References
Aliabadian, M., Kaboli, M., Förschler, M. I., Nijman, V., Chamani, A.,
Tillier, A., . . . Zuccon, D. (2012). Convergent evolution of
morphological and ecological traits in the open-habitat chat complex
(Aves, Muscicapidae: Saxicolinae). Molecular Phylogenetics and
Evolution, 65 (1), 35-45.
Allendorf, F. W., & Luikart, G. (2009). Conservation and the
genetics of populations . West Sussex, UK: John Wiley & Sons.
Arnaud‐Haond, S., Teixeira, S., Massa, S. I., Billot, C., Saenger, P.,
Coupland, G., . . . Serrao, E. (2006). Genetic structure at range edge:
low diversity and high inbreeding in Southeast Asian mangrove
(Avicennia marina ) populations. Molecular Ecology, 15 (12),
3515-3525.
Avise, J. C. (2009). Phylogeography: retrospect and prospect.Journal of Biogeography, 36 (1), 3-15.
Avise, J. C., & Walker, D. E. (1998). Pleistocene phylogeographic
effects on avian populations and the speciation process.Proceedings of the Royal Society of London. Series B: Biological
Sciences, 265 (1395), 457-463.
Baguette, M., & Schtickzelle, N. (2006). Negative relationship between
dispersal distance and demography in butterfly metapopulations.Ecology, 87 (3), 648-654.
Bandelt, H.-J., Forster, P., & Röhl, A. (1999). Median-joining networks
for inferring intraspecific phylogenies. Molecular Biology and
Evolution, 16 (1), 37-48.
Barker, F. K., Barrowclough, G. F., & Groth, J. G. (2002). A
phylogenetic hypothesis for passerine birds: taxonomic and biogeographic
implications of an analysis of nuclear DNA sequence data.Proceedings of the Royal Society of London B: Biological Sciences,
269 (1488), 295-308.
Bates, M. F., Tolley, K. A., Edwards, S., Davids, Z., Da Silva, J. M.,
& Branch, W. R. (2013). A molecular phylogeny of the African plated
lizards, genus Gerrhosaurus Wiegmann, 1828 (Squamata:
Gerrhosauridae), with the description of two new genera. Zootaxa,
3750 (5), 465-493.
Bazinet, A. L., Zwickl, D. J., & Cummings, M. P. (2014). A gateway for
phylogenetic analysis powered by grid computing featuring GARLI 2.0.Systematic Biology, 63 (5), 812-818.
Bech, N., Boissier, J., Drovetski, S., & Novoa, C. (2009). Population
genetic structure of rock ptarmigan in the ‘sky islands’ of French
Pyrenees: implications for conservation. Animal Conservation,
12 (2), 138-146.
Böhme, M. U., Schneeweiß, N., Fritz, U., Schlegel, M., & Berendonk, T.
U. (2007). Small edge populations at risk: genetic diversity of the
green lizard (Lacerta viridis viridis ) in Germany and
implications for conservation management. Conservation Genetics,
8 (3), 555-563.
Browne, R. A., & Ferree, P. M. (2007). Genetic structure of southern
Appalachian “sky island” populations of the southern red-backed vole
(Myodes gapperi ). Journal of Mammalogy, 88 (3), 759-768.
Bruford, M., Hanotte, O., Brookfield, J., & Burke, T. (1992).
Singlelocus and multilocus DNA fingerprint. In A. R. Hoelzel (Ed.),Molecular genetic analysis of populations: a practical approach(pp. 225-270). Oxford: IRL Press.
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J.
F. (2018). Runs of homozygosity: windows into population history and
trait architecture. Nature Reviews Genetics, 19 (4), 220.
Ceballos, G., & Ehrlich, P. R. (2002). Mammal population losses and the
extinction crisis. Science, 296 (5569), 904-907.
Chamberlain, D., Arlettaz, R., Caprio, E., Maggini, R., Pedrini, P.,
Rolando, A., & Zbinden, N. (2012). The altitudinal frontier in avian
climate impact research. Ibis, 154 (1), 205-209.
Cowling, R., & Heijnis, C. (2001). The identification of Broad Habitat
Units as biodiversity entities for systematic conservation planning in
the Cape Floristic Region. South African Journal of Botany,
67 (1), 15-38.
Cowling, R. M. (1992). The ecology of fynbos: nutrients, fire and
diversity : Oxford University Press Southern Africa.
Cowling, R. M., Procheş, Ş., & Partridge, T. C. (2009). Explaining the
uniqueness of the Cape flora: incorporating geomorphic evolution as a
factor for explaining its diversification. Molecular Phylogenetics
and Evolution, 51 (1), 64-74.
Dantas, G. P., Oliveira, L. R., Santos, A. M., Flores, M. D., De Melo,
D. R., Simeone, A., . . . Valdés-Velásquez, A. (2019). Uncovering
population structure in the Humboldt penguin (Spheniscus
humboldti ) along the Pacific coast at South America. PLoS One,
14 (5), e0215293.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012).
jModelTest 2: more models, new heuristics and parallel computing.Nature Methods, 9 (8), 772.
Ericson, P. G., & Johansson, U. S. (2003). Phylogeny of Passerida
(Aves: Passeriformes) based on nuclear and mitochondrial sequence data.Molecular Phylogenetics and Evolution, 29 (1), 126-138.
Ericson, P. G., Klopfstein, S., Irestedt, M., Nguyen, J. M., &
Nylander, J. A. (2014). Dating the diversification of the major lineages
of Passeriformes (Aves). BMC Evolutionary Biology, 14 (1), 8.
Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new
series of programs to perform population genetics analyses under Linux
and Windows. Molecular ecology resources, 10 (3), 564-567.
Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of
molecular variance inferred from metric distances among DNA haplotypes:
application to human mitochondrial DNA restriction data. Genetics,
131 (2), 479-491.
Ferreri, M., Qu, W., & Han, B. (2011). Phylogenetic networks: a tool to
display character conflict and demographic history. African
Journal of Biotechnology, 10 (60), 12799-12803.
Fjeldså, J., & Bowie, R. C. (2008). New perspectives on the origin and
diversification of Africa’s forest avifauna. African Journal of
Ecology, 46 (3), 235-247.
Foltz, D., Nguyen, A., Kiger, J., & Mah, C. L. (2008). Pleistocene
speciation of sister taxa in a North Pacific clade of brooding sea stars
(Leptasterias ). Marine Biology, 154 (3), 593-602.
Frankham, R. (2015). Genetic rescue of small inbred populations:
meta‐analysis reveals large and consistent benefits of gene flow.Molecular Ecology, 24 (11), 2610-2618.
Fuchs, J., Fjeldså, J., Bowie, R. C., Voelker, G., & Pasquet, E.
(2006). The African warbler genus Hyliota as a lost lineage in
the Oscine songbird tree: molecular support for an African origin of the
Passerida. Molecular Phylogenetics and Evolution, 39 (1), 186-197.
Gizaw, A., Kebede, M., Nemomissa, S., Ehrich, D., Bekele, B., Mirré, V.,
. . . Brochmann, C. (2013). Phylogeography of the heathers Erica
arborea and E. trimera in the afro-alpine ‘sky islands’ inferred
from AFLPs and plastid DNA sequences. Flora-Morphology,
Distribution, Functional Ecology of Plants, 208 (7), 453-463.
Grubb, P. (1982). Refuges and dispersal in the speciation of African
forest mammals. Biological diversification in the tropics ,
537-553.
Hasegawa, M., Kishino, H., & Yano, T.-a. (1985). Dating of the
human-ape splitting by a molecular clock of mitochondrial DNA.Journal of Molecular Evolution, 22 (2), 160-174.
IUCN. (2017). The IUCN Red List of Threatened Species., Version
2017-3 .
Jackson, M. M., Gergel, S. E., & Martin, K. (2015). Effects of climate
change on habitat availability and configuration for an endemic coastal
alpine bird. PLoS One, 10 (11), e0142110.
Johnson, N. K., & Cicero, C. (2004). New mitochondrial DNA data affirm
the importance of Pleistocene speciation in North American birds.Evolution, 58 (5), 1122-1130.
Kimura, M. (1980). A simple method for estimating evolutionary rates of
base substitutions through comparative studies of nucleotide sequences.Journal of Molecular Evolution, 16 (2), 111-120.
Knapp, S., & Mallet, J. (2003). Refuting refugia? Science,
300 (5616), 71-72.
Knowles, L. L., & Richards, C. L. (2005). Importance of genetic drift
during Pleistocene divergence as revealed by analyses of genomic
variation. Molecular Ecology, 14 (13), 4023-4032.
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: molecular
evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution, 33 (7), 1870-1874.
Kupfer, J. A., & Cairns, D. M. (1996). The suitability of montane
ecotones as indicators of global climatic change. Progress in
Physical Geography, 20 (3), 253-272.
Laikre, L. (2010). Genetic diversity is overlooked in international
conservation policy implementation. Conservation Genetics, 11 (2),
349-354.
Lee, A. T. K., & Barnard, P. (2016). Endemic birds of the Fynbos biome:
a conservation assessment and impacts of climate change. Bird
Conservation International, 26 (1), 52-68.
Leigh, J., & Bryant, D. (2015). PopART: Full-feature software for
haplotype network construction. Methods in Ecology and Evolution,
6 (9), 1110-1116.
Lexer, C., Mangili, S., Bossolini, E., Forest, F., Stölting, K. N.,
Pearman, P. B., . . . Salamin, N. (2013). ‘Next generation’biogeography:
towards understanding the drivers of species diversification and
persistence. Journal of Biogeography, 40 (6), 1013-1022.
Liu, Y., Chen, G., Huang, Q., Jia, C., Carey, G., Leader, P., . . .
Olsson, U. (2016). Species delimitation of the white‐tailed rubythroatCalliope pectoralis complex (Aves, Muscicapidae) using an
integrative taxonomic approach. Journal of Avian Biology, 47 (6),
899-910.
Lonsinger, R. C., Schweizer, R. M., Pollinger, J. P., Wayne, R. K., &
Roemer, G. W. (2015). Fine-scale genetic structure of the ringtail
(Bassariscus astutus ) in a Sky Island mountain range.Journal of Mammalogy, 96 (2), 257-268.
Luo, S., Wu, Y., Chang, Q., Liu, Y., Yang, X., Zhang, Z., . . . Zou, F.
(2014). Deep phylogeographic divergence of a migratory passerine in
Sino‐Himalayan and Siberian forests: the Red‐flanked Bluetail
(Tarsiger cyanurus ) complex. Ecology and evolution, 4 (7),
977-986.
Martens, J., Tietze, D., & Sun, Y. (2005). Molecular phylogeny ofParus (Periparus ), a eurasian radiation of tits (Aves:
Passeriformes: Paridae). Zoological Abhandlungen, 55 , 103-120.
Martens, J., Tietze, D. T., & Päckert, M. (2011). Phylogeny,
biodiversity, and species limits of passerine birds in the
Sino-Himalayan region—a critical review. Ornithological
Monographs, 70 (1), 64-94.
Masta, S. E. (2000). Phylogeography of the jumping spiderHabronattus pugillis (Araneae: Salticidae): recent vicariance of
sky island populations? Evolution, 54 (5), 1699-1711.
McCormack, J. E., Bowen, B. S., & Smith, T. B. (2008). Integrating
paleoecology and genetics of bird populations in two sky island
archipelagos. BMC Biology, 6 (1), 28.
McCormack, J. E., Huang, H., Knowles, L. L., Gillespie, R., & Clague,
D. (2009). Sky islands. Encyclopedia of Islands, 4 , 841-843.
Miller, M. A., Pfeiffer, W., & Schwartz, T. (2010). Creating the
CIPRES Science Gateway for inference of large phylogenetic trees. Paper
presented at the 2010 Gateway Computing Environments Workshop (GCE),
Louisiana, USA.
Milne, R., Cunningham, S. J., Lee, A. T. K., & Smit, B. (2015). The
role of thermal physiology in recent declines of birds in a biodiversity
hotspot. Conservation Physiology, 3 (1), cov048.
Nei, M. (1978). Estimation of average heterozygosity and genetic
distance from a small number of individuals. Genetics, 89 (3),
583-590.
Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J., & De Meester, L.
(2013). Drivers of population genetic differentiation in the wild:
isolation by dispersal limitation, isolation by adaptation and isolation
by colonization. Molecular Ecology, 22 (24), 5983-5999.
Picker, M., & Samways, M. (1996). Faunal diversity and endemicity of
the Cape Peninsula, South Africa—a first assessment.Biodiversity & Conservation, 5 (5), 591-606.
Pirie, M., Oliver, E., de Kuppler, A. M., Gehrke, B., Le Maitre, N.,
Kandziora, M., & Bellstedt, D. (2016). The biodiversity hotspot as
evolutionary hot-bed: spectacular radiation of Erica in the Cape
Floristic Region. BMC Evolutionary Biology, 16 (1), 190.
Quick, L. J., Meadows, M. E., Bateman, M. D., Kirsten, K. L.,
Mäusbacher, R., Haberzettl, T., & Chase, B. M. (2016). Vegetation and
climate dynamics during the last glacial period in the
fynbos-afrotemperate forest ecotone, southern Cape, South Africa.Quaternary International, 404 , 136-149.
Ramakrishnan, U., Hadly, E. A., & Mountain, J. L. (2005). Detecting
past population bottlenecks using temporal genetic data. Molecular
Ecology, 14 (10), 2915-2922.
Ribera, I., & Vogler, A. P. (2004). Speciation of Iberian diving
beetles in Pleistocene refugia (Coleoptera, Dytiscidae). Molecular
Ecology, 13 (1), 179-193.
Scridel, D., Brambilla, M., Martin, K., Lehikoinen, A., Iemma, A.,
Matteo, A., . . . Pedrini, P. (2018). A review and meta‐analysis of the
effects of climate change on Holarctic mountain and upland bird
populations. Ibis, 160 (3), 489-515.
Sekercioglu, C. H., Schneider, S. H., Fay, J. P., & Loarie, S. R.
(2008). Climate change, elevational range shifts, and bird extinctions.Conservation Biology, 22 (1), 140-150.
Sharratt, N. J., Picker, M. D., & Samways, M. J. (2000). The
invertebrate fauna of the sandstone caves of the Cape Peninsula (South
Africa): patterns of endemism and conservation priorities.Biodiversity & Conservation, 9 (1), 107-143.
Sittenthaler, M., Kunz, F., Szymusik, A., Grünschachner‐Berger, V.,
Krumböck, S., Stauffer, C., & Nopp‐Mayr, U. (2018). Fine‐scale genetic
structure in an eastern Alpine black grouse Tetrao tetrixmetapopulation. Journal of Avian Biology, 49 (5), jav-01681.
Stervander, M., Ryan, P. G., Melo, M., & Hansson, B. (2019). The origin
of the world’s smallest flightless bird, the Inaccessible Island RailAtlantisia rogersi (Aves: Rallidae). Molecular
Phylogenetics and Evolution, 130 , 92-98.
Tajima, F. (1989). The effect of change in population size on DNA
polymorphism. Genetics, 123 (3), 597-601.
Travis, J. M., Delgado, M., Bocedi, G., Baguette, M., Bartoń, K., Bonte,
D., . . . Penteriani, V. (2013). Dispersal and species’ responses to
climate change. Oikos, 122 (11), 1532-1540.
Van Dyck, H., & Baguette, M. (2005). Dispersal behaviour in fragmented
landscapes: routine or special movements? Basic and Applied
Ecology, 6 (6), 535-545.
Varvio, S.-L., Chakraborty, R., & Nei, M. (1986). Genetic variation in
subdivided populations and conservation genetics. Heredity,
57 (2), 189.
Verboom, G. A., Bergh, N. G., Haiden, S. A., Hoffmann, V., & Britton,
M. N. (2015). Topography as a driver of diversification in the Cape
Floristic Region of South Africa. New Phytologist, 207 (2),
368-376.
Vörös, J., Ursenbacher, S., Kiss, I., Jelić, D., Schweiger, S., &
Szabó, K. (2017). Increased genetic structuring of isolatedSalamandra salamandra populations (Caudata: Salamandridae) at the
margins of the Carpathian Mountains. Journal of Zoological
Systematics and Evolutionary Research, 55 (2), 138-149.
Whitten, R. G. (1979). Comments on the theory of Holocene refugia in the
culture history of Amazonia. American Antiquity, 44 (2), 238-251.
Wishart, M., & Day, J. (2002). Endemism in the freshwater fauna of the
south-western Cape, South Africa. Internationale Vereinigung für
theoretische und angewandte Limnologie: Verhandlungen, 28 (4),
1762-1766.
Woodroffe, R., & Ginsberg, J. R. (1998). Edge effects and the
extinction of populations inside protected areas. Science,
280 (5372), 2126-2128.
Xia, X. (2018). DAMBE7: New and improved tools for data analysis in
molecular biology and evolution. Molecular Biology and Evolution,
35 (6), 1550-1552.
Zuccon, D., & Ericson, P. G. (2012). Molecular and morphological
evidences place the extinct New Zealand endemic Turnagra capensisin the Oriolidae. Molecular Phylogenetics and Evolution, 62 (1),
414-426.