Araneae, Zodariidae )
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Biogeography of the Caribbean Cyrtognatha Spiders Klemen Čandek1,6,7, Ingi Agnarsson2,4, Greta J
www.nature.com/scientificreports OPEN Biogeography of the Caribbean Cyrtognatha spiders Klemen Čandek1,6,7, Ingi Agnarsson2,4, Greta J. Binford3 & Matjaž Kuntner 1,4,5,6 Island systems provide excellent arenas to test evolutionary hypotheses pertaining to gene fow and Received: 23 July 2018 diversifcation of dispersal-limited organisms. Here we focus on an orbweaver spider genus Cyrtognatha Accepted: 1 November 2018 (Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine Published: xx xx xxxx its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifcally, we test if Cyrtognatha biogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampled Cyrtognatha individuals, using models with and without a founder event parameter. Our results suggest a radiation of Caribbean Cyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola, Cyrtognatha subsequently dispersed to, and diversifed on, the other islands of the Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event. -
Transcriptome Characterization of the Aptostichus Atomarius Species Complex Nicole L
Garrison et al. BMC Evolutionary Biology (2020) 20:68 https://doi.org/10.1186/s12862-020-01606-7 RESEARCH ARTICLE Open Access Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex Nicole L. Garrison1*, Michael S. Brewer2 and Jason E. Bond3 Abstract Background: Mygalomorph spiders represent a diverse, yet understudied lineage for which genomic level data has only recently become accessible through high-throughput genomic and transcriptomic sequencing methods. The Aptostichus atomarius species complex (family Euctenizidae) includes two coastal dune endemic members, each with inland sister species – affording exploration of dune adaptation associated patterns at the transcriptomic level. We apply an RNAseq approach to examine gene family conservation across the species complex and test for patterns of positive selection along branches leading to dune endemic species. Results: An average of ~ 44,000 contigs were assembled for eight spiders representing dune (n = 2), inland (n = 4), and atomarius species complex outgroup taxa (n = 2). Transcriptomes were estimated to be 64% complete on average with 77 spider reference orthologs missing from all taxa. Over 18,000 orthologous gene clusters were identified within the atomarius complex members, > 5000 were detected in all species, and ~ 4700 were shared between species complex members and outgroup Aptostichus species. Gene family analysis with the FUSTr pipeline identified 47 gene families appearing to be under selection in the atomarius ingroup; four of the five top clusters include sequences strongly resembling other arthropod venom peptides. The COATS pipeline identified six gene clusters under positive selection on branches leading to dune species, three of which reflected the preferred species tree. -
Distribution of Spiders in Coastal Grey Dunes
kaft_def 7/8/04 11:22 AM Pagina 1 SPATIAL PATTERNS AND EVOLUTIONARY D ISTRIBUTION OF SPIDERS IN COASTAL GREY DUNES Distribution of spiders in coastal grey dunes SPATIAL PATTERNS AND EVOLUTIONARY- ECOLOGICAL IMPORTANCE OF DISPERSAL - ECOLOGICAL IMPORTANCE OF DISPERSAL Dries Bonte Dispersal is crucial in structuring species distribution, population structure and species ranges at large geographical scales or within local patchily distributed populations. The knowledge of dispersal evolution, motivation, its effect on metapopulation dynamics and species distribution at multiple scales is poorly understood and many questions remain unsolved or require empirical verification. In this thesis we contribute to the knowledge of dispersal, by studying both ecological and evolutionary aspects of spider dispersal in fragmented grey dunes. Studies were performed at the individual, population and assemblage level and indicate that behavioural traits narrowly linked to dispersal, con- siderably show [adaptive] variation in function of habitat quality and geometry. Dispersal also determines spider distribution patterns and metapopulation dynamics. Consequently, our results stress the need to integrate knowledge on behavioural ecology within the study of ecological landscapes. / Promotor: Prof. Dr. Eckhart Kuijken [Ghent University & Institute of Nature Dries Bonte Conservation] Co-promotor: Prf. Dr. Jean-Pierre Maelfait [Ghent University & Institute of Nature Conservation] and Prof. Dr. Luc lens [Ghent University] Date of public defence: 6 February 2004 [Ghent University] Universiteit Gent Faculteit Wetenschappen Academiejaar 2003-2004 Distribution of spiders in coastal grey dunes: spatial patterns and evolutionary-ecological importance of dispersal Verspreiding van spinnen in grijze kustduinen: ruimtelijke patronen en evolutionair-ecologisch belang van dispersie door Dries Bonte Thesis submitted in fulfilment of the requirements for the degree of Doctor [Ph.D.] in Sciences Proefschrift voorgedragen tot het bekomen van de graad van Doctor in de Wetenschappen Promotor: Prof. -
Deep Molecular Divergence in the Absence of Morphological And
MEC1233.fm Page 899 Thursday, March 22, 2001 10:50 AM Molecular Ecology (2001) 10, 899–910 DeepBlackwell Science, Ltd molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus J. E. BOND,* M. C. HEDIN,† M. G. RAMIREZ‡ and B. D. OPELL§ *Department of Zoology — Insect Division, Field Museum of Natural History, Roosevelt Road at Lake Shore Drive, Chicago, IL 60605 USA, †Department of Biology, San Diego State University, San Diego, CA 92182 – 4614 USA, ‡Department of Biology, Loyola Marymount University, 7900 Loyola Boulevard, Los Angeles, CA 90045 – 8220 USA, §Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060 USA Abstract Aptostichus simus is a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplo- type and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6 –12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morpho- logical features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. If a time-limited genealogical perspective is employed, A. simus would be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity. -
Species Delimitation and Phylogeography of Aphonopelma Hentzi (Araneae, Mygalomorphae, Theraphosidae): Cryptic Diversity in North American Tarantulas
Species Delimitation and Phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): Cryptic Diversity in North American Tarantulas Chris A. Hamilton1*, Daniel R. Formanowicz2, Jason E. Bond1 1 Auburn University Museum of Natural History and Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America, 2 Department of Biology, The University of Texas at Arlington, Arlington, Texas, United States of America Abstract Background: The primary objective of this study is to reconstruct the phylogeny of the hentzi species group and sister species in the North American tarantula genus, Aphonopelma, using a set of mitochondrial DNA markers that include the animal ‘‘barcoding gene’’. An mtDNA genealogy is used to consider questions regarding species boundary delimitation and to evaluate timing of divergence to infer historical biogeographic events that played a role in shaping the present-day diversity and distribution. We aimed to identify potential refugial locations, directionality of range expansion, and test whether A. hentzi post-glacial expansion fit a predicted time frame. Methods and Findings: A Bayesian phylogenetic approach was used to analyze a 2051 base pair (bp) mtDNA data matrix comprising aligned fragments of the gene regions CO1 (1165 bp) and ND1-16S (886 bp). Multiple species delimitation techniques (DNA tree-based methods, a ‘‘barcode gap’’ using percent of pairwise sequence divergence (uncorrected p- distances), and the GMYC method) consistently recognized a number of divergent and genealogically exclusive groups. Conclusions: The use of numerous species delimitation methods, in concert, provide an effective approach to dissecting species boundaries in this spider group; as well they seem to provide strong evidence for a number of nominal, previously undiscovered, and cryptic species. -
Systematics of the Californian Euctenizine Spider Genus Apomastus
CSIRO PUBLISHING www.publish.csiro.au/journals/is Invertebrate Systematics, 2004, 18, 361–376 Systematics of the Californian euctenizine spider genus Apomastus (Araneae:Mygalomorphae:Cyrtaucheniidae): the relationship between molecular and morphological taxonomy Jason E. Bond East Carolina University, Department of Biology, Howell Science Complex–N211, Greenville, NC 27858, USA. Email: [email protected] Abstract. The genus Apomastus Bond & Opell is a relatively small group of mygalomorph spiders with a limited geographic distribution. Restricted to the Los Angeles Basin, San Juan Mountains, and San Joaquin Hills, Apomastus occupies a fragile habitat rapidly succumbing to urban encroachment. Although originally described as monotypic, the genus was hypothesised to contain at least one additional species. However, females of the two reputed species are morphologically indistinguishable and the authors were unable confidently to assign specific status to populations for which they lacked male specimens. Using an approach that combines geographic, morphological and molecular data, all known populations are assigned to one of two hypothesised species. Mitochondrial DNA cytochrome c oxidase I sequences are used to infer population phylogeny, providing the evolutionary framework necessary to resolve population and species identity issues. Conflicts between the parsimony and Bayesian analyses raise questions about species delineation, species paraphyly, and the application of molecular taxonomy to these taxa. Issues relevant to the conservation of Apomastus species are discussed in light of the substantive intraspecific species divergence observed in the mtDNA data. The type species, Apomastus schlingeri Bond & Opell, is redescribed and a second species, Apomastus kristenae, sp. nov., is described. Additional keywords: conservation genetics, cytochrome oxidase, molecular systematics, molecular taxonomy, phylogeography, species paraphyly, spider taxonomy. -
Phylogenomic Analysis and Revised Classification of Atypoid Mygalomorph Spiders (Araneae, Mygalomorphae), with Notes on Arachnid Ultraconserved Element Loci
Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci Marshal Hedin1, Shahan Derkarabetian1,2,3, Adan Alfaro1, Martín J. Ramírez4 and Jason E. Bond5 1 Department of Biology, San Diego State University, San Diego, CA, United States of America 2 Department of Biology, University of California, Riverside, Riverside, CA, United States of America 3 Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America 4 Division of Arachnology, Museo Argentino de Ciencias Naturales ``Bernardino Rivadavia'', Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina 5 Department of Entomology and Nematology, University of California, Davis, CA, United States of America ABSTRACT The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non- Submitted 1 February 2019 orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Accepted 28 March 2019 Published 3 May 2019 Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. -
A Reconsideration of the Classification of the Spider Infraorder Mygalomorphae (Arachnida: Araneae) Based on Three Nuclear Genes and Morphology
A Reconsideration of the Classification of the Spider Infraorder Mygalomorphae (Arachnida: Araneae) Based on Three Nuclear Genes and Morphology Jason E. Bond1*, Brent E. Hendrixson2, Chris A. Hamilton1, Marshal Hedin3 1 Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America, 2 Department of Biology, Millsaps College, Jackson, Mississippi, United States of America, 3 Department of Biology, San Diego State University, San Diego, California, United States of America Abstract Background: The infraorder Mygalomorphae (i.e., trapdoor spiders, tarantulas, funnel web spiders, etc.) is one of three main lineages of spiders. Comprising 15 families, 325 genera, and over 2,600 species, the group is a diverse assemblage that has retained a number of features considered primitive for spiders. Despite an evolutionary history dating back to the lower Triassic, the group has received comparatively little attention with respect to its phylogeny and higher classification. The few phylogenies published all share the common thread that a stable classification scheme for the group remains unresolved. Methods and Findings: We report here a reevaluation of mygalomorph phylogeny using the rRNA genes 18S and 28S, the nuclear protein-coding gene EF-1c, and a morphological character matrix. Taxon sampling includes members of all 15 families representing 58 genera. The following results are supported in our phylogenetic analyses of the data: (1) the Atypoidea (i.e., antrodiaetids, atypids, and mecicobothriids) is a monophyletic group sister to all other mygalomorphs; and (2) the families Mecicobothriidae, Hexathelidae, Cyrtaucheniidae, Nemesiidae, Ctenizidae, and Dipluridae are not monophyletic. The Microstigmatidae is likely to be subsumed into Nemesiidae. -
Molecular Species Delimitation in the Primitively Segmented Spider Genus Heptathela Endemic to Japanese Islands
bioRxiv preprint doi: https://doi.org/10.1101/812214; this version posted April 26, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands Xin Xua,b,*,+, Matjaž Kuntnerb,c,d,e,+, Jason E. Bondf, Hirotsugu Onog, Simon Y. W. Hoh, Fengxiang Liub, Long Yub, Daiqin Lii,* aCollege of Life Sciences, Hunan Normal University, Changsha, Hunan, China bState Key Laboratory of Biocatalysis and Enzyme Engineering, Centre for Behavioural Ecology and Evolution, School of Life Sciences, Hubei University, Wuhan, Hubei, China cEvolutionary Zoology Laboratory, Department of Organisms and Ecosystems Research, National Institute of Biology, Ljubljana, Slovenia dEvolutionary Zoology Laboratory, Biological Institute ZRC SAZU, Ljubljana, Slovenia eDepartment of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D.C., USA fDepartment of Entomology and Nematology, University of California at Davis, Davis, California, USA gDepartment of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba- shi, Ibaraki-ken, 305-0005, Japan hSchool of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia iDepartment of Biological Sciences, National University of Singapore, Singapore +Xin Xu and Matjaž Kuntner should be considered joint first authors *Corresponding authors: Xin Xu, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China. Tel: +86-1857-0334-875; E-mail address: [email protected] Daiqin Li, Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543. -
An Evaluation of Sampling Effects On
Molecular Phylogenetics and Evolution 71 (2014) 79–93 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: A case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae) ⇑ Chris A. Hamilton a, , Brent E. Hendrixson b, Michael S. Brewer c, Jason E. Bond a a Auburn University Museum of Natural History, Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA b Department of Biology, Millsaps College, Jackson, MS 39210, USA c Division of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA article info abstract Article history: The North American tarantula genus Aphonopelma provides one of the greatest challenges to species Received 16 August 2013 delimitation and downstream identification in spiders because traditional morphological characters Revised 29 October 2013 appear ineffective for evaluating limits of intra- and interspecific variation in the group. We evaluated Accepted 11 November 2013 the efficacy of numerous molecular-based approaches to species delimitation within Aphonopelma based Available online 23 November 2013 upon the most extensive sampling of theraphosids to date, while also investigating the sensitivity of ran- domized taxon sampling on the reproducibility of species boundaries. Mitochondrial DNA (cytochrome c Keywords: oxidase subunit I) sequences were sampled from 682 specimens spanning the genetic, taxonomic, and Biodiversity geographic breadth of the genus within the United States. The effects of random taxon sampling com- DNA barcoding Species delimitation pared traditional Neighbor-Joining with three modern quantitative species delimitation approaches GMYC (ABGD, P ID(Liberal), and GMYC). -
An Analysis of the Secondary Structure of the Mitochondrial Large Subunit Rrna Gene (16S) in Spiders and Its Implications for Phylogenetic Reconstruction
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 2003 An Analysis of the Secondary Structure of the Mitochondrial Large Subunit rRNA Gene (16S) in Spiders and Its Implications for Phylogenetic Reconstruction Stacey DeWitt Smith University of Nebraska - Lincoln, [email protected] Jason E. Bond East Carolina University Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub Part of the Life Sciences Commons Smith, Stacey DeWitt and Bond, Jason E., "An Analysis of the Secondary Structure of the Mitochondrial Large Subunit rRNA Gene (16S) in Spiders and Its Implications for Phylogenetic Reconstruction" (2003). Faculty Publications in the Biological Sciences. 111. https://digitalcommons.unl.edu/bioscifacpub/111 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. 2003. The Journal of Arachnology 31:44±54 AN ANALYSIS OF THE SECONDARY STRUCTURE OF THE MITOCHONDRIAL LARGE SUBUNIT rRNA GENE (16S) IN SPIDERS AND ITS IMPLICATIONS FOR PHYLOGENETIC RECONSTRUCTION Stacey D. Smith1: Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 USA Jason E. Bond: East Carolina University, Department of Biology, Howell Science Complex, Greenville, North Carolina 27858 USA ABSTRACT. We investigated the pattern of molecular variation with respect to secondary structure in the 16S ribosomal RNA gene and its phylogenetic implications for arachnids with a focus on spiders. Based on a model by Gutell et al. -
The Role of History in the Diversification of the Funnel-Web
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2004 The Role of History in the Diversification of the unnel-webF Spiders, Agelenopsis Aperta, and its Congeners Nadia Antoine Ayoub University of Tennessee, Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Ecology and Evolutionary Biology Commons Recommended Citation Ayoub, Nadia Antoine, "The Role of History in the Diversification of the unnel-webF Spiders, Agelenopsis Aperta, and its Congeners. " PhD diss., University of Tennessee, 2004. https://trace.tennessee.edu/utk_graddiss/1885 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Nadia Antoine Ayoub entitled "The Role of History in the Diversification of the unnel-webF Spiders, Agelenopsis Aperta, and its Congeners." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Ecology and Evolutionary Biology. Susan E. Riechert, Major Professor We have read this dissertation and recommend its acceptance: