burbrink, Leaché, (Fujita, coalescence multilocus dispute evolutionar the contrary, On 2015). al., et Fontaneto 2015; Flot, & (Dellicour rate mutation high a have used markers molecular the and small, are sizes population low, are rates speciation when results congruent yield delimitation different the 2013) Satler, & Pelletier,Reid, (Carstens, methods by required assumptions various of violations to due well arising is known, methods delimitation species different among Inconsistency addressed. explicitly never Articleal et Lefébure see (but taxa among differs substitution of rate the because case-specific is thresholds of use the Moreover, p, uncorrected (e.g., calculated are distances genetic how on depend thresholds of value the because appropriate always not is cross-referencing 2017) 2016 bGMYC and PTP over preferred was ABGD of conservative efficiency (e.g., methods the different ranking by hypothesis species particular a for opted 2014), al., et Weiss 2015; number species of estimate rough a provided either authors cases, 2014) al., et Weiss 2016; al., et Katouzian 2017; al., et Eme 2017; Fišer, & Rendoš, Trontelj, conservative more be to turned ), ), or drew on other studies to justify the choice of a particular threshold value. Unfortunately, Unfortunately, value. threshold particular a of choice the justify to studies other on drew or ), reconsidered the results within spatial context (presence of syntopy syntopy of (presence context spatial within results the reconsidered (as alluded to above) to alluded (as yug pce wt lre fetv pplto szs a b a ore of source a be can sizes population effective large with species young ily . , 2006). Oddly, reasons for the discordant number of species number were were number species of number discordant the for reasons Oddly, 2006). , . A (Copilaş . highly promising solution for the issue seems to be genome-wide genome-wide be to seems issue the for solution promising highly Steps towards integrative taxonomy were made in 55 of the 122 122 the of 55 in made were taxonomy integrative towards Steps Ciocianu & Petrusek, 2015; Delić, Švara, Delić, 2015; Petrusek, & -Ciocianu K . 2P Molecular species delimitation methods generally generally methods delimitation species Molecular , patristic distances) (Richards et al., 2012). 2012). al., et (Richards distances) patristic ,

(Copilaş (Delić, Trontelj, et al., al., et Trontelj, (Delić, -Ciocianu & Petrusek, Petrusek, & -Ciocianu

et al., 2017; Delić, Delić, 2017; al., et ; Katouzian et al., al., et Katouzian . such such In , and and This article isThis article by protected copyright. All rights reserved. Accepted issues. important three envision we 2017), al., et (Morinière libraries barcoding of development as such issues technical from Aside research. biodiversity into species cryptic of integration the to as well as understanding mechanistic the to more contribute can practices Taxonomic ofspecies cryptic taxonomy the for challenges 4.4 Future 2011). &Leys, (King sequences COI with diagnostic diagnoses morphological complemented study one and 2015) al., et Murphy 2017; al., et Trontelj, species diagnose to sequences DNA upon solely relied studies two Only species. amphipod described of number thetotal 1% to only contributed taxonomy DNA-complemented words, In other named. and described were species cryptic these 21of only Yet, 5). (Fig. period time same the during period the in discovered method the on depending (295-315 304 The Articlewere species cryptic cases, most In species 4.3 Namingcryptic 2004). &Cothran, Wellborn 2013; etal., Meleg &Relyea,2013; Schmidenberg, Henderson, w ones, genetic except species, cryptic between difference biological No complex. species in single a Differences for reported were complexes. size genome species cryptic five in behavior mating from inferred explicitly were barriers Reproductive 4C). (Fig. well as data ecological and morphological with supplemented mostly were inferences Molecular group. research a by publications consecutive of series a in occurred often complexes species cryptic of exploration integrative note, To examined. species nominal (42%) 2000-2015 as detected in only four of the 55 nominal species (Cothran, (Cothran, species nominal 55 the of four only in detected un represented 17% of the 1822 amphipod species described described species amphipod 1822 the of 17% represented -named, even when supported by multiple lines of evidence. evidence. of lines multiple by supported when even -named, , excluding nominal species) species of amphipods amphipods of species species) nominal excluding

of morphological crypsis crypsis morphological (Delić, (Delić, This article isThis article by protected copyright. All rights reserved. Accepted explanations. evolutionary sound have longasincongruences as congruence by supported those as robust as hypotheses species yield can data among incongruences Yet 2010). al., et (Padial evidence of lines multiple by supported hypotheses species rigor taxonomy increase can 2008) al., et (Herrel differ ecologically near genetically diverge some why conversely, genetically or difference, morphological without lineages some why understanding in fields Further, other 5). with (section speciation science linking biodiversity and 2012) al., et (Butlin process speciation the in rules strengthening This processes. divergent of spectrum full the unveil to DNA) multiple physiology, and ecology, (morphology, data speciation, multiple confront appropriately of nature heterogeneous the appreciate fully can theory in grounded practices Only 2007). Queiroz, (de theory evolutionary and practice taxonomic between generally, more or, process speciation the and hypotheses species between link the strengthen can taxonomy Second, recent divergence Article the and 2016) Roos, & Wheeler, Amann, (Raupach, years few next the within standard become may delimitation species multilocus thus affordable, and accessible readily becoming are technologies sequencing high-throughput Fortunately, 2012). al., et Nahavandi 2010; Dattagupta, & Wörheide, 2012) Tiedemann, & Ketmaier, Nahavandi, 2013; 2011, Pálsson, broaden & (Kornobis homoplasy low and variability to impediment major suitable both exhibiting markers A nuclear of number low the is species. methods two the of implementation non-monophyletic delimit to designed both are methods coalescent multilocus and Haploweb 2007). Carstens, & Knowles 2015; Flot, & (Dellicour time long a take can sorting Lineage monophyly. reciprocal reach species evolving before e.g., divergence, early detect to enough sensitive are that methods evolutionar are species cryptic whether testing First, Aog mhpd, ny w mres ( markers two only amphipods, Among . hypothesis may increase increase may hypothesis importance (see 3.1). (see 3.1). in importance ITS , , EF1α y young requires using species delimitation delimitation species using requires young ily is ) apparently meet these conditions (Flot, (Flot, conditions these meet apparently ) a major step towards discovery of general general of discovery towards step major a as

in more robust than single line evidence evidence line single than robust more species with large population sizes sizes population large with species . Some taxonomists consider consider taxonomists Some ly -identical populations populations -identical original name need to be molecularly diagnosed as well as diagnosed molecularly be to nameneed original the retaining isthat species species cryptic of description molecular the of corollary An important 2016) Renner, 2013; &Schrödl, (Jörger taxonomy in continuity and repeatability ensure to available This article isThis article by protected copyright. All rights reserved. on data to communicate asaneffort species, cryptic potential entities, including circumscribed In separation lineage evidence of of lines additional with be strengthened to need hypotheses species DNA analysis for preserved improperly or lost thelatter are if holotypes supplement or can replace that co-types or neotypes phylogeny) in nodes (i.e., distances genetic than rather substitutions diagnostic on rely should diagnosis First, details. technical two recommend works recent and 2016) 2011;Renner, DeSalle, & (Goldstein are diagnosed species how on vary aspects Technical collections. into deposited and defined broad thesestudies All 2011). &Sundberg, Strand 2016; Renner, etal.,2015; Murphy Schrödl, 2013; 2008;Jörger& Humphreys, Edward, & Berry, M.S.Harvey, 2009; &Rouse, Cooper, Kupriyanova, 2008;Halt, Giribet, Edgecombe & 2010; et Cook al., Wheeler, 2014; & (Clouse rare still generally are data molecular onlyon relying descriptions but 1993) Knowlton, 2011; & DeSalle, (Goldstein notnew is sequences using DNA species diagnosing of idea traits. The ofmorphological use tothe ofspecies diagnosis limitthe not does ) ICZN (http://iczn.org/code, 2012) (Jugovic et al., questionable be may diagnoses valueofsuch the practical and 2010) etal., 2009;Schlick-Steiner Zagmajster, challenging is species cryptic morphologically traitsamong diagnostic morphological criteria. Finding morphological basedon described until nameless speciesremain cryptic that isparadoxical It theirresearch. in binomials Linnaean use science that biodiversity of fields other 2015) Panteetal., 2013; Schrödl, no matter species, Third, novel

Accepted Morard cases, such Article . Second , detailed alignment construction, sequences and final alignments must be made made be must alignments final and sequences construction, detailed alignment

et et al. .

( Finally, formal naming sometimes is not considered desirable when when desirable considered is not sometimes naming Finally, formal 2016) if morphologically cryptic, can be described and named (Jörger (Jörger & named and described be can cryptic, morphologically . . This practice is one way to communicate cryptic species with with cryptic species to communicate way is one practice This proposed an interim nomenclature system to codify genetically genetically codify to system nomenclature interim an proposed Indeed, The International Code of Zoological Nomenclature Nomenclature Zoological of Code International The Indeed, . This step may require designation designation may require step This

ly agree that holotypes should be be should holotypes that agree (C. Fišer & Fišer (C. of

. . This article isThis article by protected copyright. All rights reserved. can untested An species. mechanisms cryptic of Accepteddistribution even an produce to space across These other each compensate invariant. themselves are species cryptic causing mechanisms the that imply necessarily not does space across distributed homogeneously are species cryptic that Finding 2015) Vila, & Dinca, Dapporto, only can bedetected distribution heterogeneous an perhaps Voda, 2016; al., et Gill 2017; al., et (Eme conflicting is regions geographic across species cryptic of distribution homogenous for evidence The 2016). Poulin, & León heterogeneously be may actually species cryptic problems meta Their assessments”. biodiversity in error regions, and taxa among distributed homogeneously were species cryptic that found authors The regions. biogeographical and phyla metazoan major across species cryptic of proportion the in variation for test to species Pfenninge few. are analyses Global-scale analyses 5.1.1 Global-scale Article depend strongly now we science, biodiversity in species cryptic for account to (2007) al. et Bickford by plea the Following natureconservation for consequences and revisited patterns 5.1 Biodiversity RESEARCH INBIODIVERSITY DIVERSITY 5. CRYPTIC research. to biodiversity silent remains taxonomy DNA by uncovered species ofcryptic majority the that acknowledge only we can Presently, stakeholders. multiple biodiversity for genetic diversity re ii a ubr f idvriyrltd issues biodiversity-related of number a visit Totl & ie, 2009) Fišer, & (Trontelj ed on the scale of the analysis. the analysis. of scale the on and concluded “that cryptic metazoan diversity can be treated as random random as treated be can diversity metazoan cryptic “that concluded and , and additional analyses almost almost analyses additional and , r and Schwenk (2007) conducted a meta-analysis of cryptic cryptic of meta-analysis a conducted (2007) Schwenk and -analysis was later criticized for several methodological methodological forseveral criticized later was -analysis dis tributed across animal phyla (Pérez-Ponce de de (Pérez-Ponce phyla animal across tributed . Notably, the number of examined studies studies examined of number the Notably, at

global geographic scales. scales. geographic global a decade later suggested that that suggested later decade

; This article isThis article by protected copyright. All rights reserved. Accepted Notably, 2013). al., et Zettler 2013; al., et Weston 2013; McEwen, & Major, Dickinson, Soucek, 2013; Soto-Adames, & Wetzel, Giordano, Soucek, Major, 2012; Bundschuh, & Schulz, Schwenk, Thielsch, Feckler, 2013; Bundschuh, & Schulz, Feckler, 2014; al., et (Feckler assessment health ecosystem in indicators biological of use the and 2009), Wilhelm, & Anderson, (Venarsky, measures conservation 2015) coexistence species and overlap niche ecological of extent the 2009), al., et (Trontelj size range geographic species a to limited not are but include these scope phylogenetic or geographic in either limited are studies Most limitedanalyses phylogenetically and 5.1.2 Geographically spiders. or isopods suchas characters, 2009) al., et Fišer 1977; Dahl, amphipods: (e.g., ecology to related characters somatic functional on based been has explained causing and particular, quantified mechanisms Article be to mentioned awaits three groups taxonomic the different in of crypsis morphological importance relative the diversity, cryptic of address explicitly that study single a of aware not are we but information, visual on rely not do that taxa in frequent more be may species cryptic that suggested (1993) Knowlton phyla. some in overrepresented are species cryptic why unclear is also It (Bic selection convergence morphological glaciations, Pleistocene (e.g., the species ancestral of ranges (e.g., fragmented perturbations climatic recent where regions in predominate mechanisms neutral selectively that is hypothesis te tegh f ieasraie arn (aiad t l, 2015) al., et (Galipaud pairing size-assortative of strength the , PNC kford et al., 2007; Trontelj & Fišer,2009) Trontelj& etal.,2007; kford may well explain the morphological similarity in organisms, the taxonomy of which which of taxonomy the organisms, in similarity morphological the explain well may . In contrast, it may be less important in species delimited essentially on sexual sexual on essentially delimited species in important less be may it contrast, In ) operate more frequently in environments with strong directional directional strong with environments in frequently more operate Fišer t al. et 21) wees eeto-ae mcaim ( mechanisms selection-based whereas 2010), , ed this question. Analogous to geographic aspects aspects geographic to Analogous question. this . . (Ž. Fišer, Altermatt, Zakšek, Knapič, & Fišer, Fišer, & Knapič, Zakšek, Altermatt, Fišer, (Ž.

eet divergence recent . In the amphipod literature, literature, amphipod the In , the effectiveness of of effectiveness the hypothesis PNC . In ) , This article isThis article by protected copyright. All rights reserved. Accepted cryptic members. community other to cryptic be not may species cryptic Apparently, 2007). Lunt, & Whiteley, Potter, Ironside, Rock, 2010; Bastrop, & Zettler, Jürss, Blank, Krebes, 2011; Bastrop, & Blank, Krebes, 2016; Jokela, & Westram, Altermatt, Eisenring, 2009; Hervant, & Douady, Gravot, one along requirements 2015) al., et Fišer ecological ( requirements same the have species cryptic morphologically whether is aspect important Another 2017). (Eme etal., 1989) Stevens, region; in thePalearctic latitudes higher species at morphological of size range increasing of pattern the (i.e., effect Rapoport so-called the size, range study One determined. of patterns scale continental affect not does cryptic species of that consideration however, indicates, be to yet has regions geographical across distributed homogeneously are ranges morphospecies of fragmentations asymmetrical and symmetrical Whether 2006). al., et Lefébure 2011; Martin, & Broyer, De Sonet, Nagy, (Havermans, species morphological the of that as were reported Article species morphological of sizes range large “symmetrically” general, In 2008). al., et Villacorta 2009a; al., et Trontelj 2013; al., et Meleg 2010; Cooper, & Austin, Humphreys, Adams, Bradford, 2013; et al., Bradford 2011; Pons, & Juan, Fornós, Jaume, Bauzà-Ribot, (e.g., Europe and Islands Canary Australia, from amphipods groundwater and 2006) Hebert, & Threloff, Witt, 2013; Austin, & Guzik, Adams, (Murphy, America North and Australia springs desert 2009), Coleman, & Linse, Maas, Lörz, 2012; explicitly corresponding addressed was of species morphological that than smaller is species cryptic of size range the whether of question The when for patterns. accounted biodiversity andexplaining documenting be must that error of source a as species cryptic consider studies these all Hyalella “ asymmetrical i.e. species imply different vulnerabilities to fish predation (Cothran, Henderson, et al., al., et Henderson, (Cothran, predation fish to vulnerabilities different imply species divided into a series of smaller ranges for cryptic species. Yet, some studies studies some Yet, species. cryptic for ranges smaller of series a into divided . Almost all detailed ecological studies showed that cryptic species differed in their their in differed species cryptic that showed studies ecological detailed all Almost . , Grinnellian niche) and play similar roles in ecosystems (i.e., Eltonian niche) niche) Eltonian (i.e., ecosystems in roles similar play and niche) Grinnellian , ” fragmentation where the range of at least one cryptic species was as large large as was species cryptic one least at of range the where fragmentation

r oe iesos f hi Grinnellian their of dimensions more or in amphipods from Antarctic Antarctic from amphipods

niche (Colson-Proch, Renault, Renault, (Colson-Proch, niche deep -sea (Baird et al., al., et (Baird -sea St udies on on udies (Ž. (Ž. This article isThis article by protected copyright. All rights reserved. Accepted2011) al., et (Bálint Europe throughout diversity genetic with along species of loss the cause will change climate global that indicate example, aquatic for species, cryptic of future the forecasting models Niche biodiversity. ultimately and populations local to threats underestimate can stressors multiple to species cryptic of vulnerability the ignoring Second, loss biodiversity to lead can local perturbations even and species distributed broadly than disturbances external to vulnerable more much are sizes range small with Species conceived. previously than smaller much are species many of sizes range First, conservation. nature for difficult are studies ecological and biogeographic from Results redundancy. functional of hypothesis the challenging decomposition, matter organic on effects species-specific unveiled authors these by experiment microcosm A 2016). Moens, & Derycke, Rigaux, Gingold, Meester, (De species cryptic as nematodes cryptic using study single 2015) al., et Scheffer 2017; Altermatt, & Ward, Gounand, Harvey, E. 2003; function ecosystem stabilizing in important critically be may species cryptic so, functional be may stressors various to responses and requirements environmental Articlediffer but niche) (Eltonian ecosystem the in role similar roughly a having species Cryptic are they species indicate on studies but these challenging highly of is magnitude context the ecological an of in Interpretation differences 2013). al., et Weston 2013; al., et Soucek 2013; al., amphipod subterranean et Major 2013; 2014, al., et Feckler 2012; al., et the (Feckler taxa cryptic of range a across pollutants of of species cryptic rhenorhodanensis among cold to responses al. et Colson-Proch the of species cryptic among parasites acanthocephalan 2007) 2004, Cothran, & Wellborn 2013; . Ecotoxicological tests further revealed large differences in sensitivity to a number number a to sensitivity in differences large revealed further tests Ecotoxicological

(2009) found substantial differences in behavioral, metabolic and biochemical biochemical and metabolic behavioral, in differences substantial found (2009) in sufficient to mediate stable coexistence (Box 2). (Box 2). coexistence stable to mediate sufficient a . model system explor system model Westram et al et Westram Bad Cle, 06 Dlć Totl, t l, 2017) al., et Trontelj, Delić, 2016; Collen, & (Bland . (2011) showed different susceptibilities to to susceptibilities different showed (2011) Gammarus

. ed There is an urgent need for assess for need urgent an is There differences in the functional role of of role the functional in differences fossarum co . -occurrence of cryptic cryptic of -occurrence species complex, species To our knowledge, knowledge, our To ing (Elmqvist et al., al., et (Elmqvist ly redundant. If If redundant. ing Niphargus Niphargus in their their in

and and ing a . This article isThis article by protected copyright. All rights reserved. success, similar with science biodiversity of fields all across extended be cannot OTUs addressed. being question the to relevant most are that properties species select can biologist each that view analyse diversity in OTUs of use The molecular of accuracy the on dependent methods. delimitation being still although crypsis, morphological to due bias from free are OTUs from drawn patterns and processes eco-evolutionary about Inferences undervalu and ranges, ancestral reconstruct incorrectly rates, diversification underestimating thereby species; known omitting to equivalent is studies these in diversity cryptic for account to failing Importantly, 2012). al., et (Knox relationships diversity-environment species and 2014), al., et (McInerney fauna 2013) al., et Yang L. 2016; Grabowski, & Burzyński, rates diversification of determinants explore to used were OTUs literature, amphipod the In 2. Section in presented methods using delimited are MOTUs), 2015) (Ryberg, diversity taxonomic for units as species nominal than rather clusters sequence use that are species Cryptic units taxonomic operational 5.2 Molecular conservation. in making decision and policies improving towards assist can diversity cryptic of assessments rapid 2016) al., et (Espíndola co of phylogeographies known and data environmental use These phylogeographies. predictive be may change environmental from loss potential the reduce to diversity cryptic

Accepted Article biome same the in taxa other in species cryptic of presence the predict to taxa -distributed . Such clusters, referred to as molecular operational taxonomic units (OTUs units taxonomic operational molecular as to referred clusters, Such . de facto de . In conjunction with molecular operational units (discussed below), these these below), (discussed units operational molecular with conjunction In taken into consideration by an increasing number of biodiversity studies studies biodiversity of number increasing an by consideration into taken ing oa dvriy Mra e a. 21; yo & ubik 2013) Burbrink, & Pyron 2013; al., et (Morvan diversity local s can be viewed as a logical extension of de Queiroz’s (1999) (1999) Queiroz’s de of extension logical a as viewed be can s , the geographic origin of European groundwater groundwater European of origin geographic the , (Hou, Sket, Fišer, & Li, 2011; Mamos, Wattier, Wattier, Mamos, 2011; Li, & Fišer, Sket, (Hou,

. One step in this direction direction this in step One local assemblages assemblages local of , also referred as as referred also ing es .

This article isThis article by protected copyright. All rights reserved. Accepted selection varying with gradient resource a along faster much acquired be can distinctness ecological in pinpoint could species variation via patterns richness species to contribute distinguishable factors environmental how driven) (hypothesis morphologically and (OTUs) cryptic morphologically 2006) Valentine, & Roy, (Jablonski, time in and regions geographical across vary can properties speciation different of importance relative 2011) (Wiens, dispersal and The eco-evolutionary testing in patterns. biodiversity large-scale of understanding our foster can hypotheses properties species of use broader a how discuss now We patterns. integrat complementary are bias accountable science biodiversity into of diversity cryptic integrating for source approaches a as species cryptic treating and OTUs Using criteria species different useof 5.3 Making Article & Caulk, Best, 2014; 2013). Stachowicz, 2013, Stachowicz, & Best 2009; (Kembel, from alone inferred relatedness be phylogenetic cannot assemblages local in role ecological their and protection, lack threats different to vulnerability unknown of OTUs risky. be can 2011) Blaxter, & Ghoorah, Jones, 2015; Leese, & (Elbrecht ecology community local and 2014) Nipperess, & Hose, Linke, (Asmyhr, biology 2011) al., et Safi 2012; Rahbek, & (Fritz high is species cryptic evolved convergently of proportion the when especially turnover, phylogenetic and diversity phylogenetic of patterns large-scale from derived inferences bias can species cryptic Neglecting 2016). al., et (Gill future near the in ecology in mandatory become may they although pce poete drn speciation during properties species regional number of species is ultimately determined by three processes processes three by determined ultimately is species of number regional es the various properties of speciation towards towards speciation of properties various the . Further, the contribution of speciation to species richness and the the and richness species to speciation of contribution the Further, . An . Thus, geographic variation in the proportion proportion the in variation geographic Thus, . underlying hypothesis is that morphological and and morphological that is hypothesis underlying However, applying this approach to conservation conservation to approach this applying However, a

better understanding of biodiversity biodiversity of understanding better . However, neither satisfactorily satisfactorily neither However, – speciation, extinction extinction speciation, of

This article isThis article by protected copyright. All rights reserved. Accepted theories eco-evolutionary of testing hypothesis in uncertainty this of consideration broader for door the opens notably species delimiting and conceptualizing in made progress Recent feared”. or ignored be it need neither but stamped used or ‘solved’ be is cannot uncertainty it scientific “this that which argued authors The for hypothesis. entity evolving the and criteria any using delimited taxon a between the used (2003) al. et Hey regions. geographical taxa and across each other to inrelative vary strength diversity cryptic causing mechanisms how understanding towards contribute can approach this fact, In regions. fragmented highly in species cryptic allopatric of number higher disproportionately the to due heterogeneity spatial to attributed richness species in variation geographic of proportion the variance and inferences illustrati For 2017). multi-model 2015, al., et Eme using example for (see partitioning assessed is patterns biodiversity explaining for relative the 6), (Fig. variability climate historical example and climate/productivity, present our heterogeneity, spatial of In importance Article hypotheses. species different the for patterns richness species explaining mechanisms different of importance relative the assess can one Ultimately, data). species that ecological genes, Note new (e.g., available become methods and data 6). more as refined be can hypotheses (Fig. species criteria multiple DNA-based multiple to and associated morphology on be based can hypotheses regions geographic large across collected specimens One 6 (Fig. ecological analyses criteriainto different species integrating 2015) by driven perhaps speciation, (non-ecological environment each in pressures selection similar with barrier physical a from than speciation) (ecological pressures step towards this testing consists consists testing this towards step A iprat on hr i ta tee yohssdie peitos a b tse by tested be can predictions hypothesis-driven these that is here point important An . biodiversity science. science. biodiversity in term “species uncertainty” to denote the ambiguous correspondence correspondence ambiguous the denote to uncertainty” “species term building occurrence databases in which thousands of of thousands which in databases occurrence building of

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on , DNA-based criteria increase increase criteria DNA-based , . 21; yo e al. et Pyron 2010; , in out, out, a , This article isThis article by protected copyright. All rights reserved. science biodiversity in frontiers new to way the paving Acceptedbio of fields different to approaches multi-criteria Extending delineation. species for criteria multiple used has date to study no but analyses, their into species cryptic incorporating inherently thereby (OTUs) units taxonomic operational molecular use increasingly ecology and evolution in Studies overlooked thus and un-named, or undescribed are species cryptic known of majority the Paradoxically, bias. of sources potential as or inventory species incomplete of evidence as research biodiversity in considered often are species Cryptic (3) science. biodiversity in integration properties) (species heterogeneity the of understanding our improve gener unveil can data of types multiple of analyses Comprehensive cryptic delimiting for methods species of variety ever-increasing an provides speciation the taxonomy in DNA process. grounded empirically and theoretically are that hypotheses species towards oriented are efforts research if explanations evolutionary for evidence provide can Taxonomy (2) Article largely unknown. diversity remains cryptic of explanations different of importance relative the present, At morphology. on selection directional similar to response in lineages related distantly from by converge or constrained selection, are stabilizing neutrally, evolve traits morphological whether of testing explicit need now the understand to beginning just only are We phenotypes. of They convergence morphological and conservatism niche divergence, recent lacking comprising heterogeneous, species of are set similarity morphological to negatively-defined leading mechanisms and Evolutionary distinguishability. heterogeneous morphological a to refer species Cryptic (1) 6. CONCLUSIONS iest sine a bte itgae rpi seis n clgcl n eouinr theories evolutionary and ecological in species cryptic integrate better can science diversity are as important and fascinating as mechanisms leading organisms to diversify into a multitude multitude a into diversify to organisms leading mechanisms as fascinating and important as are , and be used to explore species boundaries related to morphology, ecology, and physiology and ecology, morphology, to related boundaries species explore to used be and in resea . c fed rlig n pce binomials species on relying fields rch For example, are biodiversity patterns patterns biodiversity are example, For

‘ invisible al ities in the speciation process speciation the in ities speciation, and allow better better allow and speciation, in ’ world of cryptic species. We We species. cryptic of world . , , . . , This article isThis article by protected copyright. All rights reserved. Accepted entities. species of uncertainty scientific the thatexplicitly acknowledge policies public and principles conservation ofadaptive development the promote can explained readily be cannot that incongruences Lastly, strategies. conservation understanding better Thus, process. thespeciation in variation geographic reveal will then incongruences These incongruences. method in regions pinpoint that can methods delimitation species different using range size andgeographic richness ofspecies maps continental may include information this example, For distribution. and speciesdiversity knowledge on body of novel complex but more usinga decisions informed to make beprepared must andpolicy-makers conservationists future, the In conservation. and assessment inbiodiversity occupations and newskills consolidating multi-criteria and taxonomy integrative research basic biodiversity in alreadyevident as criteria, multiple species use of the and taxonomy integrative include must necessarily integration This biodiversity science. Article into properties) (species heterogeneity its and speciation integrating towards epiphenomenon constructive a as ofscientists generation next the viewed by be and overtime likely fade will science biodiversity context of the broader within pervasiveness cryptic species methodologies, W speciation. on research complement clearly species cryptic Importantly, beparallel. can ecological species cryptic and of phenomena (4) The proceeds? divergence lineage as change scales local at mechanisms and coexistence do lastly, space, And gradients? geographical environmental across other each to relative strength in vary diversity cryptic causing contingen morphological from inferred cy to ecological and processes generating cryptic speci cryptic generating processes and ecological to of the causes of this variation in speciation can reinforce process-oriented process-oriented reinforce can speciation in this of variation causes the ly and DNA delimited species discordant? If so, is discrepancy a a discrepancy is so, If discordant? species delimited DNA and ha ve profound implications in terms of forecasting and and forecasting in termsof implications profound e do envision that with the development of new new of development the with that do envision

es ? How do different mechanisms mechanisms different do How . Importantly, shifts to shifts Importantly, This article isThis article by protected copyright. All rights reserved. Accepted diversification species of Arerates J. (2009). & Wiens, H., Kozak,K. M., C. Berns, D.C., Adams, subterranean the in speciation Pseudo-cryptic (2015). C. & Erséus, P., Rodriguez, Achurra, A., REFERENCES program. Technology) and Science in Cooperation (European the COST by supported (CA15219), ActionDNAqua-Net fromCOST work upon based articleis This manuscript. and D.Eme, Douady, C. Datry, T. Altermatt, IZK0Z3_169642) 0184) P0- Programme (ARRS, Agency Article Research the Slovenian (no.31199UM), programme Proteus the PHC by funded was This study ACKNOWLEDGEMENTS interest. of noconflict declare Authors INTERESTS OF CONFLICT paper. the draft andhelped ideas original contributed authors data, all theliterature gathered C.F. CONTRIBUTION AUTHOR Sciences evolution? morphological of with rates correlated Zoology Comparative Clitellata, Lumbriculidae). (Annelida, Bretscher, 1900 Bichaeta of ofthestatus revision with a 1862, Claparède, Stylodrilus of species new medium: A , 276 . Anne-Nina Lörz analyzed data from Amphipoda Newsletters. We thank thank We Newsletters. Amphipoda datafrom analyzed Lörz Anne-Nina (1668), 2729 , 257, 71 – 2738. https://doi.org/10.1098/rspb.2009.0543 https://doi.org/10.1098/rspb.2009.0543 2738. – and the Swiss National Science Foundation (grant (grant Foundation Science National Swiss the and 86. https://doi.org/10.1016/j.jcz.2015.05.003 86. https://doi.org/10.1016/j.jcz.2015.05.003 J. -F. Flot for comments on early versions of the of early versions on comments for Flot -F. Proceedings of the Royal Society B: Biological Biological SocietyB: Royal the of Proceedings Zoologischer Anzeiger - A Journal of Journal of - A Anzeiger Zoologischer

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This article isThis article by protected copyright. All rights reserved. Accepted to pollutants. sensitivities with different 20 al., et Marmonier & Farley, Coyle, 2013) Renner, (Pinchuk, webs food in link key a also are they hence high; be can abundances predation) and scavenging shredding, feeding, filter (e.g., strategies feeding of range broad a use and bryozoans) and mollusks whales, on commensals and ambush-predators, sedentary builders, tube burrowers, order one ecolog diverse and highly display however, species Benthic benthic, pelagic. is are (Hyperiida) amphipods Most 2006). al., et (Lefébure convergence and stasis morphological promote to thought been long has that environment constrained highly a 2008), al., et (Väinölä groundwater to exclusive are species freshwater of 45% About 2010). Priede, & Solan, Mayor, Fujii, (Jamieson, community the of part important an represent they where zone, hadal the to zone supra-littoral the in living marine, are (80%) species Many 2). (Fig. 2013) Pavesi, & (Ketmaier habitats terrestrial inhabit even some and habitats aquatic most in thrive Amphipods differences. Article variation Within-population studied. ever if rarely were barriers reproductive patterns; setal and shapes body shapes, appendage different of basis a on delimited traditionally were species the and apparatus copulatory have not do Amphipods Verheye, Held, 2004; & Lörz 2011; al., et Hou 2008; Trontelj, & Horton, Sket, Fišer, C. (Corrigan, 2013; Hoelzel, & relationships White, Fotherby, phylogenetic nor diversity species depicts accurately neither alone morphology that indicate studies phylogenetic clade-specific and amphipods of phylogeny into classified are that species 10,000 ca. of consist Peracarida) Malacostraca: (Crustacea: Amphipods species of cryptic study for amodel as Amphipods 1 BOX six orders (Horton et al., 2016; Väinölä et al., 2008). There is no comprehensive molecular molecular comprehensive no is There 2008). al., et Väinölä 2016; al., et (Horton orders six . Lastly, amphipods are routinely used in ecotoxicological tests (Feckler et al., 2012; 2012; al., et (Feckler tests ecotoxicological in used routinely are amphipods Lastly, Aeadr Dc, OCno, 03 Mcel Dc, Ewo, 1997) Elwood, & Dick, Macneil, 2013; O’Connor, & Dick, (Alexander, akla, dUee dAo, 2016) d’Acoz, d’Udekem & Backeljau, 13) , the results of which may be biased if model species contain cryptic species species cryptic contain species model if biased be may which of results the , is often high in contrast to small between-species between-species small to contrast in high often . Species-level taxonomy is demanding. demanding. is taxonomy Species-level

ies (e.g., free-roaming species, species, free-roaming (e.g., . Local Local . This article isThis article by protected copyright. All rights reserved. niche Accepted Gómez, & Serra, Ramos-Rodríguez, (Montero-Pau, space, rotifers including organisms, model various using niche ecological their in overlap coexistence their explain cannot differentiation significantly species cryptic that Assuming syntopy. even or livesympatry to in were found species cryptic amphipod the of 20% than less no view; this support largely phyla animal many from studies Recent sea. the in species cryptic among common is co-occurrence local and sympatry that suggested (1993) Knowlton 2. BOX nature conservation. and functioning ecosystem dynamics, ecological local with evolution morphological of issue the link analysis for replicates natural provide t at ranges distributional Limited settings. ecological different under diversity cryptic generating processes in generalities 2006) al., et Witt 2016; al., 2016; al., et et Mamos Katouzian Article 2016; (Havermans, species of tens several to up varies species nominal amphipods of groups ecological all in found been have species ecology applied and patterns biodiversity global dynamics, ecological local with diversity contributing processes evolutionary linking for organism model ideal an are Amphipods are etal.,2014). Dodd 2000; (Dick &Platvoet, amphipods fauna native athreat to andpose species invasive Some 2004). Grabowski, & Konopacka, Jazdzewski, 2007; Konopacka, & Bacela, & Pilgrim (Grabowski, decades recent in ranges distributional their expanded 2013; substantially have 2010), Darling, Darling, & Lee, Reusser, Blum, Pilgrim, 2004; MacIsaac, & Hebert, Grigorovich, Witt, (Cristescu, species cryptic some including species, of tens some Yet, 2009). Lowry, & ranges (Myers distributional limited have species amphipod most larvae, pelagic free of absence the In Co -occurrence of cryptic species crypticspecies of -occurrence he species level coupled with ubiquitous distribution at the genus level level genus the at distribution ubiquitous with coupled level species . A s a . key functional group in ecosystems, amphipods naturally naturally amphipods ecosystems, in group functional key Ecological diversity of amphipods allows for testing testing for allows amphipods of diversity Ecological

(Chesson, 2000). Several studies addressed this issue issue this addressed studies Several 2000). (Chesson,

. The number of cryptic species within within species cryptic of number The to . Cryptic Cryptic cryptic cryptic This article isThis article by protected copyright. All rights reserved. more non-randomly or random are co-occurrences Accepted species whether testing by puzzle the solve to attempted authors Some differences. meaningful ecologically into translated be can traits biological issue; general a up brought review This etal.,2004). Zhang D. Y. 2016; Hanski, & (Ruokolainen rare is species when growth population favors interference breeding 2007) 2004, Cothran, & (Wellborn competitor stronger the of strength the regulates predation selective where iii) 2003), al., et Ortells 2011; Serra, & Montero-Pau 2011; al., et (Montero-Pau scales annual or seasonal daily, over species occurring 2012) (Eis other each outcompete locally and gradients environmental along disperse species when i) i.e., trade-offs; subtle more are differences found cases other whereas 2006), Racey, & (Nicholls habitat foraging for preferences differential strong showed study One case. to case from varies differentiation species of degree The differentiated. ecologically are species cryptic thatco-occurring showed studies exception, little With Article natureconservation. for implications unveil studies These 2012). Arlettaz, & Ashrafi, Braunisch, Bontadina, Rutishauser, 2006; Racey, & Nicholls 2011; Bontadina, & Arlettaz, Rutishauser, Beck, (Ashrafi, bats and 2004) Hanski, & Lin, Zhang, Y. (D. wasps fig 2016), Tinsley, & Goulson, Whitehorn, (Scriven, bees bumble 2012), Gauthier, & Clouet, 2004) Cothran, & Wellborn 2015; al., et Fišer Ž. 2016; al., et Eisenring 2011; Nozais, & Charles, Dufresne, & Vergilino, Dionne, 2013; Relyea, Wellborn, Chapman, Stiff, Cothran, 2015; Relyea, & Noyes, Cothran, 2013; al., et Henderson, (Cothran, amphipods different 2008), al., et Derycke 2016; al., et Meester De 2011; Moens, & Bonte, Derycke, Meester, (De nematodes 2003), Serra, & Gomez, Ortells, 2011; Serra, & Montero-Pau 2011; i) hn eprl lcutos n niomna fcos le cmeiie tegh f co- of strength competitive alter factors environmental in fluctuations temporal when ii) , ed emerging commonalities in co-occurrence patterns and unsolved issues with important important with issues unsolved and patterns co-occurrence in commonalities emerging enring et al., 2016; Ž. Fišer et al., 2015; Pfenninger & Nowak, 2008; Rutishauser et al., al., et Rutishauser 2008; Nowak, & Pfenninger 2015; al., et Fišer Ž. 2016; al., et enring (Ž. Fišer et al., 2 al., et Fišer (Ž. 015; Wellborn & Cothran, 2004). Co-occurrence Co-occurrence 2004). Cothran, & Wellborn 015; , chironomids (Pfenninger & Nowak, 2008), bugs (Saleh, Laarif, Laarif, (Saleh, bugs 2008), Nowak, & (Pfenninger chironomids i.e., whether and how statistically significant differences in in differences significant statistically how and whether , and iv) when, under various scenarios, heterospecific heterospecific scenarios, various under when, iv) and

is based on different different on based This article isThis article by protected copyright. All rights reserved. Accepted motion: Brownian Glossary non- initially between interactions competitive 2012) &Gravel, Mouquet, Canard, Mouillot, Poisot, 2006; & Callaway, (Lortie species competing intensify and space ecological reshape may conditions environmental altered that expected be can it mesocosms, in other which each species outcompete of co-occurrence long-term mediate factors local if example, For to species. cryptic responses species predict we can 2016) al., et e.g., (Sinclair change environmental questions; many for implications Article important has community a in growth population and differentiation species of degree the between relationship marina 2015) al., et (Cothran mesocosms experimental in abundance low at introduced were they when growth population positive showed amphipod the In conditions. laboratory under co-existence for tested that systems model two only of aware are We demanding. quite species, cryptic of case the in are, that experiments controlled laboratory requires test This 2010). McPeek, abundance low at system the in present initially if grow can population species’ a that 2012) al., et Saleh 2012; al., et Rutishauser data distributional to respect with frequent/rare either facilitated or suppressed population growth (De Meester et al., 2011) al., et Meester (De growth population suppressed or facilitated either

species is linearly related to the amount of time since divergence. divergence. oftimesince the amount to related species is linearly at andoccurs non-directional be to expected is phenotype in mean Change drift. genetic to due traits of evolution andgradual neutral A model of trait evolution trait of model A . In . contrast, interactions among species of the nematode nematode the of species among interactions contrast, . . The best evidence for coexistence was a demonstration demonstration a was coexistence for evidence best The , This question extends beyond the issue of co-occurring co-occurring of issue the beyond extends question This sometimes called random walk, which assumes assumes which walk, random called sometimes Hyalella (Ž. Fišer et al., 2015; Pfenninger & Nowak, 2008; 2008; Nowak, & Pfenninger 2015; al., et Fišer (Ž. a constant rate, whereas variance among variance whereas rate, constant , none of the three co-occurring species species co-occurring three the of none ,

. An ambiguous ambiguous An (Siepielski & & (Siepielski Pelloditis Pelloditis .

This article isThis article by protected copyright. All rights reserved. Acceptedtaxon species vs. Species concept Integrative taxonomy niche ecological Eltonian for requirements species on niche grounded ecological of A concept . niche ecological Grinellian group Paraphyletic Monophyletic Article group Polyphyletic crypsis Morphological White noise Orstein-Uhlenbeck entities. “Species taxon” entities. “Species semantic nature. is of term species theecosystem. in role it plays species. genetic, morphological, behavioral and ecological evidence of lineage separation. separation. lineage of evidence ecological and behavioral morphological, genetic, environment; biotic breeds. inwhich conditions with parametrized is aniche specific habitat; descendants. analysis. molecular prior without apart be told cannot differentiation morphological whose species those term for this use we this review relationships. phylogenetic from independent is that change phenotypic evolutionary which generates trait optima, moving around constantly revolves traits phenotypic Evolutionary changes are constrained by a constant force towards an adaptive optimum. optimum. an adaptive towards force aconstant by constrained are changes Evolutionary stabilizing selection. to aphenotype of theresponse describing model is analternative

model

group: group: : : : model A group of organisms deriv oforganisms group A A model of trait evolution represent trait evolution of A model A group of organisms derived from derived from oforganisms group A : An interdisciplinary approach in delimiting species, based on confrontation of onconfrontation based delimiting species, in approach interdisciplinary : An : A group of organisms composed of composed organisms group of A Extreme similarity of morphological phenotypes of two or more species. In species. more or two of phenotypes morphological of similarity Extreme : A concept of ecological niche defined by the place a species takes in its takes in a species place the by niche defined ecological of A concept : : A model of trait evolution trait of A model i.e., “its relationship towards food andenemies” food towards relationship “its i.e., : Several authors argued that much of the confusion related to the to related confusion the of much that argued authors Several : has practical value. It is an elementary unit in biodiversity biodiversity elementary unit in is an It practicalvalue. has The “species concept” treats species as evolutionary evolutionary as treats species concept” “species The from different ancestors. ancestors. different ed from , sometimes also called also sometimes a ing common ancestor, which excludes some some excludes which ancestor, common a a process in which variation of of variation inwhich a process common ancestor and all its descendant its descendant all ancestor and common

a a “rubber a species persists and persists species and the functional and thefunctional - band”, band”, which which a This article isThis article by protected copyright. All rights reserved. at available photos Commons, Creative under (licensed with permission used Hillewaert and Hans evolutionary of importance relative the diff crypsis morphological underlying whether mechanisms question the pose naturally They groups. ecological these all in found were species Cryptic plankton. gelatinose within often pelagial, live semi colonized (G) successfully talitroids of lines (F) cyamids and (E) leucothoids in live that feeders filter are (C) corophiids sediments; soft in burrow commonly (B) ampeliscids depth; m 5000 below depths at sea 2 FIGURE gradients. andenvironmental space across biodiversity to contribute mechanisms the three how reveal turn in may latter The research. biodiversity into species cryptic of integration and crypsis understanding fosters taxonomy Integrative are sections practices. three taxonomic directs mechanisms the causal for quest how The science. biodiversity show into integrated Arrows (italics). literature the from retrieved information quantitative as well as (headings) addressed topics main the provide we section, each For science. 1 FIGURE Figures Acceptedhttps://www.fli Article the process of speciation. speciation. of the process the reason “ Forthis speciation. of the context on depends and isunclear, taxon species concept and between species correspondence The methods. by delimitation individuated and research,

The three sections of a research agenda for integrating cryptic species in biodiversity biodiversity in species cryptic integrating for agenda research a of sections three The (as part of BOX 1). BOX of part (as ckr.com/photos/bathyporeia/albums/72157639365477036 species taxon species A snapshot of Amphipoda diversity. Lyssianasoids (A) live in the deep deep the in live (A) Lyssianasoids diversity. Amphipoda of snapshot A ,

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This article isThis article by protected copyright. All rights reserved. Accepted size. sample small corrected for criterion information AICc: Akaike’s phylogeography; & phylogenetics Bayesian BP&P: approaches; Yule-coalescent mixed generalized multi different where regions and using factors environmental causal for space, tested and pinpointed be can operate mechanisms speciation in mapped be can datasets Alternative criteria. different to according hypotheses species different to assigned be can Individuals patterns. biodiversity scale 6 FIGURE time. through species increases cryptic undescribed but discovered of proportion the that shows panel Lower period. time same the over Information) Supplementary (source rate discovery species cryptic shows panel Middle 39). 30- vol. Newsletters Amphipoda (source: 2015 and 2000 between description species of rates shows Article5 FIGURE complexes). cryptic species containing species described 55 = (n taxonomy DNA from inferred hypotheses species cryptic test to used data Non-molecular C) studies); 76 = (n delimitation species to methods Molecular B) studies); 76 = (n markers molecular of 4 FIGURE see text. betweenstudies, vary ofdivergence estimation usedfor methods the note that Please publications. 3 FIGURE -model inferences and variance partitioning. PTP: Poisson tree processes models; GMYC: GMYC: models; processes tree Poisson PTP: partitioning. variance and inferences -model Age distribution of 43 cryptic species of amphipods, extracted from 29 out of 120 reviewed reviewed outof120 29 from extracted species ofamphipods, 43cryptic of distribution Age An overview of practices in taxonomy to delimit cryptic species of amphipods. A) Number Number A) amphipods. of species cryptic delimit to taxonomy in practices of overview An A general methodology for integrating multiple species criteria into the analysis of large- of analysis the into criteria species multiple integrating for methodology general A Rates of species description and discovery of cryptic species of amphipods. Upper panel panel Upper amphipods. of species cryptic of discovery and description species of Rates

This article isThis article by protected copyright. All rights reserved. Accepted Article

This article isThis article by protected copyright. All rights reserved. Accepted Article

This article isThis article by protected copyright. All rights reserved. Accepted Article

This article isThis article by protected copyright. All rights reserved. Accepted Article

This article isThis article by protected copyright. All rights reserved. Accepted Article

This article isThis article by protected copyright. All rights reserved. Accepted Article