References
Alvarez, N., Thiel-Egenter, C., Tribsch, A., Holderegger, R., Manel, S.,
Schönswetter, P., Taberlet, P., Brodbeck, S., Gaudeul, M., Gielly, L.,
Küpfer, P., Mansion, G., Negrini, R., Paun, O., Pellecchia, M., Rioux,
D., Schüpfer, F., Van Loo, M., Winkler, M., Gugerli, F., & IntraBioDiv
Consortium (2009). History or ecology? Substrate type as a major driver
of spatial genetic structure in Alpine plants. Ecology
Letters , 12(7) , 632- 640.
Andújar, C., Serrano, J. & Gómez-Zurita, J. (2012). Winding up the
molecular clock in the genus Carabus (Coleoptera: Carabidae):
assessment of methodological decisions on rate and node age estimation.BMC Evolutionary Biology , 12 , 40.
Bankevich, A., S. Nurk, Antipov, D., Gurevich, A. A., Dvorkin, M.,
Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A.
D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev,
M. A., & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm
and its applications to single-cell sequencing. Journal of
Computational Biology , 19 , 455- 477.
Barton, N. H., & Hewitt, G. M. (1985). Analysis of hybrid zones.Annual Review of Ecology and Systematics , 16 , 113- 148.
Basagic, H. J., & Fountain, A. G. (2011). Quantifying 20th century
glacier change in the Sierra Nevada, California. Arctic,
Antarctic, and Alpine Research , 43(3) , 317- 330.
Battey, C. J., Ralph, P. L., & Kern, A. D. (2020). Space is the place:
effects of continuous spatial structure on analysis of population
genetic data. Genetics , 215 , 193- 214.
Beerli, P. (2015). How to use MIGRATE or why are Markov chain Monte
Carlo programs difficult to use. Population Genetics for Animal
Conservation , 17 , 42- 79.
Belmecheri, S., Babst, F., Wahl, E. R., Stahle, D. W., & Trouet, V.
(2016). Multi-century evaluation of Sierra Nevada snowpack. Nature
Climate Change , 6(1) , 2- 3.
Bidegaray-Batista, L., Sánchez-Gracia, A., Santulli, G., Maiorano, L.,
Guisan, A., Vogler, A. P., & Arnedo, M. A. (2016). Imprints of multiple
glacial refugia in the Pyrenees revealed by phylogeography and
palaeodistribution modelling of an endemic spider. Molecular
Ecology , 25 , 2046- 2064.
Bohonak, A. J. (1999). Dispersal, gene flow, and population structure.The Quarterly Review of Biology , 74 , 21- 45.
Bouckaert, R. R. (2010). DensiTree: making sense of sets of phylogenetic
trees. Bioinformatics , 26 , 1372- 1373.
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C-H., Xie, D.,
Suchard, MA., Rambaut, A., & Drummond, A. J. (2014). BEAST 2: A
Software Platform for Bayesian Evolutionary Analysis. PLoS
Computational Biology , 10(4) , e1003537.
doi:10.1371/journal.pcbi.1003537
Bradburd, G., Coop, G., & Ralph, P. (2018). Inferring continuous and
discrete population genetic structure across space. Genetics ,210 , 33- 52.
Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., &
RoyChoudhury, A. (2012). Inferring species trees directly from biallelic
genetic markers: bypassing gene trees in a full coalescent analysis.Molecular Biology and Evolution , 29 , 1917- 1932.
Carling, M. D., Lovette, I. J., & Brumfield, R. T. (2010). Historical
divergence and gene flow: coalescent analyses of mitochondrial,
autosomal and sex-linked loci in Passerina buntings .Evolution , 64 : 1762- 1772.
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A.
(2013). Stacks: an analysis tool set for population genomics.Molecular Ecology , 22 , 3124- 3140.
Clement, M., Snell, Q., Walker, P., Posada, D., & Crandall, K. (2002).
TCS: estimating gene genealogies. Brigham Young University, Provo, UT.
Coffman, A. J., Hsieh, P. H., Gravel, S., & Gutenkunst, R. N. (2016).
Computationally Efficient Composite Likelihood Statistics for
Demographic Inference. Molecular Biology and Evolution ,33(2) , 591- 593. https://doi.org/10.1093/molbev/msv255
Dahl, E. (1987). The nunatak theory reconsidered. Ecological
Bulletins , 77-94.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E.,
DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S.
T., McVean, G., Durbin, R., & 1000 Genomes Project Analysis Group.
(2011). The variant call format and VCFtools. Bioinformatics ,27 , 2156- 2158.
DeChaine, E. G., & Martin, A. P. (2006). Using coalescent simulations
to test the impact of Quaternary climate cycles on divergence in an
alpine plant‐insect association. Evolution , 60(5) , 1004-
1013.
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha,
S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: ultrafast
universal RNA-seq aligner. Bioinformatics , 29 , 15- 21.
Dufresnes, C., Berroneau, M., Dubey, S., Litvinchuk, S. N., & Perrin,
N. (2020). The effect of phylogeographic history on species boundaries:
a comparative framework in Hyla tree frogs. Scientific
Reports , 10 , 1- 12.
Dynesius, M., & Jansson, R. (2000). Evolutionary consequences of
changes in species’ geographical distributions driven by Milankovitch
climate oscillations. Proceedings of the National Academy of
Sciences , 97(16) , 9115- 9120.
Elshire, R.J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K.,
Buckler, E. S., & Mitchell, S. E. (2011). A robust, simple
genotyping-by-sequencing (GBS) approach for high diversity species.PLoS ONE , 6 , e19379.
François, O. & Durand, E. (2010). Spatially explicit Bayesian
clustering models in population genetics. Molecular Ecology
Resources , 10(5) , 773- 784
Frichot, E., Mathieu, F., Trouillon, T., Bouchard, G., & François, O.
(2014). Fast and efficient estimation of individual ancestry
coefficients. Genetics , 196, 973-983.
Galbreath, K. E., Hafner, D. J., & Zamudio, K. R. (2009). When cold is
better: climate-driven elevation shifts yield complex patterns of
diversification and demography in an alpine specialist (American pika,Ochotona princeps ). Evolution , 63 , 2848- 2863.
Gereben, B. A. (1995). Co-occurrence and microhabitat distribution of
six Nebria species (Coleoptera: Carabidae) in an alpine glacier
retreat zone in the Alps, Austria. Arctic and Alpine Research ,27(4) , 371- 379.
Gompert, Z., Fordyce, J. A., Forister, M. L., Shapiro, A. M., & Nice,
C. C. (2006). Homoploid hybrid speciation in an extreme habitat.Science , 314(5807) , 1923- 1925.
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante,
C. D. (2009). Inferring the joint demographic history of multiple
populations from multidimensional SNP frequency data. PLoS
Genetics , 5, e1000695.
He, Z., Li, X., Yang, M., Wang, X., Zhong, C., Duke, N. C., Wu, C. I.,
& Shi, S. (2019). Speciation with gene flow via cycles of isolation and
migration: insights from multiple mangrove taxa. National Science
Review , 6(2) , 275- 288.
Hewitt, G. M. (1999). Post-glacial re-colonization of European biota.Biological Journal of the Linnean Society , 68 , 87- 112.
Holderegger, R., & Thiel‐Egenter, C. (2009). A discussion of different
types of glacial refugia used in mountain biogeography and
phylogeography. Journal of Biogeography , 36 , 476- 480.
Homburg, K., Drees, C., Gossner, M. M., Rakosy, L., Vrezec, A., and
Assmann, T. (2013). Multiple glacial refugia of the low-dispersal ground
beetle Carabus irregularis : molecular data support predictions of
species distribution models. PLoS One , 8 , e61185.
Huang, C. C., Hsu, T. W., Wang, H. V., Liu, Z. H., Chen, Y. Y., Chiu, C.
T., Huang, C. L., Hung, K. H., & Chiang, T. Y.. (2016). Multilocus
analyses reveal postglacial demographic shrinkage of Juniperus
morrisonicola (Cupressaceae), a dominant alpine species in Taiwan.PLoS One , 11 , e0161713.
Huang, Z. S.,. Yu, F. L, Gong, H. S., Song, Y. L., Zeng, Z. G., &
Zhang, Q. (2017). Phylogeographical structure and demographic expansion
in the endemic alpine stream salamander (Hynobiidae:Batrachuperus ) of the Qinling Mountains. Scientific
Reports , 7 , 1871.
Jansson, R., & Dynesius, M. (2002). The fate of clades in a world of
recurrent climatic change: Milankovitch oscillations and evolution.Annual Review of Ecology and Systematics , 33(1) ,
741-777.
Kavanaugh, D. H. (1985). On wing atrophy in carabid beetles (Coleoptera:
Carabidae), with special reference to Nearctic Nebria . In G. E.
Ball (Ed.), Taxonomy, Phylogeny and zoogeography of beetles and
ants. A Volume Dedicated to the Memory of Philip Jackson
Darlington, Jr.(1904-1983). Series Entomologica , 33 , 408-431.
Kavanaugh, D. H. (2015). A new species of Nebria Latreille
(Insecta: Coleoptera: Carabidae: Nebriini) from the Spring Mountains of
Southern Nevada. Proceedings of the California Academy of
Sciences , 62 , 441–450.
Keightley, P. D., Ness, R. W., Halligan, D. L., & Haddrill, P. R.
(2014). Estimation of the spontaneous mutation rate per nucleotide site
in a Drosophila melanogaster full-sib family. Genetics ,196 , 313-320.
Keightley, P. D., Pinharanda, A., Ness, R. W., Simpson, F.,
Dasmahapatra, K. K., Mallet, J., Davey, J. W., & Jiggins, C. D. (2015).
Estimation of the spontaneous mutation rate in Heliconius
melpomene . Molecular Biology and Evolution , 32 ,
239-243.
Kikvidze Z, Brooker RW, Butterfield BJ, Callaway RM, Cavieres LA, Cook
BJ, Lortie CJ, Michalet R, Pugnaire FI, Xiao S, Anthelme F, Bjork RG,
Cranston BH, Gavilan RG, Kanka R, Lingua E, Maalouf JP, Noroozi J,
Parajuli R, Phoenix GK, Reid A, Ridenour WM, Rixen C, Schob C. 2015. The
effects of foundation species on community assembly: A global study on
alpine cushion plant communities. Ecology , 96 , 2064–
2069.
Kleckova, I., Konvicka, M., & Klecka, J. (2014). Thermoregulation and
microhabitat use in mountain butterflies of the genus Erebia :
importance of fine-scale habitat heterogeneity. Journal of Thermal
Biology , 41 , 50- 58.
Knowles, L. L. (2001). Did the Pleistocene glaciations promote
divergence? Tests of explicit refugial models in montane grasshopprers.Molecular Ecology , 10(3) , 691- 701.
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD:
Analysis of Next Generation Sequencing Data. BMC Bioinformatics ,15 , 356.
Kosiński, P., Sękiewicz, K., Walas, Ł., Boratyński, A., & Dering, M.
(2019). Spatial genetic structure of the endemic alpine plantSalix serpillifolia : genetic swamping on nunataks due to
secondary colonization? Alpine Botany , 129 , 107- 121.
Karney, C. F. F. (2013). Algorithms for geodesics. Journal of
Geodesy , 87 , 43- 55.
Kubow, K. B., Robinson, C. T., Shama, L. N., & Jokela, J. (2010).
Spatial scaling in the phylogeography of an alpine caddisfly, Allogamus
uncatus, within the central European Alps. Journal of the North
American Benthological Society , 29 , 1089- 1099.
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular
Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.Molecular Biology and Evolution , 33 , 1870- 1874.
Leigh, J. W., & Bryant, D. (2015). PopArt: full-feature software for
haplotype network construction. Methods in Ecology and Evolution ,6 (9) , 1110- 1116.
Liu, X. (2020). Human prehistoric demography revealed by the polymorphic
pattern of CpG transitions. Molecular Biology and Evolution ,
msaa112
Liu, X., & Fu, Y. X. (2015). Corrigendum: Exploring population size
changes using SNP frequency spectra. Nature Genetics ,47 , 1099.
Lohse, K., Nicholls, J. A., & Stone, G. N. (2011). Inferring the
colonization of a mountain range—refugia vs. nunatak survival in high
alpine ground beetles. Molecular Ecology , 20(2) , 394-
408.
Merkle, E., & You, D. (2018). nonnest2: tests of non-nested models.
Retrieved 04 August, 2020, from
https://cran.r-project.org/web/packages/nonnest2
Massatti, R., & Knowles, L. L. (2014). Microhabitat differences impact
phylogeographic concordance of codistributed species: Genomic evidence
in montane sedges (Carex L.) from the Rocky Mountains.Evolution , 68 , 2833- 2846.
Nguyen, L.T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015).
IQ-TREE: a fast and effective stochastic algorithm for estimating
maximum-likelihood phylogenies. Molecular Biology and Evolution ,32 , 268- 274.
Nielsen, R., & Wakeley, J. (2001). Distinguishing migration from
isolation: a Markov chain Monte Carlo approach. Genetics ,158(2) , 885- 896.
Nielsen, R., & Slatkin, M. (2007). Likelihood analysis of ongoing gene
flow and historical association. Evolution , 54(1) , 44-
50.
Oppold, A. M., & Pfenninger, M. (2017). Direct estimation of the
spontaneous mutation rate by short-term mutation accumulation lines in.Evolution Letters , 1 , 86- 92.
Pan, D., Hülber, K., Willner, W., & Schneeweiss, G. M. (2020). An
explicit test of Pleistocene survival in peripheral versus nunatak
refugia in two high mountain plant species. Molecular Ecology ,29 , 172- 183.
Paun, O., Schönswetter, P., Winkler, M., Consortium, I. & Tribsch, A.
(2008), Historical divergence vs. contemporary gene flow: evolutionary
history of the calcicole Ranunculus alpestris group
(Ranunculaceae) in the European Alps and the Carpathians.Molecular Ecology , 17 : 4263- 4275.
Portik, D. M., Leaché, A. D., Rivera, D., Barej, M. F., Burger, M.,
Hirschfeld, M., Rödel, M. O., Blackburn, D. C., & Fujita, M. K. (2017).
Evaluating mechanisms of diversification in a Guineo‐Congolian tropical
forest frog using demographic model selection. Molecular Ecology ,26 , 5245- 5263.
Qu, Y., Zhang, R., Quan, Q., Song, G., Li, S.H. & Lei, F. (2012).
Incomplete lineage sorting or secondary admixture: disentangling
historical divergence from recent gene flow in the Vinous‐throated
parrotbill (Paradoxornis webbianus ). Molecular Ecology ,21 : 6117- 6133.
Rambaut, A. (2012). FigTree v1. 4. Available from
https://beast.community/figtree
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A.
(2018). Posterior summarization in Bayesian phylogenetics using Tracer
1.7. Systematic Biology , 67 , 901.
Rood, D. H., Burbank, D. W., & Finkel, R. C. (2011). Chronology of
glaciations in the Sierra Nevada, California,
from 10Be surface exposure dating. Quaternary
Science Reviews , 30 : 646- 661.
Rougemont, Q., & Bernatchez, L. (2018). The demographic history of
Atlantic salmon (Salmo salar ) across its distribution range
reconstructed from approximate Bayesian computations. Evolution ,72 : 1261- 1277
Rovito, S. M. (2010). Lineage divergence and speciation in the Web‐toed
Salamanders (Plethodontidae: Hydromantes ) of the Sierra Nevada,
California. Molecular Ecology , 19(20) , 4554- 4571.
Rovito, S. M., & Schoville, S. D. (2017). Testing models of refugial
isolation, colonization and population connectivity in two species of
montane salamanders. Heredity (Edinb), 119 , 265- 274.
Rubidge, E. M., Patton, J. L., & Moritz, C. (2014). Diversification of
the Alpine Chipmunk, Tamias alpinus , an alpine endemic of the
Sierra Nevada, California. BMC evolutionary biology ,14(1) , 34.
Schönswetter, P., & Schneeweiss, G. M.. (2019). Is the incidence of
survival in interior Pleistocene refugia (nunataks) underestimated?
Phylogeography of the high mountain plant. Ecology Evolution ,9 , 4078- 4086.
Schoville, S. D., & Roderick, G. K. (2009). Alpine biogeography ofParnassian butterflies during Quaternary climate cycles in North
America. Molecular Ecology , 18 , 3471- 3485.
Schoville, S. D., & Roderick, G. K. (2010). Evolutionary
diversification of cryophilic Grylloblatta species
(Grylloblattodea: Grylloblattidae) in alpine habitats of California.BMC Evolutionary Biology , 10 , 163.
Schoville, S. D., Roderick, G. K., & Kavanaugh, D. H. (2012). Testing
the ‘Pleistocene species pump’in alpine habitats: lineage
diversification of flightless ground beetles (Coleoptera: Carabidae:
Nebria) in relation to altitudinal zonation. Biological Journal of
the Linnean Society , 107 , 95- 111.
Schneeweiss, G. M., & Schoenswetter, P. (2011). A re‐appraisal of
nunatak survival in arctic‐alpine phylogeography. Molecular
Ecology , 20 (2), 190-192.
Segarra‐Moragues, J. G., Palop‐Esteban, M., González‐Candelas, F., &
Catalán, P. (2007). Nunatak survival vs. tabula rasa in the Central
Pyrenees: a study on the endemic plant species Borderea pyrenaica(Dioscoreaceae). Journal of Biogeography , 34 , 1893-
1906.
Schönswetter, P., Stehlik, I., Holderegger, R., & Tribsch, A. (2005).
Molecular evidence for glacial refugia of mountain plants in the
European Alps. Molecular Ecology , 14(11) , 3547- 3555.
Sim, Z., Hall, J. C., Jex, B., Hegel, T. M., & Coltman, D. W. (2016).
Genome-wide set of SNPs reveals evidence for two glacial refugia and
admixture from postglacial recolonization in an alpine ungulate.Molecular Ecology , 25 , 3696- 3705.
Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H., & Flook, P.
(1994). Evolution, weighing, and phylogenetic utility of mitochondrial
gene sequences and a compilation of conserved polymerase chain reaction
primers. Annals of the Entomological Society of America ,87 , 651- 701.
Starcová, M., Vohralík, V., Kryštufek, B., Bolfíková, B. Č., & Hulva,
P. (2016). Phylogeography of the Alpine shrew, Sorex alpinus(Soricidae, Mammalia). Journal of Vertebrate Biology ,65 , 107- 116.
Stehlik, I., Blattner, F. R., Holderegger, R., & Bachmann, K. (2002).
Nunatak survival of the high Alpine plant Eritrichium nanum (L.)
Gaudin in the central Alps during the ice ages. Molecular
Ecology , 11(10) , 2027- 2036.
Stoltz, M., Bauemer, B., Bouckart, R., Fox, C., Hiscott, G., & Bryant,
D. (2019). Bayesian inference of species trees using diffusion models.
arXiv preprint arXiv:1909.07276.
Theissinger, K., Bálint, M., Feldheim, K. A., Haase, P., Johannesen, J.,
Laube, I., & Pauls, S. U. (2013). Glacial survival and post‐glacial
recolonization of an arctic–alpine freshwater insect
(Arcynopteryx dichroa , Plecoptera, Perlodidae) in Europe.Journal of Biogeography , 40 , 236- 248.
Thiel‐Egenter, C., Alvarez, N., Holderegger, R., Tribsch, A., Englisch,
T., Wohlgemuth, T., Colli, L., Gaudeul, M., Gielly, L., Jogan, N.,
Linder, H.P., Negrini, R., Niklfeld, H., Pellecchia, M., Rioux, D.,
Schönswetter, P., Taberlet, P., van Loo, M., Winkler, M., and Gugerli,
F. (2011), Break zones in the distributions of alleles and species in
alpine plants. Journal of Biogeography , 38 : 772- 782.
Vuong, Q. H. (1989). Likelihood ratio tests for model selection and
nonnested hypotheses. Econometrica , 57(2) , 307- 333.
Wachter, G. A., Papadopoulou, A., Muster, C., Arthofer, W., Knowles, L.
L., Steiner, F. M., & Schlick-Steiner, B. C. (2016). Glacial refugia,
recolonization patterns and diversification forces in Alpine-endemicMegabunus harvestmen. Molecular Ecology , 25 ,
2904- 2919.
Wallis, G. P., Waters, J. M., Upton, P., & Craw, D. (2016). Transverse
Alpine Speciation Driven by Glaciation. Trends in Ecology &
Evolution , 31, 916-926.
Warmuth, V. M., & Ellegren, H. (2019). Genotype‐free estimation of
allele frequencies reduces bias and improves demographic inference from
RADSeq data. Molecular Ecology Resources , 19 , 586- 596.
Weir, B. S., & Cockerham, C. C. 1984. Estimating F‐statistics for the
analysis of population structure. Evolution , 38 , 1358-
1370.
Weng, Y. M., Yang, M. M., & Yeh, W. B. (2016). A comparative
phylogeographic study reveals discordant evolutionary histories of
alpine ground beetles (Coleoptera, Carabidae). Ecology and
Evolution , 6 , 2061- 2073.
Zaman, K., Hubert, M. K., & Schoville, S. D. (2019). Testing the role
of ecological selection on colour pattern variation in the butterfly
Parnassius clodius. Molecular Ecology , 28 , 5086- 5102.