Posted on Authorea 6 May 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158880203.33695479 | This a preprint and has not been peer reviewed. Data may be preliminary. 04 tvn,18) rae adae Fn e,20;Rsnwi,19;Trog,17) n higher and 1973), Terborgh, 1995; higher Rosenzweig, Whittaker, 2011), 2006; Ree, 2012; Stevens, & 2014; Fine, (Fine al., & area et Jetz land Kreft, & greater Lamanna 2003; Gerstner, 1989), 2010; Stein, Alexandre, Stevens, 1967; al., (Janzen, 2014; & heterogeneity et environmental Diniz-Filho, tropical higher (Buckley that 2007), Porter, 1878). niches Nogu´es-Bravo, Araujo, including Wallace, (Hawkins, & of perspectives, 1995; diverse array productivity & Rosenzweig, from wider Roy, primary provided toward 1992; Jablonski, a been Rohde, poles 1959; have have 1993; the Hutchinson, pattern regions biogeography, Schluter, from this 1859; in & of diversity Darwin, explanations Ricklefs pattern 1957; species Potential 1966; pervasive Darlington, increasing Pianka, most 2006; of 2006; Gillooly, the pattern Valentine, & pondered striking (Allen have a equator scientists gradient, the years, diversity hundred latitudinal two the than more For INTRODUCTION 1. Paleo-distributions, Learning, Machine Demography, Historical Phylogenomics, words Key tropical in speciation complexity studying the to highlights to approaches study integrative us This of allowing advantage maximum, hypothesis. the glacial barrier and river last tropics the the African regions. of during the favor in habitat analyses in dynamics suitable migration hypotheses diversification divergence. of river-refuge and of their and contraction demographic since refuge major Our populations the a among both Miocene. flow for reject gene late support to to no barriers mid found strong geograph- the represented we have Additionally, corresponding from rivers ranging species, that Toxicodryas times interpretation both divergence our this within supported and of structure barriers, analysis genetic demographic river historical population to and significant ically phylogenomic revealed comprehensive results a Our conduct to range genus. paleo-distribution modeling phylogeographic stability species river-refuge dated selection, climate and used model We and refuge, demographic Toxicodryas. estimates, river, learning-based genomic genus de- machine classic with snake widely analyses, African the questions clustering Central been of these population and has answer predictions West inferences, to rainforests arboreal the approach the tropical tested integrative in we in diversification an diversity Here, on take hypotheses species to modeling. of possible distribution levels become paleo-species it high and has the sequencing recently shaping Only in decades. refugia for and bated rivers of roles relative The Abstract 2020 6, May 5 4 3 2 1 Peterson Townsend Sterkhova Viktoria Allen Kaitlin sub-Saharan arboreal, snakes in African diversification drove refugia, not Rivers, uemfu aukne-LinzIsiu ¨rEouin-udBiodiversit¨atsforschung Biodiversitatsforschung und f¨ur und Evolutions- Leibniz-Institut Evolutions- - fur f¨ur Naturkunde Leibniz-Institut Museum - Naturkunde Naturelles fur Sciences Museum en Recherche Paso de El Centre at Texas of University Kansas of University 1 l Greenbaum Eli , 1 1 hfneaKusamba Chifundera , n aeBrown Rafe and , 2 alHime Paul , 1 3 akOie R¨odel Mark-Oliver , 1 atrPui aodo Nkonmeneck Tapondjou Paulin Walter , 1 4 oansPenner Johannes , Toxicodryas 5 , 1 , Posted on Authorea 6 May 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158880203.33695479 | This a preprint and has not been peer reviewed. Data may be preliminary. rad ey,21) rmts(lffr ta. 04 ase l,21;Ts,20) rg Bl tal., et al., (Bell et frogs Leache 2008), 2019; Tosi, Bauer, 2013; & Colyn, al., Welton, et Missoup, Greenbaum, et Ley Nicolas, Tapondjou, Haus important 2011; (Allen, 2013; 2004; an al., lizards al., played al., et 2018), have et et Nicolas al., to Hardy (Clifford 2015; et barrier suggested al., primates 2011; Jongsma important are et Drews Hardy, 2012), 2017; an Refugia (Bohoussou Denys, Wieczorek, & represent rodents & 2010). 2019; Doucet, to of Cruaud, Dawson, diversification Rodel, Debout, appear & the & not 2014; Dormontt, in Augustin do al., role Harris, Penner, but et Lowe, 2015), 2010), 2011; (Dauby 2014; al., Rodel, important species al., et al. & (Jacquet be plant et shrews Hillers to many 2003), Penner Zimkus, shown for al., 2018; et 2000; been of Telfer al., have Channing, 2015; drivers et al., alone & as et (Charles Rivers both (Mitchell frogs primates or species. of and refugia, species animal rivers, some and to of for de plant barriers mid & importance the Stankiewicz disparate the 2015; to across supported al., dating diversification have et younger, (Flugel, studies much Rift phylogeographic be African Numerous to East Stankiewicz appears the 2015; River of Cotterill, Congo uplift generally & the the 2006). Eckardt, are to of Wit, (Flugel, but & corresponding course old unknown Stankiewicz and present quite 2005; are Miocene the is Goudie, rivers late mya; basin 2006), these (80–35 the Congo Wit, of Cenozoic Congo, the de many Early while the the of & However, to Ogooue, ages Mesozoic 2006). the exact Late Wit, Sanaga, The the de the to 1). Volta, back the date (Fig. to include Rivers estimated Africa Cross Central the and and (Robbrecht, West Niger taxa in plant barriers and river 2013) Major al., et 1996), al., (Maley, Levinsky et data Levinsky 1991; core Verheyen, 2018; Voelker, pollen & 1996). located & by Gautier-Hion, refuge, are Boano, supported (Colyn, fluvial Pavia, refugia Harvey, been mammal (Huntley, major hypothesized has bird a 2013), River, these multiple however, Congo of of Rift), the patterns Many Albertine distributional around Wegmann, the and forests 1). and Penner, gallery Line Fig. 2016; the Volcanic 2017; in today Greenbaum, Cameroon located the al. & used (e.g., et Behangana, & areas widely Portik Musher, highland Castro, 2011, 1991), still Castellanos, in Larson, Huntley, Rodel, Sosef, are 2017; 2018; & Greenbaum, 1963; that Schmidt al., & Richards, Hillers, Africa et species Behangana, 1994; Kusamba, 1995; sub-Saharan Jongsma and Hughes, Brenac, 2019; Wilde, for 1991) 2017; & Voelker, Sowunmi, De refugia al., Maley, et 1983; & rainforest Bell Girese, Livingstone, Ketner, several (e.g. & 1988; Rietkerk, proposed Maley Riollet, 1991; (1996) 1987; & 1987, Maley Brenac, Bonnefille (Colyn, & data 1988; Maley distribution 1991; the (Brenac, 1989, of records political 1987, testing core Maley, given rigorous rainforests pollen and African 2016), on Central 1986), and Based al. West O’Hara, the et & for Tolley Mayr neglected recently. been 2019; 1994; only has Siddig, until Fjeldsa, hypotheses DeMenocal, these 2017; see 1985; from (Greenbaum, Cracraft, but stemming Africa predictions 1991; 2004; (Amorim, tropical However, Plana, Amazon in the 1997; 2006). instability on Weir, 1969, primarily 2001; Haffer, was 2008; Hollingsworth, the Haffer, focus 2004; in & 2000; scientific al., Pennington, used early et Pennington, widely Gascon the Richardson, been because (e.g. have 2005; production hypotheses Silva, its of “river-refuge These & mechanisms Patton amalgamate the 1993). 1969, vegetation and an driven 1992, biodiversity climate (Haffer, Neotropical Haffer and (i.e. and of patches barriers 1992; study 1970); cycles river Clutton-Brock, forest of Williams, climate combination & a small & (Ayres dry by Vanzolini changes promoted in or was 1973; divergence speciation cold Wallace, which Vanzolini, and in Earth’s 1967; 1982; hypothesis” isolation during Sick, Prance, fragmented causing 1942; 1982; forests cycles), Mayr, 1974, which glaciation 1977; in river Hershkovitz, Pleistocene across hypothesis” 1863; diverged the explain populations “refuge Bates, to and the literature species 1992; which classical 1853); Clutton-Brock, in the Sukumaran, & hypothesis” “river in (Ayres Wiens, the proposed barriers 2004; 2006; Amazon: been the Donoghue, al., have in & diversity mechanisms et species diversification Wiens Jablonski allopatric 2007; 2005; major Schluter, Owens, Three & & Weir Orme 2009). 2017; Cardillo, Brown, al., & et tropical (e.g. Pyron, recent major Smith biodiversity in more high 2006; processes In their speciation Ricklefs, 2007). on explain Soeller, focused to & have researchers Jaramillo, rainforests biogeography, Diniz-Filho, tropical Hawkins, historical 2017; of Noss, studies & (Harrison stability climatic 2 Posted on Authorea 6 May 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158880203.33695479 | This a preprint and has not been peer reviewed. Data may be preliminary. loigu osudyrjc h rdcin frfgahptee nfvro h rviigrl friverine of METHODS role AND prevailing group MATERIALS forest-associated the 2. arboreal, of and generally favor this paleo-distribution in snakes. in hypotheses African Species diversity refugia endemic maintaining and of of Pleistocene, dispersal. the structuring, predictions since shaping, the recent or in reject during to barriers contraction soundly western habitat barriers to the suitable of us strongest that that suggestion allowing suggest the no finding analyses show of migration modelling a stability no and one climate Pleistocene, of divergence, represents models of the support River time predate analyses the Congo demographic times since be Historical populations diversification could hypothesis. among alone river-barrier hypotheses, migration the and distributions three of refugial population predictions the the with although with of aligns that, distributions any historical demonstrate with paleo-distribution of results with congruent congruence Our combined the are determine data hypotheses. et and to and genetic river-refugial Portik location These modeling analyses, the 2019; stability as structure barriers. well climate al., dispersal population as and present et divergence inference, and of Leache phylogeographic past timing 2017; the of dated identify permeability al., integrate to we et modeling to demographic study, (Bell avenues learning-based this machine new speciation In opened rainforest have 2017). tropical sequencing river-refugia al., of DNA and hypotheses genome-scale refugia and classic river, modeling testing the paleo-climate of in predictions mak- advances competing Africa, Recent Central the and testing West for species across addition, system broadly these suitable In arboreality, and hypotheses. a system general distribution. genus fluvial their forest Nagy River mainly this of with Congo 2019; ing feeding Because the correlated Jackson, arboreal, within strongly & 2018). primarily distributed Chippaux distributions Menegon, widely are have 1998; & genus to Luiselli, Hinkel, this predicted & Howell, in are Barieenee, Spawls, snakes, (Akani, species 2011; eating chameleons Both al., egg and et 2013). African frogs the al., bats, to birds, et genus on (Pyron sister support the weak as with them recover analyses genus phylogenetic Asian the in placed expansion blandingii of T. genus patterns of genus The show snake timing to the ses. the use expected Finally, we be study, this would rivers. In but Pleistocene. by rivers the or subdivided of to barriers, additionally ages dating rivers and contraction by to and bounded locations relatively correspond and refugial should be population refugia splits to to rainforest hypothesis: population confined of predicted river-refugia locations been are locations (3) the have with populations cycles; with will concordant glaciation and correlated be Pleistocene be periods should should the dry distributions distributions to to cold, corresponding population corresponding during old, possibly hypothesis: relatively refugia young, refuge be rainforest should (2) hypothesized populations rivers; of of the ages distributions of the population ages between and boundaries barriers the three riverine hypothesis: these to river diversi- (1) correspond between species forests (Colinvaux,should regarding African distinguishing predictions tropics tropical following in 1998), the the alone. make patterns hypotheses data Brenac, for fication diversification phylogeographic records allopatric & on major fossil Maley relying three The and when 1996; core especially Bush, difficult, pollen & been sparse (Hofer, has Miller, systems the hypotheses riverine and Moreno, evolutionary and et 2011; montane 2000), Portik combinationin Oliveira, with al., 2010; in 1999, De refugia Marks, et simultaneouslyor of Borcard, 2010; Gonder overlap roles Fujita, & spatial 2015; & played the Bersier, Leache have al., of 2019; may et because al., 2014; However, both Bohoussou et al., and Leache diversification. that 2011; et refugial 2018; suggesting Ley both al., al., match 2013; 2017), et et patterns al., Jongsma al., Barej divergence et 2014; cases, 2007; Hardy al., some 2009; et al., In al., al., Jacquet et et 2010). et (Anthony & al., (Born Gomez Heuertz, et predictions 2016; plants Lowe Duminil, riverine al., Dauby, rainforest 2016; et Hardy, 2010; and Faye & al., 2015; 2016), Heuertz, et Ley, al., al., Dainou et et 2013; Duminil Heuertz, (Gaubert 2010; & Hardy, pangolins Hardy, 2008), Gonzalez-Martinez, Bowie, Budde, 2011; & (Fjeldsa birds 2017), and Toxicodryas .pulverulenta. T. Boiga ossso w ag,ra-agd eoosWs n eta fia species, African Central and West venomous rear-fanged, large, two of consists Shit 93,adsm uhr tl lsiyte ssc,btrecent but such, as them classify still authors some and 1923), (Schmidt, h aooi lcmn fti eu sucran hywr originally were They uncertain. is genus this of placement taxonomic The Toxicodryas samdlsse ots h rdcin fteehypothe- these of predictions the test to system model a as 3 Dasypeltis Toxicodryas albeit , is Posted on Authorea 6 May 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158880203.33695479 | This a preprint and has not been peer reviewed. Data may be preliminary. pce n o h eu sawoei re oblnemsigdt n ubro oyopi loci. between polymorphic dissimilarity of of Because number each used. and was for data 0.8 separately missing = POPULATIONS r balance in and to was needed, tested was this order were processing data, in parameters further our Further whole no For and a 15. respectively) population. as = the genus n of the and 0.8) Within number maximum for 5 = while the (the (r = and 3 which n 80% M species at at and across parameters be stack) recom- formation) available the a to their were loci identified form to found loci during we According to allowed until polymorphic needed formation) mismatches of (2017). catalog reads of number during al. number of allowed range et number (the mismatches Paris a minimum M of assembly in tested varied (the Final we we out m CSTACKS, 2017), laid kept loci. in al., we methods orthologous USTACKS, et single-copy the in Shafer putatively on of mendations, 2017; based recovery Catchen, selected the & were optimize Stevens, parameters to (Paris, parameters taxa assembly across for of widely one vary including can sets, over data data 20 ddRAD < to separate STACKS score three lenta used uncalled produce quality we an to Phred Next, aimed with average We length. read with read any read pairs. total remove any read the sites, Illumina of discard cut stitched 15% and enzyme of each RAD-Tags, restriction windows demultiplex and by both sliding parameters: demultiplexed barcodes for following and rescue check the quality-filtered barcode, base, with were the STACKS in-line recapitulating reads in second, by Stitched the function library of process_radtags Hohenlohe, genome. complement 2019) reverse the the Weisrock, (Catchen, the with & in with 2.4 individual pair Reece, fragments prior read Briggler, of Illumina libraries, (Hime, orientation an v. approach strand-specific from original read-stitching read STACKS generates a first protocol used the using ddRAD join we assembly, to processed the and Because were filtering read 2013). libraries to Cresko, ddRAD & (with Amores, the lane HiSeqX Bassham, from Illumina one reads on Illumina sequencing each of for bp concentration amounts Biolabs). and equimolar (487–595 England distribution post-ligation in (bp) size 10% New combined Resulting fragment a (Phusion?, were pairs final MA). pools polymerase the base Beverly, Library high-fidelity determine 541 Science, to a pool. used (Sage of with was length cycles TapeStation Prep? Agilent eight insert An Pippin for mean a amplified oligonucleotide a were with custom to products standards using size-selected internal barcoded were with individually range) samples and Pooled enzymes (Agencourt) restriction beads adapters. the AmpureXP using total with digested a individual, bead-cleaned double each was For DNA (2012). and genomic Hoekstra CCTGCAGG-3’) version and of modified Fisher, ng Kay, a Weber, 300–500 following Peterson, individual of of each protocol with for ddRADseq markers v.5 the nuclear MAFFT of anonymous in genome-wide sequenced aligned v5.6.7 also were We Geneious 2002). sequences Kuma, in resulting & manually and (Katoh edited 2012) parameters were default al., Electropherograms et the system. cytochrome Kearse using electrophoresis gene (http://www.geneious.com, capillary extracted mitochondrial 3730 and the ABI and (Sigma-Aldrich) an cyt c-mos 2005; Burbrink, gene RNAlater? & Crother, nuclear or The ethanol (Promega). 95% b system in RSC preserved assembly Maxwell were locus S1. Table and samples in processing, presented Tissue bioinformatic are collection, specimen each data catalog of for Museum Genetic countries (DRC). data 2.2 the species Congo locality the including each and of Africa of numbers, Republic Central range accession Democratic and known GenBank West and the of numbers, Gabon, blocks of Cameroon, representative Ghana, forest was Guinean Liberia, lower Guinea, Sampling and S1). upper Table the (see throughout museums various from of and specimens 20 obtained We Sampling 2.1 eePRapie o ahidvda sn tnadpies(-o:S7 6;Lwo,Slowinski, Lawson, S68; S67, (c-mos: primers standard using individual each for PCR-amplified were ) n obnddt e opiigbt pce.Bcueteoptimal the Because species. both comprising set data combined a and , Phi .blandingii T. pk-nad10b ardedreads). paired-end bp 150 and spike-in X and Msp .pulverulenta T. rsrcinst ’CG-’.Tersligdul ieto rdcswr then were products digestion double resulting The 5’-CCGG-3’). site (restriction I Toxicodryas b 41B 170 ubik asn lwnk,20)adsqecdon sequenced and 2000) Slowinski, & Lawson, Burbrink, H15720; L4910B, : h ecn isn aawslw(%ad73 isn data missing 7.3% and (5% low was data missing percent the , (seven .blandingii T. 4 n 13 and .pulverulenta T. .blandingii T. enovo de enovo de Sbf sebyo ddRADseq of assembly sebefitrdand filtered assemble n for one , rsrcinst 5’- site (restriction I hog fieldwork through ) .pulveru- T. b (cyt Posted on Authorea 6 May 2020 | CC BY 4.0 | https://doi.org/10.22541/au.158880203.33695479 | This a preprint and has not been peer reviewed. Data may be preliminary. n rae ismlrt arxuigteBDDFSpormi h ESpcae(ekv tal., et (Petkova package EEMS the 2015), in al., program et (Chang BED2DIFFS PLINK the using filetype using bed matrix correct Stephens, dissimilarity the & compare a to Novembre, (Petkova, output to created isolation-by-distance stacks similarity of model and filtered genetic EEMS model where our genetic using converted regions a We sets identify population under to data 2016). expected a order three than in uses quickly our dissimilarity more of that genetic decays each expected approach to in an rates diversity migration genetic Surfaces), effective and Migration flow Effective gene of (Estimated patterns spatial using visualized diversity We 2014) genetic Minh, and & substitution migration 2017). 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(2016). the Baele, Muller 10,000 Xie, at Drummond, and every one Mahlow, logged calibration, Head, and for on conducted fossils based the two placement at constant and of one a ages and use assuming Mya), the prior cyt 30.9 tree allow and age: Yule (minimum to a (c-mos and outgroups set clock species as data log-normal The used relaxed Sanger a rate. our used birth We on lineage 2019). analysis al., calibrated et (Bouckaert time 2.5.2 Bayesian a steps conducted 100,000 We by followed plotted was steps and 2017). analyses (Francis, set 2005) 10,000 Phylogenetic (Evanno, 2.3.0 of data 2.4 method v. burn-in Each Evanno MCMC pophelper the package using a 2000). evaluated R and were Donnelly, v. the K Results through STRUCTURE & per 2013). method Stephens, runs al., Bayesian et Pritchard, 10 the (Porras-Hurtado with 2003; using the K=1–10 Pritchard, tested select for Francois, also used & evaluated and & were was Stephens, coefficients, Bouchard, v. admixture function Trouillon, admixture (Falush, Mathieu, LEA and sNMF individual Frichot, 2.3.4 structure using The 2016; estimate (Francois, Population inferred replicates, entropy package. cross 20 were 3.4 2014). minimized with individuals that 1–10, v. 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(Fig. localities ldsadtetwo the and clades .pulveru- T. Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. oprsno I ausfo h eu-ee ACaaye ugse oa ffiegntcclusters, genetic five of total a suggested analyses DAPC genus-level in the populations from two values with BIC of comparison late A the in structure place Population taken 3.3 have to estimated 2). is (Fig. in Fossil-calibrated species clades 3). two each (Fig. the of within River with Congo Pliocene, Diversification the to Mya). of Miocene 18.3 south and age north that of (median Africa, suggests lineages Central divergent dating in three two tree divergence of revealed and Sanger lineages Africa analyses two-locus divergent West two Our same from S2). supported These Fig. both respectively. identical 2; trees were Africa, (Fig. SNP sets Central throughout ddRAD data nodes 2848-locus SNP internal and our supported Sanger and our strongly of with topology, analyses in in coverage estimated of relationships phylogenetic depth dating Broad-scale mean divergence per-sample and effective structure an and Phylogenetic 83.6x data, 3.2 of missing coverage per- 7.3% of with mean 20.7% depth effective loci 77.9x with 4471 an per-sample of of loci and mean consisted 2848 individuals), effective set all of an data across consisted 78.7x and loci set of data, missing data coverage missing of ddRAD outgroup of proportion genus-level the depth as for our sample c-mos defined above), of (here Methods, exception data (see the missing with filtering samples After all in . represented were genes assembly Both cyt locus and c-mos and concatenated processing, Our bioinformatic collection, data as 2014). Genetic well al., 3.1 as et Yannic distributions 2013; mid-Holocene Models Moritz, and RESULTS & maps. LGM McGuire, presence-absence 3. potential Hollingsworth, Peterson, create estimate Devitt, & to to (Devitt, 5% (Soberon summed maps to extrapolation stability were thresholded model continuous and outputs. period GCMs. for 3.4 logistic time three QGIS test the each and for in to from replicates mid-Holocene visualized used and were bootstrap LGM was Models the ten index to chosen 2005). with (MOP) projected parameters were the parity Maxent they and mobility-oriented present, in records the The run These occurrence in & run of were were set 2011). Lew, Models models full Seifert, After the (Anderson, & calibration. using 5% (Warren species model each complexity creation. during for [?] model model created E minimize were final models to for of Final used 2 rates set omission [?] parameter of the 2008), determined scores 2019). significant Soberon, models al., = on AICc & based (linear et and chosen classes Papes, Cobos and 2003), feature 2006) h; (Peterson, Peterson, Schapire, five = & scores of hinge Anderson, combinations ROC and (Phillips, all Maxent t, partial combining and in = run by 10), threshold were and (0.1–1.0 species models p, 8 multipliers Candidate each = and regularization for product 1, possible q, models of 17 = intervals candidate 1–4), at quadratic 1479 1–5, 2–6 l, al., created 0.1, 1–6, et we of (PCAs (Cobos species. intervals models, predictors kuenm each at package environmental our for R of calibrate points the sets to using occurrence three done order around were In buffer evaluation 1000-kilometer and 2019). a projection, creation, as Africa. calibration, sub-Saharan defined Model of were bioclim extent present areas Lira- the on calibration for performed (Escobar, Model LGM order were models the In (PCAs) Maximum MPI-ESM-P. to Glacial distribution analyses and projected Last component MIROC-ESM, in and the principal CCSM4, variables artifacts for autocorrelation, (GCMs): used spatial create were models reduce variables to circulation to 15 general known same three are The under which (LGM) 2014). Peterson, bio19 & Medina-Vogel, and Noriega, bio18, bio9, bio8, .pulverulenta T. ± 14.6x. iegn rud70Ma n h w eta fia ldsdvrigaon . Mya 4.1 around diverging clades African Central two the and Mya, 7.0 around diverging .blandingii T. b .blandingii T. aast(agrdt e eefe)cnitdo 27b,icuigindels. including bp, 1237 of consisted hereafter) set data (Sanger set data ± 36.Our 13.6x. n he in three and .blandingii T. and .blandingii T. .pulverulenta T. .pulverulenta T. 7 iegn rud86Ma h etArcnclade African West the Mya, 8.6 around diverging aastcnitdo 21lc ih5.0% with loci 7231 of consisted set data acigtecae dnie nthe in identified clades the matching , iegdi h al omid-Miocene to early the in diverged ± 20.Our 12.0x. .blandingii T. .pulverulenta T. otalongicaudae Contia .pulverulenta T. nWs and West in , one , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. 06.Ol eetyhsi eoepsil otk nitgaieapoc oaseigteequestions 2019). these al., Leach´e answering et 2017; to al., approach et integrative (Portik an modeling take distribution to Collevatti, paleo-species possible & and Terribile, become sequencing Lima-Ribeiro, it genomic Vitorino, R 1986; with has Irion, has O’Hara, recently rainforests Colinvaux, & tropical Only 1991; Mayr in diversity 1997; Amorim, 2016). species 1969, of (e.g. Haffer, levels 2004; decades high DeMenocal, for the shaping debated in been widely refugia have and been may rivers of expansion roles relative northward The of potential degrees greatest lesser the was DISCUSSION but day with 4. present Africa, range, 7c). the Central species past Africa. (Fig. in expansion the West time to range scale in of northward through LGM time possible edges No stable any the the Africa. remained at on Central from has southern estimated found habitat species in only change each suitable is distribution of persistent for habitat distribution of suitable core in areas the Instability that the suggest 7b). estimating present (Fig. maps the sets stability data all climate for genus Continuous Paleodistribution distribution the present-day for the habitat 7). to suitable of similar of range highly (Fig. contraction the habitats southern while and Angola, woodland northern into Africa. and slight Central a rainforest and West suggested in both LGM from the for for documented ranges models species overlapping widely both suggested with and modeling matrix distribution S3. confusion and Species The S2 Tables (2020). in Carstens modeling found & Distribution be Smith 3.6 can by error model obtained out-of-bag per those The votes to of S3). similar number and are S2 rate (Tables error support out-of-bag low very received for contact rate as secondary with flow divergence gene and without divergence identified for pulverulenta we model selection, best model the demographic flow learning-based gene machine of Using analysis for individually and EEMS modeling S4). ran Demographic (Fig. also 3.5 We species levels individual 5b). higher each (Fig. and for rainforest Africa sizes Guinean Central sample Upper of the coast blandingii of in the species T. in for supported both diversity suggested for were African were data West River diversity all of Congo lower-than-expected analyzed western simultaneously of we the Areas when and higher- 5a). dispersal of Gap to areas barriers Dahomey as well major The as as migration, diversity. to genetic barriers present-day lower-than-expected several or identified we 2016). analyses (Puechmaille, EEMS uneven our diversity Through or genetic small and are preferable migration sizes be analyses sample Contemporary may multivariate-based and when 3.4 equilibrium because STRUCTURE Hardy-Weinberg as analyses about such assumptions remaining make methods our not Bayesian for do over DAPC populations and for five LEA as three, used such We of highest by LEA. instead second detected from the populations, as two not those supported suggested was in were and two populations populations clades and Three level, between African genus Central admixture the the at however, combined populations identical; two suggested was STRUCTURE Similarly, methods DAPC. clustering of two samples the of Gabonese sample the Cameroonian for the in identified for populations at clusters two three genetic the and distinct to two corresponding identified level, LEA, genus method, the admixture-based Our S3). (Fig. analyses phylogenetic .blandingii T. ihapseirpoaiiyo .3(i.6.Frbt pce,mdl ersnign divergence no representing models species, both For 6). (Fig. 0.63 of probability posterior a with and .pulverulenta T. .blandingii T. a 73 n 28 for 22.8% and 17.3% was .pulverulenta T. oiora pulverulenta Toxicodryas .pulverulenta T. .blandingii T. ihapseirpoaiiyo .8 n iegnewt eeflwfor flow gene with divergence and 0.68, of probability posterior a with u hs nlssaemr icl oitrrtbcueo h small the of because interpret to difficult more are analyses these but , Toxicodryas ssgetdb AC(i.4.Alwaon famxuewas admixture of amount low A 4). (Fig. DAPC by suggested as .blandingii T. eandsal Fg a.TemdHlcn itiuinwas distribution mid-Holocene The 7a). (Fig. stable remained Fg ) h ouainasgmn fidvdasbetween individuals of assignment population The 4). 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Data may be preliminary. oe Fg b,epaiigtebooia elt fti are o oetascae,piaiyarboreal primarily forest-associated, for barrier this of reality biological the for barrier emphasizing in dispersal 5b), diversity a (Fig. genetic as lower model identified the previously support in been also flow R has areas gene which to (e.g. and barriers species rainforests, as Guinean arboreal Gap lower and Dahomey 2011). the upper Jump, the and role & River the (Hampe but Congo literature 2002), western genus the Dynesius, the in & support during attention Jansson analyses form little 2011; to Migration received Jump, able has has are & refugia diversification refugia Hampe that driving older 1997; likely in (Haffer, possible is 2004; refugia change it of of climatic Jacobs, Pleistocene, the of role 2016; of the period al., oscillations byany surrounding climate this et characterized research dramatic in change (Herbert the most divergences climatic on Africa Although global 2015), focused population sub-Saharan 2014). of al., of throughout al., time et locations a et shifts (Jacquet and also Menegon vegetation shrews was timing and Miocene 2003), the including cooling the al., while species barriers, dramatic However, et many river Telfer to with 2018). 2015; barrier correspond al., well-known al., study a et et been (Charles Mitchell has frogs 2012; river and Wood, Congo The & splits (Harcourt 2015). distribution et al., primates African Zimkus Central et 2018; to (W (Jacquet West al., cobras shrews similar et other forest and and Jongsma for in 2019), 2017; noted al., seen al., been et been et have (Portillo have Eocene- snakes times (Bell late terrestrial divergence frogs the and Miocene including 2017), in late taxa al., Plateau to African Adamawa West mid the in and Similar of Central barrier 2016). formation widespread al., potential the et The to another (Fagny back 2). Oligocene River, dates early Sanaga (Fig. likely but The Pliocene history, 2006). geological the known Wit, to de Miocene & Stankiewicz late African Central the the in in in the barrier place barrier from a derived took River, of predictions diversification Congo the side reject intraspecific and either to subsequent wider, on fail and found also is phylogeny be river time-calibrated can hypothesis. the a species river-barrier where from both west estimates from the time clades Divergence in of stronger samples 3) DRC be (Fig. eastern to river the seems this In levels barrier stronger. River Minor is Congo 4). current the of (Fig. clades species, clusters two the both genetic the between analyses between distinct occurred structure Of and have five population River, species. to Our supporting this River. appear to analyses Congo admixture in needed western phylogenetic of structure the be with by genetic will concordant separated shaping analyses Africa, are in Central population comparative in role and as distributed deterministic sampling interpreted are Leach´e most additional 2019; been the but al., three frequently Leach´e played et the 2017), 2018; have river al., al., rivers which et et Both Jongsma determine Portik DRC. 2008; 2010; allopatrically (Blackburn, the Fujita, situated vertebrates & in terrestrial generally River other are within in Congo species barriers clades the each two strongly or divergent, within The deeply Cameroon clades barriers. two sympatric, reveal river broadly set across data are genus SNP species RADseq the recognized 2848-locus of in and lineages analysis last set supported phylogenetic data the Sanger first during two-locus the contraction our represents habitat suitable study and for This ages support the of diversification on lack Species based a 4.1 hypotheses as river-refuge well and terrestrial refuge as maximum. for the populations genus glacial over hypotheses snake the hypothesis river-refuge African of river and arboreal locations the the refuge, for system: river, study support classic novel strong the a of using predictions diversification faunal alternate tested we Here Toxicodryas .blandingii T. .pulverulenta T. Fg a.TeDhmygpi aua aan eini etArc htseparates that Africa West in region savanna natural a is gap Dahomey The 5a). (Fig. .blandingii T. dvrec ie 86Ma,dtsbc otemdlt icn (Fl Miocene mid-late the to back dates Mya), ˜8.6 time: (divergence dl mrc,Pne,Shiz ae,21;Shne&Htee,20) Both 2005). Hutterer, & Schunke 2014; Barej, & Schmitz, Penner, Emmrich, ¨ odel, oiora blandingii Toxicodryas lds n sdsrbtdi etArc abi ihlmtdsmln)adtwo and sampling) limited with (albeit Africa West in distributed is one clades, se ta. 08,fos(ecee l,21) iad Alne l,2019), al., et (Allen lizards 2019), al., et (Leache frogs 2018), al., et uster ¨ n he in three and .blandingii T. Toxicodryas .pulverulenta T. .blandingii T. and .pulverulenta T. ntesml olce tteSng ie Fg ) In 4). (Fig. River Sanaga the at collected sample the in .pulverulenta T. .pulverulenta T. 9 hnepce ne ueisolation-by-distance pure a under expected than r eaae ihrb h aaaRvrin River Sanaga the by either separated are dvrec ie 41Ma,adapotential a and Mya), ˜4.1 time: (divergence Fg ;Fg 2.Atog oa,tetwo the today, Although S2). Fig. 2; (Fig. Toxicodryas ldssprtdb h etr Congo western the by separated clades iegdi h al omid-Miocene, to early the in diverged .blandingii T. hlgntcaaye of analyses Phylogenetic . Toxicodryas gle l,2015; al., et ugel ¨ a poorly a has , efound We . Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ao,adi etArc rfga9 –,ad13rsetvl,Fg.1 ) e,ordtdphylogenies dated our Yet, of 2). predictions 1, contraction Figs. habitat respectively, and age 1–3 population and to River, Pleistocene Congo 5–8, difficult the the 9, distribution extremely around reject where (refugia refugia it models system, hypothesized Africa study makes paleo-distribution with West our and 1), populations in in salient of Fig. and particularly association 2000; is the Gabon, difficulty 1999; suggested (Leach´e This have alone 2017). al., may data areas al., et data distribution et with with Portik refugia (Hofer mechanisms 2019; of diversification zones al., different association et of riparian the importance and or relative Africa, the relief Central untangle and surface 2017). West high al., in refugia et barriers of (but surrounding Portik geographic phylogeography hypotheses 2019; gene of mitochondrial complexity al., and Leach´e of The et concepts in era African examples the the tropical during multilocus of of sets recent, hypotheses many data more to single-locus so see have by respect approaches evaluated that with Barnes, such been However, noteworthy Lister, study. only in Stewart, is have this power 2008; of it of Bennett, focus diversification, & lack the Fjelds˚a Provan species and not & 2002; (e.g. pitfalls are Madison, and The sets & Dal´en, (e.g. 2010), Knowles 1986). & data (e.g., diversification O’Hara, DNA elsewhere & of discussed mitochondrial descriptive, Mayr mechanisms been this 1969; single-locus in infer Haffer, conducted only were 1997; to employing studies Lovett, refugial attempted usually rainforest they manner, of & observed majority which pattern-based Knowles commonly The 2001). from biogeographers 2009; statistical Templeton, 2003), Knowles, 2000; distributions and Taberlet, Avise, 2014; species modeling, & Ellegren, Jordan, of paleo-distribution 2007; Tallmon, patterns phylogenies, Richards, England, & Luikart, dated 2002; (Carstens data, Madison, demography genomic historical of of availability analyses the to Prior studies species diversification in species shifts Integrative Southward replacement habitat. a 4.3 habitat. forest suggesting savannah (1981), montane White strict with of to rainforest shifts lowland distribution surrounding shift forest of woodlands dramatic predicted dryer with more to correspond a may shifted suitability of composition instead rainforest that refugia, of hypothesis stability rainforest The the rainforest. habitat supports and widespread woodland Pleistocene inferred both the in our distribution contrast, their Africa In by reflected Central 2017). DRC as al., in southern et contraction the Portik habitat habitat in 2019; and substantial stability al., for (Leach´e Angola suggested et Pleistocene potential have northern the frogs greatest today’s during on into The of studies south 7c). ranges paleo-distribution the (Fig. core Similar to that years be suggested 22,000 to mapping past appears 7). stability the (Fig. species habitat for for this our stable occurred in and climate remained expansion 7a), suitable have (Fig. of species LGM contraction 1981). both the 2019). substantial White, Jackson, during no & 2001; species (Chippaux that 1996, Africa either suggested al., Central and modeling et West Colinvaux paleo-distribution in forest; distributions Our overlapping dry widely savannas to exhibit by species wet more two replaced of from possibility was (i.e., the rainforest emphasized composition have African Toxicodryas forest others Central widely while in 1998), been the shifts Brenac, has of & subtle Pleistocene much Maley the 1996; that Maley, during 2004; argued refugia (DeMenocal, have rainforest authors surrounding Some habitat intervening debated. represent the of the they nature of that The likely light stability justified. is habitat In variation is and phenotypic it S3). revision of Paleo-distributions clades, (Table taxonomic analyses 4.2 five formal and species these if data both determine morphological between of to in flow underway surveys gene confidence African thus, are and, Central of high lineages two lack with evolutionary the and distinct out in times clades ruled River divergence between two was Congo Miocene barriers the flow the between dispersal gene across flow riverine flow Contemporary gene gene that without minor suggest divergence with further indicating analyses strong, demographic are both Our that gap. fact Dahomey the despite vertebrates Toxicodryas pce r eeal hrceie sabra cosrifrs n odadhbtt n the and habitats woodland and rainforest across arboreal as characterized generally are species a edet h eaieyrdcddpnec fabra nkso os habitats, moist on snakes arboreal of dependence reduced relatively the to due be may Toxicodryas 10 pce aebe on nfrs ace ihnthe within patches forest in found been have species .blandingii T. .pulverulenta T. Toxicodryas ldsaddivergence and clades aia through habitat lds(i.6). (Fig. clades Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. nhn,N . ono-ae . ery . lffr,S . breh,K . ui,C . Bruford, . . . E., C. Tutin, A., K. Abernethy, L., S. distributions: Clifford, species’ K., Jeffrey, of M., models Johnson-Bawe, predictive M., Evaluating N. (2003). Anthony, T. models. A. optimal Peterson, selecting & for D., Criteria Lew, levels P., High R. theory. Anderson, (2019). the Testing M. simulations: A. model Refuge Bauer, (1991). 35 & S. J., D. African D. L. West Amorim, Welton, and E., Central Greenbaum, within P., structure 231–234. at W. phylogenetic biodiversity Tapondjou, hidden and N. rates of E., speciation in K. gradients Allen, of latitudinal feeding Assessing (2006). and F. scale. reproduction J. global habitat, Gillooly, the on & Observations P., (1998). A. Allen, L. Luiselli, & F., blandingii An I. models. Boiga spThin: Barieenee, niche (2015). C., ecological P. in G. R. use Akani, Anderson, for records & occurrence B., species Vilela, 541–545. of A., , thinning Radosavljevic, spatial A., for package R. R Boria, E., M. Konomou, with permits. Aiello-Lammens, R. assistance necessary Maougnan, for all Fulton D. for Samuel, Machon, authorities Daniel, M. Guinean References Pepe, Mazumdar, the Bayo, S. as Papa, well Rene, Sao as Langlois, work Ibrahim, D. the field thankful Mohamed, and to is Oumar, 3064/1-2) as JP A. RO well 01LC0017). BIOTA-West, & Marcel, as W08 183/4-1 Science Barej (BMBF-Project VE Michael National Research (DFG US to and Foundation Education the Research support. of and German fellowship Ministry Paso, the postdoctoral Federal for El from funds Institute funding at Biodiversity research Texas received KU of MOR M.D., the Sladen Exploration University thanks Reed, and Percy the PMH Research K. the (DEB-1145459). WW-R018-17), la Geographic Foundation Grant, by and National pour Alonda, two 8556-08 University, supported Seed Congolais Villanova F.I. (nos. was Group at Institut Grants Akuku, EG Biology and Specialist of permits. F. Naturelles Department Amphibian and the and Sciences IUCN/SSC from support en J., an Recherche project Luhumyo, and Fund, provided de Arts M. Memorial Centre Nature Liberal Marcel, companions The la of field A.M. M’Mema. de their College Conservation A. Zigabe, thank the CK late M. and of the EG Fund Aristote, Kansas. and Scholar of M.M. Faculty University Illumina Muninga, Foundation the Docking for of funding Science W.M. the Institute Partial National Biodiversity KU. from the at the States came and collection by United Sciences study data supported genomic at this of was Wynn in course including: Lab the Addison sequencing study, during Brown and 1557053) this The Zoology, and of for History. 1654388 Comparative Museum extractions (DEB Natural of University and of State Museum tissues Louisiana Museum at at lent National Zimkus Parker that Seth We Breda Studies institutions Sciences, modeling. Science, Graduate of and niche Natural Academy of regarding people California Office advice the at for the Scheinberg of Cobos and Lauren all Marlon Institute to and Biodiversity sequencing, grateful Kansas ddRAD are of with University associated the funding thank for to Earth. like of would ecosystems We imperiled other and Mittermeier, 1988) that 2000; Biodiversity Myers, Mittermeier, ACKNOWLEDGMENTS processes Global 2011; & evolutionary with Gascon, Myers, & cases and Mittermeier, many Brooks, of 2017; environmental in Larsen, maintenance Romportl, of Turner, coincide & and which inference (Hrdina, partitioning, areas, to Hotspots tropical production, Conservation lead in the biodiversity may pattern-based of terrestrial pure landscapes of understanding accumulate beyond nuanced complex importance Moving more the in biodiversity. and highlight diversity to species hypotheses results deeper concentrated competing These a geographically among hypothesis. inference, of distinguish barrier levels statistically river high to approach the explain multidisciplinary of integrative, favor an in using hypotheses refugial the 803–812. , Clbia)i ot-atr Nigeria. south-eastern in (Colubridae) clg Letters Ecology , 9 947–954. , clgclModelling Ecological 11 mhbaRpii,19, Amphibia-Reptilia, , 162 211–232. , Trachylepis eit rsliad Entomologia de Brasileira Revista 430–436. skinks. Salamandra cgah,38 Ecography, , 55 , , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ases .C,&Rcad,C .(07.Itgaigcaecn n clgclncemdln ncompar- in modeling niche ecological rates: and coalescent diversification Integrating in bias (2007). latitudinal L. C. for phylogeography. Testing Richards, ative & (2005). C., F. B. P. Carstens, I. birds Owens, World New & using L. example D. An C. Orme, M., Cardillo, polytypic the of phylogeography DNA Mitochondrial ( (2000). 2118. Snake B. Rat J. Slowinski, American & North R., Lawson, T., rainforest F. tropical Burbrink, ancient The (2013). M. C. Heuertz, McCain, Africa. & Equatorial J., . O. . . Hardy, C., L., tree S. B. Gonzalez-Martinez, Anacker, B., P., K. mammals. S. Budde, in Harrison, Sciences gradient Biological J., diversity B: latitudinal N. Society the Kraft, Royal and D., conservatism the D. niche Ackerly, 11.000 Phylogeny, J., et (2010). T. 25.000 M. Davies, entre B., Cameroun L. l’Ouest Buckley, dans Pondichery Franwise. de climat Langue Francais du Palynologues l’Institut et Ass. . de . vegetation Techniques . Symposium Xeme la A., Actes de BP. Evolution Gavryushkina, ans (1988). M., P. analysis. Fourment, Brenac, evolutionary Bayesian S., for platform Duchene, software advanced An Biology J., Computational 2.5: Barido-Sottani, BEAST (2019). for T.G., M. implications Matschiner, Vaughan, Paleoclimatic (Burundi): Africa. R., sequence tropical Bouckaert, in pollen BP Kashiru yr The 40,000 (1988). last G. the Riollet, (2015). V. & Nicolas, R. . Bonnefille, .. J., Kennis, K., J. Peterhans, refugia. genus M., rodent M.-H. role Colyn, the of B., Chevallier, the phylogeography Akpatou, for & The R., Evidence Cornette, M., H., Domain: Hossaert-McKey, Forest K. of Bohoussou, J., Guinea differentiation Lower E. intraspecific the the Wickings, of in S., history refugia biogeographical Ossari, of the D., into McKey, Insights N., (2011). Alvarez, C., Born, Phylogeny R. frogs: K. African Evolution of Zamudio, and history life Phylogenetics and . Molecular size . ( . body frogs of squeakers M., evolution reed and Burger, of Biogeography in C., Islands. (2008). incursions Guinea D. C. marine D. of Blackburn, Blackburn, and Gulf F., fragmentation the M. and forest Barej, Africa climate-driven G., Central to from Badjedjea, responses L., Idiosyncratic J. (2017). Parra, C., R. Bell, R (1863). & H.W. W., Bates, Boehme, H., Hinkel, A., Hillers, M., African Menegon, off–the A., Schmitz, F., primates M. Amazonian Barej, in size range species and boundaries Naturalist River American (1992). T.H. Clutton-Brock, & J.M.C. Ayres, Africa. Press. Central versity in (2000). diversity C. genetic J. gorilla shaping Avise, Sciences in of rivers Academy and National refugia the Pleistocene of of Proceedings role The (2007). W. M. ypoi globulifera Symphonia ora fBiogeography of Journal Arthroleptis meohyu superciliaris Amietophrynus Heredity hlgorpy h itr n omto fspecies of formation and history The Phylogeography: h auaito h ie Amazon. River the on Naturalist The , 140 vlto:ItrainlJunlo rai Evolution Organic of Journal International Evolution: , 15 3–537. 531– , .f Cuica)wsntrsrce opsuae litcn eui nAtlantic in refugia Pleistocene postulated to restricted not was (Clusiaceae) f. L. n ogfigrdfos( frogs long-fingered and ) , e1006650. , 111 lpeobsoleta Elaphe , 66–76. , 42 Ecology . 2049–2061. , , Malacomys , 49 utrayResearch Quaternary 277 806–826. , pce ope fgattoads. giant of complex species :Aciiu ftesbpce concept. subspecies the of critique A ): , uomaklaineana Aucoumea 2131–2138. , 86 , , 25 USA 2278–2287. , ugssmlil forpclPesoeelwadforest lowland Pleistocene Afrotropical multiple suggests oeua Ecology Molecular 12 91–103. , Cardioglossa , 104 odn K onMurray. John UK: London, 20432–20436. , , 30 . 19–35. , siae rmmtcodildata. mitochondrial from estimated ) oeua Ecology Molecular rvu el eto e cecs& Sciences des Section la de Travaux , 26 abig,M:HradUni- Harvard MA: Cambridge, . 5223–5244. , Zootaxa , 61 dl .O 21) Dusted (2011). M.-O. ¨ odel, 1439–1454. , Evolution , 2772 , 20 1–32. , 131–142. , rceig of Proceedings , 54 2107– , PLoS . Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. rpia atrso ih reseisi tatcCnrlArc rvd nihsit h atdnmc of dynamics past phylogeo- the Congruent into (2014). insights J. provide O. Africa Hardy, Central Atlantic & in T., Stevart, species cover. K., tree phy-forest G. eight and Koffi, of polymorphism M., patterns graphical Heuertz, DNA rainforest: J., Chloroplast mature Duminil, in G., Dauby, (2010). widespread J. species O. tree Hardy, African & Central olens M., a Heuertz, of J., logeography Duminil, G., Dauby, Life for Struggle the in Races (1859). C.R. Darwin, refugia Forest Inc. Sons, & (2010). high Wiley M. (1957). with John tree Heuertz, Jr. African J., & wide-spread P. J., a Darlington, in O. isolation Hardy, historical American G., support capacity, Mahy, South sequences colonization cpDNA J.-L., the and Doucet, within NSSRs J.-P., differentiation revisited: Bizoux, of K., patterns Dainou, and Basin. biogeography endemism. in Zaire of Historical history the Areas palaeoenvironmental avifauna: in (1985). of refuge J. re-appraisal fluvial Cracraft, A major a (1991). cas for Le W. Verheyen, Evidence 403–407. speciation: & la Africa: A. pour zoo- Central Zaire Gautier-Hion, Interpretations fleuve M., du Zaire: Colyn, bassin du du cuvette zoogeographique Siens. la L’importance Primates be de des (1991). to ombrophiles M. paradigm forets M. A des Colyn, Primates distribution. (2001). de Les N. modeles Amazonian J. des (1987). of geographiques Mello, hypothesis pollen M. De refuge long M. & Prance A Colyn, & B., Haffer M. (1996). the B. Bush, falsify M. E., data Bush, M. speciation. paleoecological & and Rasanen, Geological C., G., M. times. discarded: Irion, glacial Miller, A., in E., P. detailed cooling J. Colinvaux, for and package Forest Moreno, R E., Amazonia: An lowland P. from Kuenm: Oliveira, record De (2019). A., L. P. Osorio-Olvera, Maxent. Colinvaux, & using N., models Barve, niche T., ecological . of A. . development . Peterson, E., J., M. L. Cobos, (2019). White, ( K. E., Press. gorillas Jackson, C. University lowland & Hopkins Tutin, P., western A., J. of K. phylogeography Chippaux, Abernethy, DNA M., Mitochondrial Bawe-Johnson, (2004). M., gorilla model. J. coalescent N. E. the Anthony, D. under Wickings, L., data Portik, S. SNP . from Clifford, . Gvoˇzd´ık, . inference Quartet K., V., M. (2014). L. Fujita, formatics frog Kubatko, M., leaf-folding & African J., Burger, the rainforest Chifman, C., Guineo-Congolian in Lower Diversification D. the islands: of Blackburn, forest Hyperoliidae) and C., (Anura: sea, R. Second-generation Sky, (2015). (2018). Bell, sets J. M. data J. L., richer Lee, & K. and M., larger S. Charles, of tool Purcell, challenge S., analysis Vattikuti, the An C., to L. Stacks: Tellier, Rising C., (2013). PLINK: C. A. Chow, W. C., C. Cresko, Chang, & A., Amores, genomics. S., population Bassham, for A., set P. Hohenlohe, J., Catchen, (Annonaceae). ). oeua Ecology Molecular , Amazoniana 30 oeua Ecology Molecular 3317–3324. , nae ue oa eI fiu etae eto olge evrn 264 Tervuren, Zoologie, Section Centrale, Afrique I; de Royal Musee Annales rpclPatBiology Plant Tropical h rgno pce yMaso aua eeto,o h rsraino Favoured of Preservation the or Selection, Natural of Means by Species of Origin The iii excels Milicia , 16 oeua Ecology Molecular , 609–646. , ogorpyadteGorpia itiuino Animals of Distribution Geographical the and Zoogeography 13, odn K onMurray. John UK: London, . rihlgclMonographs Ornithological , 1551–1565. 23 (Moracea). 2299–2312. , nkso eta n etr Africa Western and Central of Snakes eu eZooi fian,True,101 Tervuren, Africaine, Zoologie de Revue , 3 , 4–13. , oeua Ecology Molecular 22 3124–3140. , 13 PeerJ , 36 Gigascience . , 49–84. , 7 ora fBiogeography of Journal . e6281. , , Science 19 4462–4477. , , ora fBiogeography of Journal , 4 274 7. , rewydnrnsuave- Greenwayodendron 85–88. , atmr,M:John MD: Baltimore, . fiau paradorsalis Afrixalus 183–96. , e ok NY: York, New . , 45 oil gorilla Gorilla 1781–1794. , –250. 1– , Bioin- , 18 , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. rnos .(06.Rnigsrcuelk ouaingntcaaye ihR. struc- with population analyses visualize genetic and population Grenoble-Alpes analyze structure-like U. to Running Genetics, app web (2016). and O. package Francois, R An (Eds.) C. Pophelper: M. Wit, river ture. (2017). De Congo & M. the F., of R. Guillocheau, patterns Francis, Basin J., drainage day M. Congo present Wit, the The De biota: of In (2015). forest Potential P. evolution. Resource African F. Neogene in Cotterill, their & species and D., forest young system F. and Africa’s Eckardt, old J., of centres. T. of evolutionary diversification Flugel, patterns as and areas Geographical montane origin (1997). specific of the C. significance J. on The Lovett, perspectives & New J., Fjeldsa, (2008). America C. South R. and Africa Bowie, avifauna. latitudinal in & birds the J., of on species Fjeldsa, young effect priorities. and species-area conservation relict for for time-integrated implications patterns a and Geographical for (1994). J. Evidence Fjeldsa, (2006). diversity. Phy- R.H. tree in (2016). Ree, gradient T. & Couvreur, P.V.A. & Fine, Y., Vigouroux, diversity. B., genetic Sonke, unique D., predicts genus Richard, the C., Adamawa of Mariac, and logeography A. Line V., Boutale, Volcanic Deblauwe, & Cameroon A., D., massif, Faye, Stumbea, volcano H., alkaline multilocus Guillou, Mbabo using Africa). M., Tchabal (Central J. of structure plateau Bardintzeff, ages population R., K–Ar Temdjim, of New F., Inference (2016). O. Nkouandou, frequencies. (2003). demographic F., allele M. K. Robust Fagny, correlated and J. loci (2013). Pritchard, Linked & M. data: Foll, M., genotype & Stephens, the V.C., D., using Falush, Sousa, data. individuals SNP E., of and clusters Huerta-Sanchez, genomic of from I., number inference Dupanloup, the L., Detecting Excoffier, (2005). study. J. simulation Goudet, the A & of STRUCTURE: software S., spread Regnaut, for Potential G., Evanno, (2014). A.T. Peterson, transference. & model strict G., Medina-Vogel, ( A., fungus Lira-Noriega, white-nose E., L. Escobar, organisms. non-model in (2015). African genomics J. in population Evolution and O. changes & sequencing Hardy, hypothesis. Genome demographic & refuge (2014). and H. forest J.-L., fragmentation Ellegren, the Doucet, population supports F., species past Walmacq, tree of C., refugia forest dating Montane rain Doumenge, molecular P., (2013). Mardulyn, Pleistocene C. S., Late Moritz, Mona, & J., A., Duminil, J. McGuire, Large-blotched D., the B. in Pliocene–Pleistocene. Hollingsworth, 1650–1665. structure the E., genetic during S. population evolution Devitt, predict faunal J., T. and Devitt, change Letters climate Science African Planetary and (2004). Earth from B. inferred P. dispersal gene DeMenocal, and tree, history Population timber African (2011). Central J. a Heredity O. Hardy, of & structure J.-L., genetic Doucet, spatial C., D. G. Debout, oeua clg Resources Ecology Molecular , fia ora fEcology of Journal African 106 , 29 88–99. , 51–63. , suoynacsdestructans Pseudogymnoascus Podococcus h mrcnNaturalist American The nentoa ora fAvne Geosciences Advanced of Journal International esailHealth Geospatial 1–9. , oeua hlgntc n Evolution and Phylogenetics Molecular , 17 Pla/rcca)i eta fia anfrss lmt stability Climate forests: rain African Central in (Palmae/Arecaceae) , , 220 LSGenetics PLOS 46 p.3537.Bri,Gray Springer. Germany: Berlin, 315–337). (pp. . 27–32. , 235–247. , 3–24. , idvriy&Conservation & Biodiversity , 9 oeua Ecology Molecular 221–229. , , nteAeia:Ueo aetadNceAt assure to A Niche and Maxent of Use Americas: the in ) 168 14 , 9 796–804. , itmnnhsbenthamianus Distemonanthus e1003905. , Ensatina Genetics ora fBiogeography of Journal , 14 idvriy&Cnevto,6 Conservation, & Biodiversity 2611–2620. , salamander. , 164 , , , 105 3 4 1567–1587. , 207–226. , 62–71. , 126–138. , uoil nPopulation in tutorials R oeua Ecology Molecular , 42 (Caesalpinioideae). rnsi Ecology in Trends 1443–1454. , elg and Geology 325–346. , , 22 , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. acut .H,&Wo,M .(02.Rvr sbrir opiaedsrbtosi Africa. in distributions primate to future. barriers as present, Rivers Past, (2012). Primatology A. M. of relicts: Wood, Journal Climate & H., A. (2011). Harcourt, S. A. B Systematics Jump, and Amazonia. Evolution, & in species A., of origin Hampe, the explain overview. to An Hypotheses , Amazonia: (2008). R. in J. speciation Haffer vertebrate of models Alternative Conservation Amazonia. and (1997). of R. history the J. in Haffer, arrow Amazonia. Biogeographie time’s de southern and Societe of cycle la Time’s birds de forest (1993). some R. J. in ZoologiaHaffer, effect” serie. “river Nova the Goeldi. (Ed.) On T. Emilio Paraense G. (1992). Prance, R. In J. theory. Haffer, refuge the of Tropics aspects the General in (1982). R. J. America. Haffer, South tropical in speciation 14 Avian Club, (1974). birds. R. forest J. Amazonian joint in Haffer, the Speciation Inferring (1969). R. (2009). J. D. Haffer, C. data. Bustamante, frequency & SNP multidimensional H., e1000695. from S. , populations Williamson, multiple D., of history R. demographic Hernandez, N., R. Gutenkunst, England. New of Press Cretaceous. University the NH: since Africa (2017). of E. Greenbaum drainage chimpanzee The of S. histories (2005). Tishkoff, and S. . structure A. . . genetic Goudie, J., the genetic F. in Lankester, Current differences T., reveals J. Kujawski, Cameroon (2009). W., populations. from M. V. Evidence Mitchell, L., Poncet, (2011). Ghobrial, A. S., & Locatelli, activities. A., K., human M. recent Kochko, Gonder, and de changes S., climatic ancient Hamon, of P., impact Hamon, of S., differentiation Dussert, Mbo Barombi C., Lake Gomez, the in matter. palaeoenvironments organic Quaternary of (2016). isotopes Late carbon 107 A. Palaeoecology, (1994). and Antunes, P. pollen from Brenac, deduced & (Cameroon) . . J. . Maley, diversification. J., P., Pleistocene Malekani, Girese, of (Pholidota, S., signatures pangolin T. traceable Dufour, P. common as Boag, K., African lineages poached Afiademanyo, cryptic . heavily . G., . the Ngua, C., of S. F., Phylogeography Lougheed, Njiokou, P., P., J. Gaubert, species. Bogart, Amazonian N., of M. USA distribution Silva, Sciences, geographic da of the L., Academy and J. barriers of Patton, Riverine estimation R., stud- (2000). efficient J. and association Malcolm, Fast ecological C., (2014). Gascon, and O. Francois, landscape & G. for coefficients. Bouchard, package ancestry T., individual Trouillon, R F., An Mathieu, E., LEA: Frichot, (2015). O. Francois, ies. & E., Frichot, 68 ehd nEooyadEvolution and Ecology in Methods 1–947. 917– , 1–390. , rceig fteNtoa cdm fSine,USA Sciences, of Academy National the of Proceedings p.62) e ok Y oubaUiest Press. University Columbia NY: York, New 6–24). (pp. . oe canephora Coffea , 65–78. , 6 451–476. , mrl ayit:ASinitsAvnue nteJnlso h Congo the of Jungles the in Adventures Scientist’s A Labyrinth: Emerald , 33 , , 168–183. , 97 42 , Genetics 69 13672–13677. , 313–333. , iree.A reni unoCnoinArcnzn:Cumulative zone: African Guineo-Congolian in Froehn A. ex. Pierre 15–45. , , 6 , 925–929. , 196 , 973–983. , 8 217–245. , 15 Science M vltoayBiology Evolutionary BMC ulctoso h utl Ornithological Nuttall the of Publications Geomorphology , 165 , oeua Ecology Molecular 108 aaoegah,Palaeoclimatology,Palaeogeography, 131–137. , 4766–4771. , ai tricuspis Manis nulRve fEcology, of Review Annual opeRnudsSeances des Rendu Compte rceig fteNational the of Proceedings aiinJunlo Biology of Journal razilian ilgclDiversification Biological , 67 437–456. , , oei oMuseu do Boletim LSGenetics PLoS 25 , 5975–5993. , 9 International eel six reveals ) Biodiversity 167. , Lebanon, . , 5 Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ucisn .E 15) oaet at oai rwyaetees ayknso animals? of kinds many so there are why or Rosalia Santa to and Homage Underestimated (2019). G. Naturalist (1959). Voelker, American E. & J., G. L. forests. Hutchinson, Musher, lowland A., Afro-tropical on A. across fragmentation Castellanos, patterns D., forest diversification K. cryptic Plio-Pleistocene Keith, of W., impact J. Huntley, the biogeography and reveals systematics The Criniger) diversity. (2018). (Aves: avian G. Voelker, Greenbuls Afro-tropical & G., Bearded Boano, the M., Pavia, of A., J. Harvey, W., J. Central Huntley, the more of Rift. taxonomy even Albertine Integrative the and (2017). in E. diversity rich Greenbaum, & hotspots–Very M., chameleon, biodiversity forest Behangana, African C., global Kusamba, F., Evaluating D. Hughes, (2017). D. herpetofaunal Romportl, of endangered. & determinants as A., Cameroon. gradient Kupe, Hrdina, and Mount Ecotones of elevational forest an (2000). primary on D. 517–533. the herpetofauna Borcard, in a & structure of L.-F., community organization Bersier, Spatial U., Improving Hofer, (1999). UFBoot2: tests. D. model (2018). null Borcard, S. by & L. revealed Vinh, L.-F., gradient & Bersier, Q., U., B. Hofer, Minh, A., approximation. Haeseler, bootstrap Von ultrafast O., high-resolution female the Chernomor, conserved Very reveal T., data D. (2005). Genomic Hoang, (2019). A. genomes. W. Jarvis, nuclear D. Weisrock, gigantic & & with S., 3467–3476. G., salamanders J. P. giant Reece, in T., Jones, heterogamety J. L., Briggler, M., J. P. areas. Parra, Hime, land global E., for S. (2016). surfaces S. climate Cameron, interpolated C. J., Kelly, R. & R., Hijmans, Caballero-Gill, ecosystems. C., modern of L. (1977). P. rise Peterson, Hershkovitz, the A., and Tzanova, cooling of T., global analysis K. phylogenetic Miocene Lawrence, molecular Late for D., dates T. calibration Fossil Herbert, Colubridae. Elapoidea, (2016). Colubroidea, J. Caenophidia, Muller, & 2: K., predictors snakes as Mahlow, history J., and birds. J. Productivity terrestrial Head, (2003). of J. gradient Alexandre, diversity conservatism, & latitudinal niche F., the Diniz-Filho, Climate, E., of (2007). E. A. Porter, S. A., B. Soeller, Hawkins, & gradient. A., diversity C. bird diversity Jaramillo, global F., Mitochondrial the A. and J. (2013). Diniz-Filho, D. A., B. Zinner, Hawkins, & C., Roos, ( M., monkeys 350–360. green , Hofreiter, African B., of Agwanda, distribution refugia. and E., the climatic Akom, in stable T., to history linked Haus, vegetation are hotspots of Endemism signatures (2017). Comparative genetic R. , (2013). Noss, of V. & Poncet, review S., Harrison, A . . . trees: J., Duminil, forest G., region. Dauby, rain Guineo-Congolian K., African Dainou, K., of Budde, phylogeography C., Born, J., O. Hardy, 119 207–214. , ora fLnsaeEcology Landscape of Journal , 93 iigNwWrdMnes(Platyrrhini). Monkeys World New Living iyni adolfifriderici Kinyongia 145–159. , ope edsGeoscience Rendus Comptes olgclJunlo h ina Society Linnean the of Journal Zoological olgclJunlo h ina Society Linnean the of Journal Zoological clg,80 Ecology, h mrcnNaturalist American The oeua ilg n Evolution and Biology Molecular , Chlorocebus 10 108–115. , Sui:Caaloia) eel neetmtdspecies underestimated reveals Chamaeleonidae), (Sauria: 976–988. , nentoa ora fClimatology of Journal International 16 , Ecology ry 1870). Gray, 345 aaotlgaElectronica Palaeontologia 284–296. , , aueGeoscience Nature , 84 hcg,I:Uiest fCiaoPress. Chicago of University IL: Chicago, 170 ora fBiogeography of Journal 3 Genes G3: 1608–1623. , mrcnJunlo Primatology of Journal American S16–S27. , , , 183 , ora fToia Ecology Tropical of Journal 35 181 672–686. , 518–522. , 400–438. , | Genomes , 9 843–847. , , , 19 naso Botany of Annals 25 | , 1–21. , Genetics 1965–1978. , 46 381–391. , , , 16 The , 9 75 , , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ec´ ,A . uia .K 21) aeinseisdlmtto nWs fia oetgco ( geckos forest African West in delimitation species Bayesian (2010). (Ser- K. fasciatus Colubroidea M. dactylus Fujita, the & of D., Phylogeny Leach´e, A. (2005). genes. F.T. nuclear Burbrink, and mitochondrial & 581–601. from B.I., evidence Crother, New frog J.B., pentes): river Slowinski, the R., of history Lawson, Evolutionary (2016). Evolution E. and Greenbaum, Phylogenetics & cular M., Behangana, D., genus Castro, B., R., Sandel, T. Larson, J., N. Kraft, gradient. C., diversity USA latitudinal Violle, the and B., space trait Functional phylogeography. Blonder, Statistical C., (2002). P. Lamanna, W. Maddison, (2012). & L., T. L. Knowles, Thierer, phylogeography. . . Statistical . analysis and , (2009). S., organization L. Sturrock, the L. for M., Knowles, platform Cheung, software desktop S., data. extendable Stones-Havas, sequence and on A., of integrated based An Wilson, alignment Basic: sequence R., Geneious multiple Moir, rapid for M., method Kearse, novel ModelFinder: A (2017). MAFFT: S. transform. (2002). L. Fourier M. fast Jermiin, Kuma, & & A., M., estimates. Haeseler, Katoh, phylogenetic von accurate K., for C. T. D. selection Wong, Blackburn, model Q., Fast B. . . . Minh, R., S., genus Ernst, Kalyaanamoorthy, the W., data. Conradie, in SNP M., frogs Burger, genome-wide of D., of biogeography C. Africa. analysis Barratt, and area- F., the Diversity M. historical for Barej, (2018). by tools M., F. New predicted G. diversity 1.3-1: Jongsma, Adegenet vertebrate in (2011). I. gradients Bioinformatics Ahmed, Global & T., (2012). Jombart, V. environment. contemporary P. tropics. and Fine, the dynamics productivity in & higher W., are Jetz, passes mountain Why Milankovitch change: climatic (1967). 233–249. recurrent H. of world D. a Janzen, in clades of fate evolution. The and (2002). oscillations M. Africa. (2015). Dynesius, across V. & Nicolas, expansion R., Forest ecological . Jansson, broad .. to (2014). C., the origin J. C. of Peterhans, forest Denys, Kerbis a history R., From Hutterer, evolutionary J., . . and Bryja, . E., Phylogeography Verheyen, J., ( C., Denys, Decher, shrew F., pygmy R., Jacquet, African West Hutterer, forest, the B., in of diversification Kadjo, Soricomorpha). evolution promote complex, M., the barriers Colyn, riverine to and V., Relevance refugia Nicolas, Africa: F., Tropical Jacquet, from studies biomes. savannah Paleobotanical and latitudinal woodland the (2004). of dynamics B.F. evolutionary Jacobs, tropics: the of Out (2006). gradient J.W. Valentine, diversity & K. Roy, D., Jablonski, 40 593–612. , , Amietia 111 oeua hlgntc n Evolution and Phylogenetics Molecular 13745–13750. , Aua yiehlde eel xesv iesfiaini eta fia highlands. African Central in diversification extensive reveals Pyxicephalidae) (Anura: , 27 Science . Bioinformatics ). rceig fteRylSceyo odnB ilgclSciences Biological B: London of Society Royal the of Proceedings 3070–3071. , uli cd Research Acids Nucleic olgc Scripta Zoologica nulRve fEooyadSystematics and Ecology of Review Annual , 314 hlspia rnatoso h oa oit B Society Royal the of Transactions Philosophical 102–106. , , , 28 99 1647–1649. , 168–181. , , 43 , , 120 131–148. , 30 rcdr olivieri Crocidura nulRve fEooy vlto,adSystematics and Evolution, Ecology, of Review Annual 17 274–285. , 3059–3066. , LSBiology PLoS aueMethods Nature Amnirana rceig fteNtoa cdm fSciences, of Academy National the of Proceedings oeua hlgntc n Evolution and Phylogenetics Molecular M vltoayBiology Evolutionary BMC ´ mva . uzr,V (2014). V. Buzzard, & . . S´ımov´a, . I., ˇ Aua aia)ars sub-Saharan across Ranidae) (Anura: ope Mmai,Soricomorpha): (Mammalia, complex , , oeua Ecology Molecular 10 33 h mrcnNaturalist American The , e1001292. , 741–777. , 14 587. , ., 359 7,3071–3077. 277, , rcdr obscurior Crocidura 1573–1583. , , 11 , 15 2623–2635. , 71. , , Hemi- Mole- , 101 37 , , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ak,B .(00.Aelwadrifrssral vltoaymsus hlgorpyo h green the of Phylogeography museums? evolutionary really rainforests lowland Are ( hylia (2010). D. (Afrique B. Ghana Marks, du polliniques. donnees Sud Premieres le Sciences dans inferieur: des montagnard l’Holocene l’Academie element a et d’un de superieur Extension Pleistocene (1983). au l’Ouest) A. de D. Livingstone, forests & BP. the J., years in Maley, 28,000 changes last climatic the and palaeoenvironments during dynamics, Cameroon Vegetation western of (1998). P. Brenac, & J., Camer- Maley, l’Ouest paleoclimatiques. de problemes Montpellier recent des discussion Quaternaire de et du l’Institut forestiers preliminaires refuges de de polliniques evidence Analyses en Mise (1987). the oun: P. from Brenac, climate & and vegetation J., Maley, in changes Quaternary. of the characteristics to forest–main Cretaceous rain Quaternary. African Upper late The during (1996). palaeoenvironments J. and Maley, vegetation forest rain (Eds.) African Change The matic M. Sarnthein, (1991). J. & Maley, Transport M. major Atmospheric the Leinen, Global and of In refugia Springer. Forest Patterns Netherlands: forest: variations. Past rain and temperature African Modern the surface Paleometeorology: in sea changes of climatic et Quaternary role Late paleo-climatiques montagnards (1989). Implications biotopes J. of des Maley, chronologiques. promise extension et et and polliniques africaine power donnees humide The Nouvelles dense biogeographiques. foret recent: (2003). la Quatemaire P. de Taberlet, au Fragmentation forest & (1987). tropical S., typing. J. African Maley, genome Jordan, putative to D., Testing genotyping Tallmon, from (2010). R., genomics: K. P. population I. England, Dawson, G., phylogeography. forest & Luikart, DNA rain E., nuclear African and Dormontt, chloroplast Central D., using of Harris, refugia history J., evolutionary A. The Lowe, (2016). genus climber J. the O. in Biogeography species Hardy, of sister & from insights phylogeog- M., Phylogeographical Comparative Heuertz, plants: rainforests. (2014). C., African J. A. central O. Ley, Hardy, in & (Marantaceae) M., lianas Roser, and C., 403. herbs Wypior, mammals. eight J., and Kohler, of G., raphy birds Dauby, African C., Climate A. of Ley, (2013). refugia C. Rahbek, of & co-occurrence Biogeography J., treefrog P. and Valdes, spatio-temporal foam-nest Ecology M., suggest A. African Haywood, models D., the Nogues-Bravo, envelope B., in M. tree testing Araujo, species I., Levinsky, model on demographic flow gene using of R rufescens diversification influence Chiromantis D., forest The Rivera, rain M., (2014). Exploring D. Z. Portik, Yang, D., & Leach´e, A. B., Rannala, study. B., simulation A R. Harris, estimation: D., African A. West Leache, the B K., in M. diffusion Fujita, species S., Agamidae). of Krishnan, inference M., Bayesian Miller, A., (2017). J. Grummer, D., Leach´e, A. yi prasina Hylia ytmtc n Biodiversity and Systematics , 19 , 44 79–98. , aaoclg fAfrica of Palaeoecology nteAfrotropics. the in ) 308–321. , . ora fBiogeography of Journal , , , 22 17 Paris 351–363. , ytmtcBiology Systematic 129–142. , , 296 rceig fteRylSceyo Edinburgh of Society Royal the of Proceedings 1287–1292. , oeua hlgntc n Evolution and Phylogenetics Molecular , , 15 18 dl .O,Pne,J,Goz´k . uia ..(2019). M.K. Fujita, . Gvoˇzd´ık, . . J., V., Penner, M.-O., ¨ odel, 192–203. , 307–334. , , 46 , 18 63 eiwo aaooayadPalynology and Palaeobotany of Review 2706–2721. , 17–30. , aueRvesGenetics Reviews Nature rpclPatBiology Plant Tropical gm agama Agama Haumania he . fr-otn,C. Ofori-Boateng, . . . W., ¨ ohme, rnir nGenetics in Frontiers p.5566.Dordrecht, 585–616). (pp. , 55 pce ru (Reptilia, group species (Marantaceae). , , , 3 4 104 178–184. , aeciaooyand Paleoclimatology eorse Travaux et Memoires 50–58. , 981–994. , 31–73. , ope Rendus Comptes , 99 157–187. , Journal Global , Cli- 5 , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. eesn .. ae,M,&Sbrn .(08.Rtikn eevroeaigcaatrsi analysis characteristic operating receiver Rethinking (2008). J. Soberon, modeling. & rapid niche and ecological M., Recent in applications (2001). Papes, M. P. trees. A.T., Hollingsworth, Neotropical Peterson, & of D., genus T. species-rich Pennington, a T., of R. diversification Pennington, E., J. conservation Richardson, amphibian for baseline (1982). spatial G.T. the Prance, Modelling biogeo- (2019) a M.-O. - Africa. revisited Rodel, West & hotspot in A M., Augustin, of (2011). J. M.-O. timing Penner, Rodel, amphibians. and & African Mechanisms M., West Schmidt, of mammals: A., analysis Hillers, graphical Amazonian M., of Wegmann, J., history Penner, (Eds.) The C. Moritz, (2005). & C.W., F. Dick, future. M. E., Bermingham, Silva, stacks. In for & map diversification. road L., A J. effective space: parameter and Patton, in Lost fast (2017). A Evolution M. J. and IQ-TREE: Catchen, Ecology & in R., (2014). J. Q. Stevens, R., B. J. Paris, Minh, & A., phylogenies. Haeseler, 268–274. maximum-likelihood von , estimating A., for H. algorithm Schmidt, stochastic Pleistocene T., African L. mouse. West-Central soft-furred Nguyen, (2012). Misonne’s C. of Denys, phylogeography & the C., by 47 Cruaud, revealed M., in evolution Colyn, forest diversity D., lowland genetic A. (2011). Missoup, shaping M. V., Colyn, in Nicolas, & refugia A., Couloux, Pleistocene P., Katuala, and J., rivers Foraging Peterhans, Africa. Kerbis of (2011). C., J. roles Denys, Kielgast, D., The & A. J., Missoup, Kolby, V., L., Nicolas, A. Lokasola, G., G. Tungaluma, C., of forests. acrobatics Z. tropical Kusamba, in T., spots” (Eds.), Z. ”Hot C. Nagy, J. biotas: biodiversity Threatened Habel, Global & (1988). (2011). E. N. Areas C. Myers, F. Gascon, Priority Zachos, & Conservation In M., of T. Protection hotspots. Brooks, and of W., Distribution role F. critical Larsen, The R., conservation: W. Turner, A., R. Mittermeier, (2000). for R. G. Fotso, role C. & positive Mittermeier, Ecoregions. a & . Terrestrial . suggests Endangered N., . Myers, Nigeria E., A., and E. R. Abwe, subspecies. Cameroon Mittermeier, S., chimpanzee in R. of chimpanzees P. evolution wild Clee, the of A., in A. genetics selection Pokempner, population L., The Ghobrial, S., (2014). (2015). Locatelli, S. Ursenbacher, W., & M. diversity. B., Mitchell, species R. of T. refuge pattern Davenport, forest current R., the W. Pleistocene Branch, shaping the J., S. supporting genus Marsden, evidence P., The S. biogeographic Loader, The M., Menegon, (1986). J. R. O’Hara, hypothesis. & E., Mayr, Press. University Columbia (1942). E. Mayr, 100–112. , p.1716.Ciao L h nvriyo hcg Press. Chicago of University The IL: Chicago, 107–126). (pp. ora fBiogeography of Journal Atheris Evolution oiora blandingii Toxicodryas caOclgc,84 Oecologica, Acta ytmtc n h rgno pce rmteVepito Zoologist. a of Viewpoint the from Species of Origin the and Systematics Srets ieia)i atArc:Pyoeyadterl frfigadciaein climate and rifting of role the and Phylogeny Africa: East in Viperidae) (Serpentes: ilgclDvricto nteTropics the in Diversification Biological , 40 , 8 55–67. , 1360–1373. , , 38 hcg,I:Uiest fCiaoPress. Chicago of University IL: Chicago, nteDmcai eulco h Congo. the of Republic Democratic the in 31–40. , 191–207. , clgclModelling Ecological iest n itiuin 17 Distribution, and Diversity oeua hlgntc n Evolution and Phylogenetics Molecular 19 M vltoayBiology Evolutionary BMC Science osos at’ ilgclyRcetadMost and Richest Biologically Earth’s Hotspots: p.32) eln emn:Springer. Germany: Berlin, 3–22). (pp. . e ok Y oubaUiest Press. University Columbia NY: York, New . , 213 , 293 rpclrifrss at rsn and present Past, rainforests: Tropical 63–72. , Environmentalist oeua ilg n Evolution and Biology Molecular 2242–2245. , roy misonnei Praomys eptlg Notes Herpetology 1077–1088. , , 15 idvriyHtpt – Hotspots Biodiversity 3. , , , 8 79 fia Zoology African 187–208. , e ok NY: York, New 12–22. , , ntropical in 4 Methods 91–92. , , 32 , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. itek . enr . eWle .(95.Ceapnoda n h td ffrs eue nGabon: in refuges forest of study the and Caesalpinioideae (1995). J. Wilde, results. De Preliminary & Press. P., Chicago Ketner, of E. M., University R. Rietkerk, Ricklefs, IL: In Chicago, influences. 350–363). historical and (pp. Regional . diversity: (Eds.) Species D. (1993). southern Schluter, D. birds. & the Schluter, passerine & of of E., rate forest R. diversification Ricklefs, Lowland the in II. variation Global (2006). vegetation. E. African R. Ricklefs, West in on summarization notes Posterior Reserve. Ecological (2018). Forest A. Bakundu (1963). M. W. Suchard, P. & Richards, G., Baele, 1.7 Tracer D., using Xie, phylogenetics J., Bayesian A. Founda- Drummond, Geospatial A., Source Squamata, Rambaut, Open of classification System. http://qgis.osgeo.org. revised Information and Geographic Project. phylogeny QGIS tion A (2020). Team (2013). Development snakes. J. QGIS and J. lizards Wiens, of & struc- species T., 4161 population F. problem. including Burbrink, correct the A., the alleviate R. recover estimators Pyron, ABC reliably new Reliable not and Subsampling does (2015). P. structure uneven: C. Resources program is Robert, sampling The & when (2016). M., ture J. Gautier, M., S. J. Puechmaille, Cornuet, forests. A., random Estoup, via choice M., model J. Marin, refugia. P., glacial Pudlo, cryptic into multilocus insights using Phylogeographic structure (2008). Evolution population D. & K. of Bennett, Inference & Greenbaum J., (2000). Provan, Eli P. Donnelly, . & . fang . M., data. on J., genotype Stephens, emphasis Penner, K., with M.-O., J. Atractaspidinae) Pritchard, Rodel, (Lamprophiidae: W., asps selection. Conradie, prey burrowing R., and of W. evolution history Branch, Evolutionary L., (2017). K. (2019). E. M. Stanley, Fujita, F., . . Portillo, model . demographic M., using Hirschfeld, frog M., forest tropical Burger, Guineo-Congolian F., selection. a M. in Barej, diversification of D., mechanisms Rivera, Evaluating D., Leach´e, A. M., D. software. Carracedo, Portik, supporting C., and Phillips, settings, C., parameter Sciences rainforest. Biological Santos, applications, Guineo–Congolian STRUCTURE: B: Y., African Series Ruiz, the London. L., in of Porras-Hurtado, evolution Society of Royal the tempo of and Transactions Mechanisms sophical concepts. of (2004). review V. A Plana, diversity: species in geographic gradients species Latitudinal of , (1966). modeling entropy R. Maximum E. Pianka, (2006). E. R. Schapire, & P., estimated R. distributions. with Anderson, structure J., S. population Phillips, spatial Visualizing (2016). RADseq: surfaces. M. digest migration Stephens, Double effective & (2012). J., E. Novembre, H. D., Petkova, Hoekstra, & S., H. Fisher, H., 7 for E. Kay, method N., inexpensive J. An Weber, K., B. Peterson, 100 e37135. , 33–46. , oeua Ecology Molecular , 16 , clgclModelling Ecological 23 608–627. , Genetics 564–571. , ultnd uemNtoa ‘itieNtrle ai,Adansonia Paris, Naturelle, d‘Histoire National Museum du Bulletin pce iest nEooia omnte:Hsoia n egahclPerspectives Geographical and Historical Communities: Ecological in Diversity Species , 155 ora fEcology of Journal enovo de aueGenetics Nature , lSONE PloS 26 945–959. , Bioinformatics 25 5263. 5245– , , icvr n eoyigi oe n o-oe species. non-model and model in genotyping and discovery 190 ytmtcBiology Systematic . , 231–259. , 14 , M vltoayBiology Evolutionary BMC , e0214889. , 48 51 , 94–100. , 123–149. , 32 20 859–866. , , 67 901–904. , . ae,M 21) noeve of overview An (2013). M. Lareu, & A., ´ , 13 rnir nGenetics in Frontiers 93. , Ecology , 359 mrcnNaturalist American oeua Ecology Molecular , rnsi Ecology in Trends 1585–1594. , , 17 87 95–105. , LSONE PLoS 2468–2478. , , 4 98. , Philo- , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ti,A,Grte,K,&Ket .(04.Evrnetlhtrgniya nvra rvro species of driver universal a as heterogeneity Environmental scales. (2014). spatial the H. and Africa—Did biomes Kreft, Central taxa, & for across K., richness model evolution Gerstner, drainage A., proposed Stein, A (2006). J. east? M. flow Wit, Congo de & evidence. J., Palynological Stankiewicz, (2018). M. Africa: Menegon, Publishing. & equatorial H., Bloomsbury Hinkel, in NY: K., environments Howell, S., Quaternary Spawls, Late Africa (1991). of Palaeoecology A. M. of Sowunmi, species New (1991). refuges. species’ M. forest and S. niches ecological M. fundamental Sosef, of models of Interpretation selection model (2005). areas. Demographic T. distributional A. (2017). Peterson, C. & spectrum. B. J., frequency Carstens, Soberon, site & more the J., of Sullivan, and identification C., forests to D. latitudinal random Tank, leads using A M., delimitation Ruffley, L., (2017). species M. T. Process-based Smith, (2020). R. C. Brumfield, B. & species. Carstens, relevant M., biologically & A. L., Cuervo, M. G., Smith, M. Harvey, birds. in F., gradient G. diversity Seeholzer, phylogeographic T., B. Africa? in Smith, dilemma conservation ongoing an Conservation data-deficiency biodiversity Nature is avifauna. for Why a (2019). para A. A. obstaculo Siddig, como Amazonia na enchentes Amazonica e Biota Rios (1967). Bioinfor- inference. H. (2017). genetic B. Sick, J. population Wolf, downstream & Evolution W., impacts C. and dramatically Wheat, Ecology data A., in Brelsford, RAD-seq I., of Maayan, S., processing Tusso, colouration matic R., C. coat Peart, of B., A. patterns Shafer, Geographic variation: of variance 169–185. The , of (2005). collection R. and the Hutterer, Lang in on & Herbert based by C., notes Congo A. field Schunke, Belgian with the Snakes, II. of Part Chapin. herpetology P. 1909–1915. the James Expedition, to Congo Museum Contributions American the (1923). P. K. Schmidt, cause. Press. (1995). primary L. the of M. for status search Rosenzweig, The taxonomic diversity: The species in (2014). gradients 514–527. Latitudinal F. (1992). M. K. Barej, Rohde, & A., (Eds.), Schmitz, J.M. Arthroleptidae). Rooy, Anura: J., de Penner, Medenbach African West M., van van two & Emmrich, In M. M.-O., refuges. X. forest Rodel, Burgt, rain der glacial van to reference G., Plants with J. African Rubiaceae L. African Maesen, of der Geography (1996). E. Robbrecht, Anomalurops aeignArclua nvriyPapers University Agricultural Wageningen p.5451.Drrct ehrad:Kluwer. Netherlands: Dordrecht, 564–581). (pp. . and ora fArcnErhSciences Earth African of Journal , Leptopelis ultno h mrcnMsu fNtrlHistory, Natural of Museum American the of Bulletin 5 idvriyInformatics Biodiversity Anomalurus 495–520. , , 22 osseaisadEvolution and Zoosystematics , , 50 8 213–238. , species: pce iest nSaeadTime and Space in Diversity Species Evolution 907–917. , 125719. , Mmai,Rdni,Anomaluridae). Rodentia, (Mammalia, .macrotis L. , 74 Begonia 216–229. , LSBiology PLoS , 2 clg Letters Ecology 1–10. , cit,16 and 1967 Schiotz, nArc n hi eeac otesuyo lca rain glacial of study the to relevance their and Africa in 21 , 44 oeua Ecology Molecular , 90 75–84. , , , il ud oEs fia reptiles African East to guide Field 91 15 21–31. , 120–151. , e2001073. , , 17 abig,U:CmrdeUniversity Cambridge UK: Cambridge, . .spiritusnoctis L. 866–880. , 9 1–146 49, onrZooiceBeitrage Zoologische Bonner , 26 4562–4573. , tsd ipsoSbea Sobre Simposio do Atas oe,20 (Amphibia: 2007 Rodel, h idvriyof Biodiversity The e York, New . Oikos Methods Journal , 65 , 53 , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. er .T,&Shue,D 20) h aiuia rdeti eetseito n xicinrtso birds of rates extinction and speciation recent in gradient latitudinal The (2007). mammals. D. model and Schluter, & of T., importance neotropical J. highland Weir, The and lowland Maxent: in accumulation in species of patterns modeling and birds. niche timing Divergent (2006). Ecological criteria. T. selection J. (2011). Weir, model N. of S. performance the Seifert, and & complexity L., D. Warren, (1878). R. the A. in Wallace, species tree (1853). Neotropical R. and a A. history for Wallace, Demographical Basin (2016). Amazon G. R. towards Collevatti, shift & LGM. range C., show L. Terribile, modelling S., M. palaeodistribution Lima-Ribeiro, C., L. Vitorino, B. (Eds.) Meggers, D. In W. forests. Duckworth, equatorial Review & in Comparative S., multiplication E. species Ayensu, and J., relief, Paleoclimates, of evolution (1973). P.E. and Vanzolini, differentiation geographic anoles: American South disjunct (1970). the E.E. the Williams, onto & window P.E. Vanzolini, phylogeographic A refugia: and Pleistocene status Conservation 418. and (2016). monkeys the B. Forest of Maritz, distribution (2008). & J. P., A. Bowles, Tosi, R., on W. reptiles. based Branch, African inference J., for demographic G. threats of Alexander, accuracy A., the K. on Tolley, limits Fundamental spectrum. (2015). frequency S. sample Y. the Song, & J., ecology. Terhorst, plant in favorableness of processes. notion and the status 501. On species (1973). test J. to Terborgh, trees gene of analyses 10, Wickings, phylogeographic Ecology, Using . Molecular . (2001). . R., R. T. A. in Templeton, Disotell, divergence W., phylogenetic M. deep Bruford, for A., evidence K. , Abernethy, Molecular L., (2003). S. J. Clifford, 4. E. S., Version Souquiere, Methods). T., Other P. Telfer, (*and Parsimony Using Associates. Analysis Sinauer Phylogenetic MA: PAUP*. Sunderland, (2003). computing. phylogenetic L. for D. library Swofford, Python A of DendroPy: responses (2010). T. Individualistic M. matics revisited: Holder, Refugia & (2010). J., Dal´en, L. Sukumaran, & time. I., and Barnes, space M., in A. species Lister, R., J. Stewart, latitudinal the on conservatism the niche tropical in and bats. 278 coexist speciation phyllostomid for species of time of many gradient effects diversity so Relative How (2011). D. range: R. Stevens, geographical in gradient latitudinal The tropics. (1989). C. G. Stevens, 12 nlschrysolepis Anolis 2528–2536. , 2019–2024. , Evolution M vltoayBiology Evolutionary BMC , mrcnNaturalist American 26 1569–1571. , Science , 60 hooeu lhoesti Chlorocebus p.2528.Wsigo .C:SihoinPress. Smithsonian C.: D. Washington 255–258). (pp. . 842–855. , 779–791. pce ru Sui,Iguanidae). (Sauria, group species rpclNtr,adOhrEssays Negro Rio Other and and Nature, Amazon Tropical the on Travels of Narrative A , 315 rceig fteRylSceyB ilgclSciences Biological B: Society Royal the of Proceedings ilgclConservation Biological 1574–1576. , , 133 rceig fteNtoa cdm fSine,USA Sciences, of Academy National the of Proceedings , 240–256. , 16 pce group. species 213–228. , rceig fteRylSceyo odnB ilgclSciences Biological B: London of Society Royal the of Proceedings r pclFrs cssesi fiaadSuhAeia A America: South and Africa in Ecosystems Forest Tropical , 22 olgclJunlo h ina Society Linnean the of Journal Zoological 204 ruvsd olga S˜ao Paulo Zoologia, de Arquivos 63–71. , odn K amla n Company. and Macmillan UK: London, . clgclApplications Ecological h mrcnNaturalist American The adilssphinx Mandrillus odn K Reeve. UK: London, . , 277 , 21 , 661–671. , . 335–342. , oeua Ecology Molecular 112 , 19 67 7682. 7677– , , , 291–298. , 154 107 Bioinfor- 408– , 481– , , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ihyspotdnds(P[].)aedntdwt lc ice oslclbae oe are nodes Fossil-calibrated circle. black a with denoted are [?]0.9) (PP nodes supported for Highly phylogeny Bayesian time-calibrated A 2. Figure Africa, Central refugia-drove-diversification-in-arboreal-sub-saharan-african-snakes and West in image2.emf 1–10) (labeled refugia file hypothesized Hosted and rivers (1996). Maley major from of adapted Locations 1. at Figure Repository Digital Digital Dryad Dryad refugia-drove-diversification-in-arboreal-sub-saharan-african-snakes the the in in image1.emf archived archived re be re file will be Hosted files will input http://datadryad.org. maxent sequences at and ddRAD Repository data for Bioclimatic http://datadryad.org. reads manuscript. Raw K.E.A., the K.E.A edited tissues. Genbank. data. R.M.B. provided the STATEMENT and J.P. analyzed AVAILABILITY R W.P.T.N and M.-O. DATA and R, J.P., P.M.H P.M.H., M.-O. K.E.A., E.G., work. C.K., manuscript. laboratory the E.G., the wrote study. performed the V.V.S. designed and P.M.H. R.M.B. and A.T.P., K.E.A., CONTRIBUTIONS AUTHOR ( frogs puddle Evolution sub-Saharan Gvoˇzd´ık,and of & biogeography V. . and . . phylogenetics R M., M., K. B. Dash, Zimkus, A., Madagascar and Channing, niche. Africa D., across ecological diversified C. their frogs Barratt, Genetic ridged maintain Mascarene F., to (2014). How M. territory: D. Barej, new S. into P., Cote, Leapfrogging L. (2017). change. Lawson, . climate . M., . future B. C., and Zimkus, Cuyler, past S., to Couturier, linked N., caribou Lecomte, in J., diversity Ortego, L., Pellissier, G., Integration Yannic, (2018). cobra C. forest Hall, the in . diversity . . 68–98. unexpected reveals E., morphology Greenbaum, and K., sequences Jackson, ( gene I., mitochondrial Ineich, and F., biogeographic of nuclear J. of history Trape, and evolutionary L., Evolutionary and Chirio, Biogeography W., Wuster, (2009). (2000). A. M. Channing, R. & C., Brown, R. olius (Ranidae). & Drewes, frogs A. M., world A. R. old Wieczorek, in Pyron, diversity richness. S., tropical species high J. and of Sukumaran, origins ecology J., biogeography, taxa. J. Historical five Wiens, (2004). for J. data M. European Evolution Donoghue, using and & (2003) richness:Ecology J. species al. J. of et Wiens, gradients Hawkins Geographical of conjecture (2007). Biogeography water-energy B. and conservation. the Ecology M. its of for Araujo, test need & A Nogu´es-Bravo, scientific D., J., the and R. archipelago Whittaker, Afromontane the Ecology of of history Journal African The (1981). F. White, aamelanoleuca Naja pce:apiaino oeua phylogeny. molecular of application species: , vial at available at available 55 dl .O,&Hles .(00.Cmlxpten fcnietlseito:molecular speciation: continental of patterns Complex (2010). A. Hillers, & O., M. ¨ odel, 883–900. , pce ope nCnrladWs fia(epne:Elapidae). (Serpentes: Africa West and Central in complex species ) , 19 , , 639–644. , 16 19 76–89. , 33–54. , https://authorea.com/users/317799/articles/447907-rivers-not- https://authorea.com/users/317799/articles/447907-rivers-not- oeua hlgntc n Evolution and Phylogenetics Molecular N eune fcmsadcyt- and c-mos of sequences DNA ora fBiogeography of Journal Toxicodryas 23 aueCiaeChange Climate Nature vlto,64 Evolution, Phrynobatrachus ihcmsadcyt and c-mos with , , 106 27 1217–1231. , 1231–1243. , 254–269. , ). b oeua Phylogenetics Molecular b ilb cesoe on accessioned be will genes. , 4 132–137. , Zootaxa rnsin Trends , Hyper- 4455 Global , Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. esi rbblte o = nlzdi E.Bto:Gorpi ersnaino ouainstructure population of representation Geographic Bottom: LEA. in K=5. analyzed for K=5 genus for the probabilities of bership structure Population 4. Figure refugia-drove-diversification-in-arboreal-sub-saharan-african-snakes image4.emf file 2. Figure Hosted to correspond colors Clade refugia. 3. Figure showed phylogenies refugia-drove-diversification-in-arboreal-sub-saharan-african-snakes RADseq intervals. image3.emf confidence 95% represent file Hosted bars Node topologies asterisk. identical an with denoted Toxicodryas vial at available at available ld itiuin vradot a fmjrrvr n yohszdrainforest hypothesized and rivers major of map a onto overlaid distributions clade https://authorea.com/users/317799/articles/447907-rivers-not- https://authorea.com/users/317799/articles/447907-rivers-not- Toxicodryas 24 o:Brpo fpplto tutr n mem- and structure population of plot Bar Top: . Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ersnsaeso o irto,adi )bu ersnsaeso ihdvriyadoag represents log orange a and on diversity plotted high are of rates areas points. migration estimated represents black and effective blue by diversity the denoted B) Genetic B) are in diversity. and and low surface of migration, migration areas low estimated of effective areas the of represents populations A) all for for surface means diversity Posterior 5. Figure Toxicodryas nA lerpeet ra fhg irto n orange and migration high of areas represents blue A) In . 25 10 cl.Sml localities Sample scale. Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ihu eeflw oe :dvrec ihscnaycnat n oe :dvrec ihgn flow. gene with divergence divergence 4: 2: Model Model and divergence, contact, no secondary 1: with for of chosen Model divergence was DelimitR. 3: 2 using Model Model tested flow, models gene demographic without Four 6. Figure .pulverulenta T. . oiora blandingii Toxicodryas n oe a hsnfrtetoCnrlArcnclades African Central two the for chosen was 4 Model and , 26 Posted on Authorea 6 May 2020 — CC BY 4.0 — https://doi.org/10.22541/au.158880203.33695479 — This a preprint and has not been peer reviewed. Data may be preliminary. ihetgenidctn upr rmol n C.C h tblt fsial aia costeLGM, stability. the low across the indicating habitat blue and suitable and GCMs of stability stability three high The indicating all C) red between GCM. with agreement one present, indicating only and from green mid-Holocene, support darkest indicating the green only with lightest from support GCMs for the indicating between habitat blue with lightest suitable (GCMs) agreement the The models and B) climate GCMs GCM. three global all one between for between agreement agreement habitat represents indicating suitable blue blue of darkest the shade A) The showing (LGM). models maximum Paleo-distribution 7. Figure Toxicodryas uigtemdHlcn.Tesaeo re represents green of shade The mid-Holocene. the during 27 Toxicodryas uigtels glacial last the during