References
[dataset] Newton, Lacie et al. (2020), Cryptic species delimitation
in the southern Appalachian Antrodiaetus unicolor (Araneae:
Antrodiaetidae) species complex using a 3RAD approach, UC Davis,
Dataset, https://doi.org/10.25338/B8Z61M
Aberer, A. J., Kobert, K., & Stamatakis, A. (2014). ExaBayes: Massively
parallel Bayesian tree inference for the whole-genome era.Molecular Biology and Evolution , 31 (10), 2553–2556.
https://doi.org/10.1093/molbev/msu236
Andrews, K. R., Good, J. M., Miller, M. R., Luikart, G., & Hohenlohe,
P. A. (2016). Harnessing the power of RADseq for ecological and
evolutionary genomics. Nature Reviews Genetics , 17 (2),
81–92. https://doi.org/10.1038/nrg.2015.28
Avise, J. C. (2009). Phylogeography: Retrospect and prospect.Journal of Biogeography , 36 (1), 3–15.
https://doi.org/10.1111/j.1365-2699.2008.02032.x
Bagley, J. C. (2019). MAGNET v0.1.5 [GitHub Package].
http://github.com/justincbagley/MAGNET
Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L.,
Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A. (2008).
Rapid SNP discovery and genetic mapping using sequenced RAD markers.PLoS ONE , 3 (10), e3376.
https://doi.org/10.1371/journal.pone.0003376
Barraclough, T. (2019). The Evolutionary Biology of Species .
Oxford University Press.
Barroso, R., Klautau, M., Solé-Cava, A. M., & Paiva, P. C. (2010).
Eurythoe complanata (Polychaeta: Amphinomidae), the ‘cosmopolitan’
fireworm, consists of at least three cryptic species. Marine
Biology , 157 (1), 69–80.
https://doi.org/10.1007/s00227-009-1296-9
Battey, C. J., & Klicka, J. (2017). Cryptic speciation and gene flow in
a migratory songbird species complex: Insights from the red-eyed vireo
(Vireo olivaceus ). Molecular Phylogenetics and Evolution ,113 , 67–75. https://doi.org/10.1016/j.ympev.2017.05.006
Bayona-Vásquez, N. J., Glenn, T. C., Kieran, T. J., Pierson, T. W.,
Hoffberg, S. L., Scott, P. A., Bentley, K. E., Finger, J. W., Louha, S.,
Troendle, N., Díaz-Jaimes, P., Mauricio, R., & Faircloth, B. C. (2019).
Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries
(2RAD/3RAD). BioRxiv . https://doi.org/10.1101/205799
Bickford, D., Lohman, D. J., Sodhi, N. S., Ng, P. K. L., Meier, R.,
Winker, K., Ingram, K. K., & Das, I. (2007). Cryptic species as a
window on diversity and conservation. Trends in Ecology &
Evolution , 22 (3), 148–155.
https://doi.org/10.1016/j.tree.2006.11.004
Bivand, R., Keitt, T., & Rowlingson, B. (2019). rgdal: Bindings
for the “geospatial” data abstraction library [R package version
1.4-4]. . https://CRAN.R-project.org/package=rgdal
Bond, J. E., Hedin, M. C., Ramirez, M. G., & Opell, B. D. (2001). Deep
molecular divergence in the absence of morphological and ecological
change in the Californian coastal dune endemic trapdoor spiderAptostichus simus . Molecular Ecology , 10 (4),
899–910. https://doi.org/10.1046/j.1365-294X.2001.01233.x
Bond, J. E., Hendrixson, B. E., Hamilton, C. A., & Hedin, M. (2012). A
reconsideration of the classification of the spider Infraorder
Mygalomorphae (Arachnida: Araneae) based on three nuclear genes and
morphology. PLoS ONE , 7 (6), e38753.
https://doi.org/10.1371/journal.pone.0038753
Bond, J. E., & Sierwald, P. (2002). Cryptic speciation in theAnadenobolus excisus millipede species complex on the island of
Jamaica. Evolution , 56 (6), 1123–1135.
Bond, J. E., & Stockman, A. K. (2008). An integrative method for
delimiting cohesion species: Finding the population-species interface in
a group of Californian trapdoor spiders with extreme genetic divergence
and geographic structuring. Systematic Biology , 57 (4),
628–646. https://doi.org/10.1080/10635150802302443
Burns, M., Starrett, J., Derkarabetian, S., Richart, C. H., Cabrero, A.,
& Hedin, M. (2017). Comparative performance of double-digest RAD
sequencing across divergent arachnid lineages. Molecular Ecology
Resources , 17 (3), 418–430.
https://doi.org/10.1111/1755-0998.12575
Caterino, M. S., & Langton-Myers, S. S. (2019). Intraspecific diversity
and phylogeography in Southern Appalachian Dasycerus carolinensis(Coleoptera: Staphylinidae: Dasycerinae). Insect Systematics and
Diversity , 3 (6). https://doi.org/10.1093/isd/ixz022
Chan, K. O., Alexander, A. M., Grismer, L. L., Su, Y.-C., Grismer, J.
L., Quah, E. S. H., & Brown, R. M. (2017). Species delimitation with
gene flow: A methodological comparison and population genomics approach
to elucidate cryptic species boundaries in Malaysian Torrent Frogs.Molecular Ecology , 26 (20), 5435–5450.
https://doi.org/10.1111/mec.14296
Coyle, F. A. (1971). Systematics and natural history of the mygalomorph
spider genus Antrodiaetus and related genera (Araneae:
Antrodiaetidae). Bull. Mus. Comp. Zool , 141 , 269–402.
Coyle, F. A. (1983). Aerial dispersal by Mygalomorph spiderlings
(Araneae, Mygalomorphae). Journal of Arachnology , 11 (2),
283–286.
Coyle, F. A. (1985). Ballooning behavior of Ummidia spiderlings.
(Araneae: Ctenizidae). Journal of Arachnology , 13 ,
137–138.
Crotti, M., Barratt, C. D., Loader, S. P., Gower, D. J., & Streicher,
J. W. (2019). Causes and analytical impacts of missing data in RADseq
phylogenetics: Insights from an African frog (Afrixalus ).Zoologica Scripta , 48 (2), 157–167.
https://doi.org/10.1111/zsc.12335
De Jesús-Bonilla, V. S., Meza-Lázaro, R. N., & Zaldívar-Riverón, A.
(2019). 3RAD-based systematics of the transitional Nearctic-Neotropical
lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae).Molecular Phylogenetics and Evolution , 137 , 64–75.
https://doi.org/10.1016/j.ympev.2019.04.019
Degnan, J. H., & Rosenberg, N. A. (2009). Gene tree discordance,
phylogenetic inference and the multispecies coalescent. Trends in
Ecology & Evolution , 24 (6), 332–340.
https://doi.org/10.1016/j.tree.2009.01.009
Delgado‐Machuca, N., Meza‐Lázaro, R. N., Romero‐Nápoles, J.,
Sarmiento‐Monroy, C. E., Amarillo‐Suárez, Á. R., Bayona‐Vásquez, N. J.,
& Alejandro, Z. (2019). Genetic structure, species limits and evolution
of the parasitoid wasp genus Stenocorse (Braconidae: Doryctinae)
based on nuclear 3RAD and mitochondrial data. Systematic
Entomology . https://onlinelibrary.wiley.com/doi/abs/10.1111/syen.12373
Derkarabetian, S., Castillo, S., Koo, P. K., Ovchinnikov, S., & Hedin,
M. (2019). A demonstration of unsupervised machine learning in species
delimitation. Molecular Phylogenetics and Evolution , 139 ,
106562. https://doi.org/10.1016/j.ympev.2019.106562
Derkarabetian, S., & Hedin, M. (2014). Integrative Taxonomy and Species
Delimitation in Harvestmen: A Revision of the Western North American
Genus Sclerobunus (Opiliones: Laniatores: Travunioidea). PLoS
ONE , 9 (8), e104982. https://doi.org/10.1371/journal.pone.0104982
Derkarabetian, S., Ledford, J., & Hedin, M. (2011). Genetic
diversification without obvious genitalic morphological divergence in
harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane
sky islands of western North America. Molecular Phylogenetics and
Evolution , 61 (3), 844–853.
https://doi.org/10.1016/j.ympev.2011.08.004
Dupérré, N., & Tapia, E. (2015). Discovery of the first telemid spider
(Araneae, Telemidae) from South America, and the first member of the
family bearing a stridulatory organ. Zootaxa , 4020 (1),
191. https://doi.org/10.11646/zootaxa.4020.1.9
Eaton, D. A. R. (2014). PyRAD: Assembly of de novo RADseq loci for
phylogenetic analyses. Bioinformatics , 30 (13), 1844–1849.
https://doi.org/10.1093/bioinformatics/btu121
Eaton, D. A. R., Spriggs, E. L., Park, B., & Donoghue, M. J. (2016).
Misconceptions on missing data in RAD-seq phylogenetics with a
deep-scale example from flowering plants. Systematic Biology ,
syw092. https://doi.org/10.1093/sysbio/syw092
Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high
accuracy and high throughput. Nucleic Acids Research ,32 (5), 1792–1797. https://doi.org/10.1093/nar/gkh340
Emerson, K. J., Merz, C. R., Catchen, J. M., Hohenlohe, P. A., Cresko,
W. A., Bradshaw, W. E., & Holzapfel, C. M. (2010). Resolving
postglacial phylogeography using high-throughput sequencing.Proceedings of the National Academy of Sciences , 107 (37),
16196–16200. https://doi.org/10.1073/pnas.1006538107
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of
clusters of individuals using the software structure: A simulation
study. Molecular Ecology , 14 (8), 2611–2620.
https://doi.org/10.1111/j.1365-294X.2005.02553.x
Faircloth, B. C., McCormack, J. E., Crawford, N. G., Harvey, M. G.,
Brumfield, R. T., & Glenn, T. C. (2012). Ultraconserved elements anchor
thousands of genetic markers spanning multiple evolutionary timescales.Systematic Biology , 61 (5), 717–726.
https://doi.org/10.1093/sysbio/sys004
Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: New 1-km spatial
resolution climate surfaces for global land areas: new climate surfaces
for global land areas. International Journal of Climatology ,37 (12), 4302–4315. https://doi.org/10.1002/joc.5086
Francis, R. M. (2017). pophelper: An R package and web app to analyse
and visualize population structure. Molecular Ecology Resources ,17 (1), 27–32. https://doi.org/10.1111/1755-0998.12509
Freudenstein, J. V., Broe, M. B., Folk, R. A., & Sinn, B. T. (2016).
Biodiversity and the species concept—Lineages are not enough.Systematic Biology , syw098. https://doi.org/10.1093/sysbio/syw098
Garg, K. M., Tizard, R., Ng, N. S. R., Cros, E., Dejtaradol, A.,
Chattopadhyay, B., Pwint, N., Päckert, M., & Rheindt, F. E. (2016).
Genome-wide data help identify an avian species-level lineage that is
morphologically and vocally cryptic. Molecular Phylogenetics and
Evolution , 102 , 97–103.
https://doi.org/10.1016/j.ympev.2016.05.028
Garrick, R. C., Newton, K. E., & Worthington, R. J. (2018). Cryptic
diversity in the southern Appalachian Mountains: Genetic data reveal
that the red centipede, Scolopocryptops sexspinosus, is a species
complex. Journal of Insect Conservation , 22 (5–6),
799–805. https://doi.org/10.1007/s10841-018-0107-3
Graham, C. F., Glenn, T. C., McArthur, A. G., Boreham, D. R., Kieran,
T., Lance, S., Manzon, R. G., Martino, J. A., Pierson, T., Rogers, S.
M., Wilson, J. Y., & Somers, C. M. (2015). Impacts of degraded DNA on
restriction enzyme associated DNA sequencing (RADSeq). Molecular
Ecology Resources , 15 (6), 1304–1315.
https://doi.org/10.1111/1755-0998.12404
Hamilton, C. A., Hendrixson, B. E., Brewer, M. S., & Bond, J. E.
(2014). An evaluation of sampling effects on multiple DNA barcoding
methods leads to an integrative approach for delimiting species: A case
study of the North American tarantula genus Aphonopelma (Araneae,
Mygalomorphae, Theraphosidae). Molecular Phylogenetics and
Evolution , 71 , 79–93.
https://doi.org/10.1016/j.ympev.2013.11.007
Harvey, M. S., Hillyer, M. J., Main, B. Y., Moulds, T. A., Raven, R. J.,
Rix, M. G., Vink, C. J., & Huey, J. A. (2018). Phylogenetic
relationships of the Australasian open-holed trapdoor spiders (Araneae:
Mygalomorphae: Nemesiidae: Anaminae): multi-locus molecular analyses
resolve the generic classification of a highly diverse fauna.Zoological Journal of the Linnean Society , 184 (2),
407–452. https://doi.org/10.1093/zoolinnean/zlx111
Hedin, M., Carlson, D., & Coyle, F. A. (2015). 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.Molecular Ecology , 24 (13), 3467–3484.
https://doi.org/10.1111/mec.13248
Hedin, M., Derkarabetian, S., Alfaro, A., Ramírez, M. J., & Bond, J. E.
(2019). Phylogenomic analysis and revised classification of atypoid
mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid
ultraconserved element loci. PeerJ , 7 , e6864.
https://doi.org/10.7717/peerj.6864
Hedin, M., & McCormack, M. (2017). Biogeographical evidence for common
vicariance and rare dispersal in a southern Appalachian harvestman
(Sabaconidae, Sabacon cavicolens ). Journal of
Biogeography , 44 (7), 1665–1678.
https://doi.org/10.1111/jbi.12973
Hedin, M., Starrett, J., & Hayashi, C. (2013). Crossing the
uncrossable: Novel trans-valley biogeographic patterns revealed in the
genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae,Antrodiaetus ) from California. Molecular Ecology ,22 (2), 508–526. https://doi.org/10.1111/mec.12130
Hendrixson, B. E., & Bond, J. E. (2005a). Two sympatric species ofAntrodiaetus from southwestern North Carolina (Araneae,
Mygalomorphae, Antrodiaetidae). Zootaxa , 872 (1), 1.
https://doi.org/10.11646/zootaxa.872.1.1
Hendrixson, B. E., & Bond, J. E. (2005b). Testing species boundaries in
the Antrodiaetus unicolor complex (Araneae: Mygalomorphae:
Antrodiaetidae): “Paraphyly” and cryptic diversity. Molecular
Phylogenetics and Evolution , 36 (2), 405–416.
https://doi.org/10.1016/j.ympev.2005.01.021
Hendrixson, B. E., & Bond, J. E. (2007). Molecular phylogeny and
biogeography of an ancient Holarctic lineage of mygalomorph spiders
(Araneae: Antrodiaetidae: Antrodiaetus ). Molecular
Phylogenetics and Evolution , 42 (3), 738–755.
https://doi.org/10.1016/j.ympev.2006.09.010
Hendrixson, B. E., DeRussy, B. M., Hamilton, C. A., & Bond, J. E.
(2013). An exploration of species boundaries in turret-building
tarantulas of the Mojave Desert (Araneae, Mygalomorphae, Theraphosidae,Aphonopelma ). Molecular Phylogenetics and Evolution ,66 (1), 327–340. https://doi.org/10.1016/j.ympev.2012.10.004
Hey, J. (2001). The mind of the species problem. Trends in Ecology
& Evolution , 16 (7), 326–329.
Hijmans, R. J. (2015). raster: Geographic data analysis and
modeling [R package version 2.5-2].
https://cran.r-project.org/package=raster
Hoffberg, S. L., Kieran, T. J., Catchen, J. M., Devault, A., Faircloth,
B. C., Mauricio, R., & Glenn, T. C. (2016). RADcap: Sequence capture of
dual-digest RADseq libraries with identifiable duplicates and reduced
missing data. Molecular Ecology Resources , 16 (5),
1264–1278. https://doi.org/10.1111/1755-0998.12566
Holland, B. S., Dawson, M. N., Crow, G. L., & Hofmann, D. K. (2004).
Global phylogeography of Cassiopea (Scyphozoa: Rhizostomeae): molecular
evidence for cryptic species and multiple invasions of the Hawaiian
Islands. Marine Biology , 145 (6), 1119–1128.
https://doi.org/10.1007/s00227-004-1409-4
Huang, H., & Knowles, L. L. (2016). Unforeseen consequences of
excluding missing data from next-generation sequences: Simulation study
of RAD sequences. Systematic Biology , 65 (3), 357–365.
https://doi.org/10.1093/sysbio/syu046
Huey, J. A., Hillyer, M. J., & Harvey, M. S. (2019). Phylogenetic
relationships and biogeographic history of the Australian trapdoor
spider genus Conothele (Araneae: Mygalomorphae: Halonoproctidae):
diversification into arid habitats in an otherwise tropical radiation.Invertebrate Systematics . https://doi.org/10.1071/IS18078
Jezkova, T., Olah-Hemmings, V., & Riddle, B. R. (2011). Niche shifting
in response to warming climate after the last glacial maximum: Inference
from genetic data and niche assessments in the chisel-toothed kangaroo
rat (Dipodomys microps ). Global Change Biology ,17 (11), 3486–3502.
https://doi.org/10.1111/j.1365-2486.2011.02508.x
Jombart, T. (2008). adegenet: A R package for the multivariate analysis
of genetic markers. Bioinformatics , 24 (11), 1403–1405.
https://doi.org/10.1093/bioinformatics/btn129
Jombart, T., & Ahmed, I. (2011). adegenet 1.3-1: New tools for the
analysis of genome-wide SNP data. Bioinformatics , 27 (21),
3070–3071. https://doi.org/10.1093/bioinformatics/btr521
Keith, R., & Hedin, M. (2012). Extreme mitochondrial population
subdivision in southern Appalachian paleoendemic spiders (Araneae:
Hypochilidae: Hypochilus ), with implications for species
delimitation. Journal of Arachnology , 40 (2), 167–181.
Kozak, K. H., & Wiens, J. J. (2010). Niche conservatism drives
elevational diversity patterns in Appalachian salamanders. The
American Naturalist , 176 (1), 40–54.
https://doi.org/10.1086/653031
Leaché, A. D., Chavez, A. S., Jones, L. N., Grummer, J. A., Gottscho, A.
D., & Linkem, C. W. (2015). Phylogenomics of Phrynosomatid lizards:
Conflicting signals from sequence capture versus restriction site
associated DNA sequencing. Genome Biology and Evolution ,7 (3), 706–719. https://doi.org/10.1093/gbe/evv026
Lemmon, A. R., Emme, S. A., & Lemmon, E. M. (2012). Anchored hybrid
enrichment for massively high-throughput phylogenomics. Systematic
Biology , 61 (5), 727–744. https://doi.org/10.1093/sysbio/sys049
Maddison, W. P. (1997). Gene trees in species trees. Systematic
Biology , 46 (3), 523–536.
Massatti, R., & Knowles, L. L. (2014). Microhabitat differences impact
phylogeographic concordance of codistributed species: Genomic evidence
in montane sedges (Carex ) from the Rocky Mountains.Evolution , 68 (10), 2833–2846.
https://doi.org/10.1111/evo.12491
Moritz, C., Fujita, M. K., Rosauer, D., Agudo, R., Bourke, G., Doughty,
P., Palmer, R., Pepper, M., Potter, S., Pratt, R., Scott, M., Tonione,
M., & Donnellan, S. (2016). Multilocus phylogeography reveals nested
endemism in a gecko across the monsoonal tropics of Australia.Molecular Ecology , 25 (6), 1354–1366.
https://doi.org/10.1111/mec.13511
Opatova, V., & Arnedo, M. A. (2014a). From Gondwana to Europe:
Inferring the origins of Mediterranean Macrothele spiders (Araneae :
Hexathelidae) and the limits of the family Hexathelidae.Invertebrate Systematics , 28 (4), 361.
https://doi.org/10.1071/IS14004
Opatova, V., & Arnedo, M. A. (2014b). Spiders on a Hot Volcanic Roof:
Colonisation Pathways and Phylogeography of the Canary Islands Endemic
Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae).PLoS ONE , 9 (12), e115078.
https://doi.org/10.1371/journal.pone.0115078
Opatova, V., Hamilton, C. A., Hedin, M., De Oca, L. M., Král, J., &
Bond, J. E. (2019). Phylogenetic systematics and evolution of the spider
infraorder Mygalomorphae using genomic scale data. Systematic
Biology , syz064 . https://doi.org/10.1093/sysbio/syz064
Ortega-Andrade, H. M., Rojas-Soto, O. R., Valencia, J. H., Espinosa de
los Monteros, A., Morrone, J. J., Ron, S. R., & Cannatella, D. C.
(2015). Insights from Integrative Systematics Reveal Cryptic Diversity
in Pristimantis Frogs (Anura: Craugastoridae) from the Upper Amazon
Basin. PLOS ONE , 10 (11), e0143392.
https://doi.org/10.1371/journal.pone.0143392
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra,
H. E. (2012). Double digest RADseq: An inexpensive method for de novo
SNP discovery and genotyping in model and non-model species. PLoS
ONE , 7 (5), e37135. https://doi.org/10.1371/journal.pone.0037135
Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2006). Maximum
entropy modeling of species geographic distributions. Ecological
Modelling , 190 (3–4), 231–259.
https://doi.org/10.1016/j.ecolmodel.2005.03.026
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of
population structure Using multilocus genotype data. Genetics ,155 (2), 949–959.
R Core Team. (2019). R: A language and environment for statistical
computing . R Foundation for Statistical Computing.
https://www.r-project.org/
Ramírez-Reyes, T., Piñero, D., Flores-Villela, O., & Vázquez-Domínguez,
E. (2017). Molecular systematics, species delimitation and
diversification patterns of the Phyllodactylus lanei complex (Gekkota:
Phyllodactylidae) in Mexico. Molecular Phylogenetics and
Evolution , 115 , 82–94.
https://doi.org/10.1016/j.ympev.2017.07.008
Reynolds, R. G., Niemiller, M. L., & Fitzpatrick, B. M. (2012). Genetic
analysis of an endemic archipelagic lizard reveals sympatric cryptic
lineages and taxonomic discordance. Conservation Genetics ,13 (4), 953–963. https://doi.org/10.1007/s10592-012-0344-z
Richardson, B. J. (2016). New genera, new species and redescriptions of
Australian jumping spiders (Araneae: Salticidae). Zootaxa ,4114 (5), 501. https://doi.org/10.11646/zootaxa.4114.5.1
Rognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016).
VSEARCH: A versatile open source tool for metagenomics. PeerJ ,4 , e2584. https://doi.org/10.7717/peerj.2584
Satler, J. D., Starrett, J., Hayashi, C. Y., & Hedin, M. (2011).
Inferring species trees from gene trees in a radiation of California
trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus ). PLoS
ONE , 6 (9), e25355. https://doi.org/10.1371/journal.pone.0025355
Schoener, T. W. (1968). The Anolis lizards of Bimini: Resource
partitioning in a complex fauna. Ecology , 49 (4), 704–726.
https://doi.org/10.2307/1935534
Soberón, J. (2007). Grinnellian and Eltonian niches and geographic
distributions of species. Ecology Letters , 10 (12),
1115–1123. https://doi.org/10.1111/j.1461-0248.2007.01107.x
Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis
and post-analysis of large phylogenies. Bioinformatics ,30 (9), 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Starrett, J., Hayashi, C. Y., Derkarabetian, S., & Hedin, M. (2018).
Cryptic elevational zonation in trapdoor spiders (Araneae,
Antrodiaetidae, Aliatypus janus complex) from the California
southern Sierra Nevada. Molecular Phylogenetics and Evolution ,118 , 403–413. https://doi.org/10.1016/j.ympev.2017.09.003
Starrett, J., & Hedin, M. (2007). Multilocus genealogies reveal
multiple cryptic species and biogeographical complexity in the
California turret spider Antrodiaetus riversi (Mygalomorphae,
Antrodiaetidae): Cryptic diversifocation in Californian A.
riversi . Molecular Ecology , 16 (3), 583–604.
https://doi.org/10.1111/j.1365-294X.2006.03164.x
Stockman, A. K., & Bond, J. E. (2007). Delimiting cohesion species:
Extreme population structuring and the role of ecological
interchangeability. Molecular Ecology , 16 (16), 3374–3392.
https://doi.org/10.1111/j.1365-294X.2007.03389.x
Sukumaran, J., & Knowles, L. L. (2017). Multispecies coalescent
delimits structure, not species. Proceedings of the National
Academy of Sciences , 114 (7), 1607–1612.
https://doi.org/10.1073/pnas.1607921114
Swets, J. (1988). Measuring the accuracy of diagnostic systems.Science , 240 (4857), 1285–1293.
https://doi.org/10.1126/science.3287615
Templeton, A. R. (1989). The meaning of species and speciation: A
genetic perspective. In Speciation and its Consequences (pp.
3–27). Sinauer.
Thomas, S. M., & Hedin, M. (2008). Multigenic phylogeographic
divergence in the paleoendemic southern Appalachian opilionidFumontana deprehendor Shear (Opiliones, Laniatores,
Triaenonychidae). Molecular Phylogenetics and Evolution ,46 (2), 645–658. https://doi.org/10.1016/j.ympev.2007.10.013
Wake, D. B. (2006). Problems with species: Patterns and processes of
species formation in salamanders. Annals of the Missouri Botanical
Garden , 93 (1), 8–23.
Walker, M. J., Stockman, A. K., Marek, P. E., & Bond, J. E. (2009).
Pleistocene glacial refugia across the Appalachian Mountains and coastal
plain in the millipede genus Narceus : Evidence from population
genetic, phylogeographic, and paleoclimatic data. BMC Evolutionary
Biology , 9 (1), 25. https://doi.org/10.1186/1471-2148-9-25
Warren, D. L., Glor, R. E., & Turelli, M. (2008). Environmental niche
equivalency versus conservatism: Quantitative approaches to niche
evolution. Evolution , 62 (11), 2868–2883.
https://doi.org/10.1111/j.1558-5646.2008.00482.x
Warren, D. L., Glor, R. E., & Turelli, M. (2010). ENMTools: A toolbox
for comparative studies of environmental niche models. Ecography .
https://doi.org/10.1111/j.1600-0587.2009.06142.x
Weisrock, D. W., & Larson, A. (2006). Testing hypotheses of speciation
in the Plethodon jordani species complex with allozymes and
mitochondrial DNA sequences: Diagnosing plethodontid salamander species.Biological Journal of the Linnean Society , 89 (1), 25–51.
https://doi.org/10.1111/j.1095-8312.2006.00655.x
Wiens, J. J., & Graham, C. H. (2005). Niche Conservatism: Integrating
Evolution, Ecology, and Conservation Biology. Annual Review of
Ecology, Evolution, and Systematics , 36 (1), 519–539.
https://doi.org/10.1146/annurev.ecolsys.36.102803.095431
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018). ASTRAL-III:
Polynomial time species tree reconstruction from partially resolved gene
trees. BMC Bioinformatics , 19 (S6).
https://doi.org/10.1186/s12859-018-2129-y
Zhang, Y., & Li, S. (2014). A spider species complex revealed high
cryptic diversity in South China caves. Molecular Phylogenetics
and Evolution , 79 , 353–358.
https://doi.org/10.1016/j.ympev.2014.05.017