da Silva Ribeiro T, Batalha-Filho H, Silveira LF, Miyaki CY, Maldonado-Coelho M. Life history and ecology might explain incongruent population structure in two co-distributed montane bird species of the Atlantic Forest. Mol Phylogenet Evol. 2020;153:106925.
PubMed
Google Scholar
Fang F, Chen J, Jiang LY, Chen R, Qiao GX. Biological traits yield divergent phylogeographical patterns between two aphids living on the same host plants. J Biogeogr. 2017;44(2):348–60.
Google Scholar
Fenker J, Tedeschi LG, Melville J, Moritz C. Predictors of phylogeographic structure among co-distributed taxa across the complex Australian monsoonal tropics. Mol Ecol. 2020. https://doi.org/10.1111/mec.16057.
Article
Google Scholar
Massatti R, Knowles LL. Microhabitat differences impact phylogeographic concordance of codistributed species: Genomic evidence in montane sedges (Carex L.) from the Rocky Mountains. Evolution. 2014;68(10):2833–46.
PubMed
Google Scholar
Massatti R, Knowles LL. Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges. Mol Ecol. 2016;25(16):3974–86.
CAS
PubMed
Google Scholar
Gittenberger E. What about non-adaptive radiation? Biol J Linn Soc. 1991;43(4):263–72.
Google Scholar
Rundell RJ, Price TD. Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation. Trends Ecol Evol. 2009;24(7):394–9.
PubMed
Google Scholar
Czekanski-Moir JE, Rundell RJ. The ecology of nonecological speciation and nonadaptive radiations. Trends Ecol Evol. 2019;34(5):400–15.
PubMed
Google Scholar
Barley AJ, White J, Diesmos AC, Brown RM. The challenge of species delimitation at the extremes: diversification without morphological change in Philippine sun skinks. Evolution. 2013;67(12):3556–72.
PubMed
Google Scholar
Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol. 2019;139:106562.
PubMed
PubMed Central
Google Scholar
Hedin M, Carlson D, Coyle F. Sky island diversification meets the multispecies coalescent–divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia. Mol Ecol. 2015;24(13):3467–84.
PubMed
Google Scholar
Niemiller ML, Near TJ, Fitzpatrick BM. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution. 2012;66(3):846–66.
PubMed
Google Scholar
Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus). Syst Biol. 2013;62(6):805–23.
PubMed
Google Scholar
Yang L, Kong H, Huang JP, Kang M. Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol. 2019;132:219–31.
PubMed
Google Scholar
Sukumaran J, Knowles LL. Multispecies coalescent delimits structure, not species. Proc Natl Acad Sci U S A. 2017;114(7):1607–12.
CAS
PubMed
PubMed Central
Google Scholar
Leaché AD, Zhu T, Rannala B, Yang Z. The spectre of too many species. Syst Biol. 2019;68(1):168–81.
PubMed
Google Scholar
Barley AJ, Brown JM, Thomson RC. Impact of model violations on the inference of species boundaries under the multispecies coalescent. Syst Biol. 2018;67(2):269–84.
PubMed
Google Scholar
Dayrat B. Towards integrative taxonomy. Biol J Linn Soc. 2005;85(3):407–17.
Google Scholar
Schlick-Steiner BC, Steiner FM, Seifert B, Stauffer C, Christian E, Crozier RH. Integrative taxonomy: a multisource approach to exploring biodiversity. Annu Rev Entomol. 2010;55:421–38.
CAS
PubMed
Google Scholar
Jacobs SJ, Kristofferson C, Uribe-Convers S, Latvis M, Tank DC. Incongruence in molecular species delimitation schemes: what to do when adding more data is difficult. Mol Ecol. 2018;27(10):2397–413.
PubMed
Google Scholar
Wiens JJ, Graham CH. Niche conservatism: integrating evolution, ecology, and conservation biology. Annu Rev Ecol Evol Syst. 2005;36:519–39.
Google Scholar
Derkarabetian S, Ledford J, Hedin M. Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America. Mol Phylogenet Evol. 2011;61(3):844–53.
PubMed
Google Scholar
Derkarabetian S, Hedin M. Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea). PLoS ONE. 2014;9(8):e104982.
PubMed
PubMed Central
Google Scholar
Derkarabetian S, Burns M, Starrett J, Hedin M. Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States. Mol Ecol. 2016;25(18):4611–31.
PubMed
Google Scholar
DiDomenico A, Hedin M. New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands. ZooKeys. 2016;586:1–36.
Google Scholar
Hedin M, Thomas SM. Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves. Mol Phylogenet Evol. 2010;54(1):107–21.
PubMed
Google Scholar
Peres EA, DaSilva MB, Antunes M Jr, Pinto-Da-Rocha R. A short-range endemic species from south-eastern Atlantic Rain Forest shows deep signature of historical events: phylogeography of harvestmen Acutisoma longipes (Arachnida: Opiliones). Syst Biodivers. 2018;16(2):171–87.
Google Scholar
Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea). ZooKeys. 2016;555:11.
Google Scholar
Thomas SM, Hedin M. Multigenic phylogegraphic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae). Mol Phylogenet Evol. 2008;46(2):645–58.
CAS
PubMed
Google Scholar
Boyer SL, Baker JM, Giribet G. Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread ‘mite harvestman’ defies DNA taxonomy. Mol Ecol. 2007;16(23):4999–5016.
PubMed
Google Scholar
Fernández R, Giribet G. Phylogeography and species delimitation in the New Zealand endemic, genetically hypervariable harvestman species, Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi). Invertebr Syst. 2014;28(4):401–14.
Google Scholar
Chambers EA, Hillis DM. The multispecies coalescent over-splits species in the case of geographically widespread taxa. Syst Biol. 2020;69(1):184–93.
PubMed
Google Scholar
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE. 2012;7(5):e37135.
CAS
PubMed
PubMed Central
Google Scholar
Starrett J, Derkarabetian S, Hedin M, Bryson RW Jr, McCormack JE, Faircloth BC. High phylogenetic utility of an ultraconserved element probe set designed for Arachnida. Mol Ecol Resour. 2017;17(4):812–23.
CAS
PubMed
Google Scholar
Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales. Syst Biol. 2012;61(5):717–26.
PubMed
Google Scholar
Banks N. A new phalangid from the Black Mountains, NC. J N Y Entomol S. 1902;10(3):142–142.
Google Scholar
Briggs TS. A new holarctic family of laniatorid phalangids (Opiliones). Pan-Pac Entomol. 1969;45(1):35–50.
Google Scholar
Goodnight CJ, Goodnight ML. New Phalangodidae (Phalangida) from the United States. Am Mus Novit. 1942;1188:1–18.
Kury AB. Annotated catalogue of the Laniatores of the New World: (Arachnida, Opiliones). Rev Ibér Aracnol. 2003;7:5–337.
Google Scholar
Derkarabetian S, Benavides LR, Giribet G. Sequence capture phylogenomics of historical ethanol-preserved museum specimens: unlocking the rest of the vault. Mol Ecol Resour. 2019;19:1531–44.
CAS
PubMed
Google Scholar
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14(8):2611–20.
CAS
PubMed
Google Scholar
Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155(2):945–59.
CAS
PubMed
PubMed Central
Google Scholar
Hedin M, McCormack M. Biogeographical evidence for common vicariance and rare dispersal in a southern Appalachian harvestman (Sabaconidae, Sabacon cavicolens). J Biogeogr. 2017;44(7):1665–78.
Google Scholar
Huang JP. What have been and what can be delimited as species using molecular data under the multi-species coalescent model? A case study using Hercules beetles (Dynastes; Dynastidae). Insect Syst Divers. 2018;2(2):3.
Google Scholar
Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. Syst Biodivers. 2020;18(3):269–80.
Google Scholar
Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol. 2021;17(5):e1008924.
CAS
PubMed
PubMed Central
Google Scholar
Yang Z, Zhu T. Bayesian selection of misspecified models is overconfident and may cause spurious posterior probabilities for phylogenetic trees. Proc Natl Acad Sci U S A. 2018;115(8):1854–9.
CAS
PubMed
PubMed Central
Google Scholar
Carnaval AC, Waltari E, Rodrigues MT, Rosauer D, VanDerWal J, Damasceno R, Prates I, Strangas M, Spanos Z, Rivera D, et al. Prediction of phylogeographic endemism in an environmentally complex biome. Proc R Soc B Biol Sci. 2014;281(1792):20141461.
Google Scholar
Espíndola A, Ruffley M, Smith L, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc R Soc B Biol Sci. 2016;283(1841):20161529.
Google Scholar
Pei J, Chu C, Li X, Lu B, Wu Y. CLADES: a classification-based machine learning method for species delimitation from population genetic data. Mol Ecol Resour. 2018;18(5):1144–56.
Google Scholar
Smith ML, Carstens BC. Process-based species delimitation leads to identification of more biologically relevant species. Evolution. 2020;74(2):216–29.
CAS
PubMed
Google Scholar
Leaché AD, Davis HR, Singhal S, Fujita MK, Zamudio KR. Phylogenomic assessment of biodiversity using a reference-based taxonomy: an example with Horned Lizards (Phrynosoma). Frontiers Ecol Evol. 2021;9:437.
Google Scholar
Campillo LC, Barley AJ, Thomson RC. Model-based species delimitation: are coalescent species reproductively isolated? Syst Biol. 2020;69(4):708–21.
CAS
PubMed
Google Scholar
Crespi EJ, Rissler LJ, Browne RA. Testing Pleistocene refugia theory: phylogeographical analysis of Desmognathus wrighti, a high-elevation salamander in the southern Appalachians. Mol Ecol. 2003;12(4):969–84.
CAS
PubMed
Google Scholar
Hedin M. Molecular phylogenetics at the population/species interface in cave spiders of the southern Appalachians (Araneae:Nesticidae:Nesticus). Molecular Biology and Evolution. 1997;14(3):309–24.
CAS
PubMed
Google Scholar
Kozak KH, Wiens JJ. Niche conservatism drives elevational diversity patterns in Appalachian salamanders. Am Nat. 2010;176(1):40–54.
PubMed
Google Scholar
Marek PE. A revision of the Appalachian millipede genus Brachoria Chamberlin 1939 (Polydesmida: Xystodesmidae: Apheloriini). Zoological Journal of the Linnean Society. 2010;159(4):817–89.
Google Scholar
Weisrock DW, Larson A. Testing hypotheses of speciation in the Plethodon jordani species complex with allozymes and mitochondrial DNA sequences. Biol J Linn Soc. 2006;89(1):25–51.
Google Scholar
Caterino MS, Langton-Myers SS. Intraspecific diversity and phylogeography in Southern Appalachian Dasycerus carolinensis Horn. Insect Syst Divers. 2019;3(6):1–12.
Google Scholar
Garrick RC, Newton KE, Worthington RJ. Cryptic diversity in the southern Appalachian Mountains: genetic data reveal that the red centipede, Scolopocryptops sexspinosus, is a species complex. J Insect Conserv. 2018;22(5–6):799–805.
Google Scholar
Keith R, Hedin M. Extreme mitochondrial population subdivision in southern Appalachian paleoendemic spiders (Araneae: Hypochilidae: Hypochilus), with implications for species delimitation. J Arachnol. 2012;40(2):167–81.
Google Scholar
Newton LG, Starrett J, Hendrixson BE, Derkarabetian S, Bond JE. Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex. Mol Ecol. 2020;29(12):2269–87.
PubMed
Google Scholar
Goodnight CJ, Goodnight ML. Speciation among cave opilionids of the United States. Am Midl Nat. 1960;64(1):34–8.
Google Scholar
Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M. A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. ZooKeys. 2018;760:1–36.
Google Scholar
Derkarabetian S, Steinmann DB, Hedin M. Repeated and time-correlated morphological convergence in cave-dwelling harvestmen (Opiliones, Laniatores) from montane western North America. PLoS ONE. 2010;5(5):e10388.
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3.
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 2013;29(22):2869–76.
CAS
PubMed
PubMed Central
Google Scholar
Burns M, Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. Comparative performance of double-digest RAD sequencing across divergent arachnid lineages. Mol Ecol Resour. 2017;17(3):418–30.
CAS
PubMed
Google Scholar
Eaton DA, Overcast I. ipyrad: interactive assembly and analysis of RADseq datasets. Bioinformatics. 2020;36(8):2592–4.
CAS
PubMed
Google Scholar
Bryson RW Jr, Savary WE, Zellmer AJ, Bury RB, McCormack JE. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Mol Ecol. 2016;25(15):3731–51.
PubMed
Google Scholar
Chifman J, Kubatko L. Quartet inference from SNP data under the coalescent model. Bioinformatics. 2014;30(23):3317–24.
CAS
PubMed
PubMed Central
Google Scholar
Swofford DL. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland: Sinauer Associates; 2003.
Google Scholar
Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008;24(11):1403–5.
CAS
PubMed
Google Scholar
Jombart T, Ahmed I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011;27(21):3070–1.
CAS
PubMed
PubMed Central
Google Scholar
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour. 2015;15(5):1179–91.
CAS
PubMed
PubMed Central
Google Scholar
Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010;11(1):94.
PubMed
PubMed Central
Google Scholar
Leaché AD, Banbury BL, Felsenstein J, De Oca ANM, Stamatakis A. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Syst Biol. 2015;64(6):1032–47.
PubMed
PubMed Central
Google Scholar
Zarza E, Connors EM, Maley JM, Tsai WL, Heimes P, Kaplan M, McCormack JE. Combining ultraconserved elements and mtDNA data to uncover lineage diversity in a Mexican highland frog (Sarcohyla; Hylidae). PeerJ. 2018;6:e6045.
PubMed
PubMed Central
Google Scholar
Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT. Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales. Syst Biol. 2014;63(1):83–95.
PubMed
Google Scholar
Blaimer BB, LaPolla JS, Branstetter MG, Lloyd MW, Brady SG. Phylogenomics, biogeography and diversification of obligate mealybug-tending ants in the genus Acropyga. Mol Phylogenet Evol. 2016;102:20–9.
PubMed
Google Scholar
Hedin M, Derkarabetian S, Blair J, Paquin P. Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). ZooKeys. 2018;769:49.
Google Scholar
Faircloth BC. Identifying conserved genomic elements and designing universal bait sets to enrich them. Methods Ecol Evol. 2017;8(9):1103–12.
Google Scholar
Hedin M, Derkarabetian S, Alfaro A, Ramírez MJ, Bond J. Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci. PeerJ. 2019;7:
PubMed
PubMed Central
Google Scholar
Faircloth BC. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics. 2016;32(5):786–8.
CAS
PubMed
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
CAS
PubMed
PubMed Central
Google Scholar
Faircloth BC. Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. 2013. https://doi.org/10.6079/J9ILL.
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821–9.
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80.
CAS
PubMed
PubMed Central
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17(4):540–52.
CAS
PubMed
Google Scholar
Talavera G, Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007;56(4):564–77.
CAS
PubMed
Google Scholar
Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T, Keane JA, Harris SR. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genom. 2016;2(4):e000056.
Google Scholar
Borowiec ML. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ. 2016;4:e1660.
PubMed
PubMed Central
Google Scholar
Grummer JA, Bryson RW Jr, Reeder TW. Species delimitation using Bayes factors: simulations and application to the Sceloporus scalaris species group (Squamata: Phrynosomatidae). Syst Biol. 2014;63(2):119–33.
PubMed
Google Scholar
Leaché AD, Fujita MK, Minin VN, Bouckaert RR. Species delimitation using genome-wide SNP data. Syst Biol. 2014;63(4):534–42.
PubMed
PubMed Central
Google Scholar
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol. 2012;29(8):1917–32.
CAS
PubMed
PubMed Central
Google Scholar
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10(4):e1003537.
PubMed
PubMed Central
Google Scholar
Kass RE, Raftery AE. Bayes factors. J Am Stat Assoc. 1995;90(430):773–95.
Google Scholar
Chang C-C, Lin C-J. LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol. 2011;2:27:1–27:27. Software available at http://www.csie.ntu.edu.tw/~cjlin/libsvm.