LITERATURE CITED
[dataset] Manthey JD, Bourgeois Y, Yonas M, Boisssinot S. Ethiopia Highland Birds GRV whole genome sequencing. National Center for Biotechnology Information Sequence Read Archive (SRA). https://www.ncbi.nlm.nih.gov/bioproject/PRJNA605410/
Amos, W., & Harwood, J. (1998). Factors affecting levels of genetic diversity in natural populations. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 353 (1366), 177-186.
Bandelt, H.-J., Forster, P., & Röhl, A. (1999). Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16 (1), 37-48.
Barber, B. R., & Klicka, J. (2010). Two pulses of diversification across the Isthmus of Tehuantepec in a montane Mexican bird fauna.Proceedings of the Royal Society of London, Series B: Biological Sciences , rspb20100343.
Belay, G., & Mori, A. (2006). Intraspecific phylogeographic mitochondrial DNA (D-loop) variation of Gelada baboon, Theropithecus gelada, in Ethiopia. Biochemical Systematics and Ecology, 34 (7), 554-561.
Boyce, A. J., Freeman, B. G., Mitchell, A. E., & Martin, T. E. (2015). Clutch size declines with elevation in tropical birds. The Auk: Ornithological Advances, 132 (2), 424-432.
Bryja, J., Kostin, D., Meheretu, Y., Šumbera, R., Bryjová, A., Kasso, M., . . . Lavrenchenko, L. A. (2018). Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient.Molecular Phylogenetics and Evolution, 118 , 75-87.
Bushnell, B. (2014). BBMap: A Fast, Accurate, Splice-Aware Aligner . Retrieved from
Charif, D., & Lobry, J. R. (2007). SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In Structural Approaches to Sequence Evolution (pp. 207-232): Springer.
Chikhi, L., Rodríguez, W., Grusea, S., Santos, P., Boitard, S., & Mazet, O. (2018). The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity, 120 (1), 13-24.
Claramunt, S., Derryberry, E. P., Remsen Jr, J., & Brumfield, R. T. (2011). High dispersal ability inhibits speciation in a continental radiation of passerine birds. Proceedings of the Royal Society B: Biological Sciences, 279 (1733), 1567-1574.
Clement, P. (2020). Brown-rumped Seedeater (Crithagra tristriata ), version 1.0. In Birds of the World (J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, and E. de Juana, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.brrsee1.01.
Collar, N. (2020). Rüppell’s Robin-Chat (Cossypha semirufa ), version 1.0. In Birds of the World (J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, and E. de Juana, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.rurcha1.01.
Collar, N., & Robson, C. (2021). Abyssinian Catbird (Sylvia galinieri ), version 1.1. In Birds of the World (J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, and E. de Juana, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.abycat1.01.1.
Cruickshank, T. E., & Hahn, M. W. (2014). Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Molecular Ecology, 23 (13), 3133-3157.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., . . . Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27 (15), 2156-2158.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: more models, new heuristics and parallel computing.Nature Methods, 9 (8), 772.
del Hoyo, J., Collar, N., & Kirwan, G. (2020). Abyssinian Thrush (Turdus abyssinicus ), version 1.0. In Birds of the World (J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, and E. de Juana, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.abythr1.01.
Derjusheva, S., Kurganova, A., Habermann, F., & Gaginskaya, E. (2004). High chromosome conservation detected by comparative chromosome painting in chicken, pigeon and passerine birds. Chromosome Research, 12 (7), 715.
Dessie, G., & Kleman, J. (2007). Pattern and magnitude of deforestation in the South Central Rift Valley Region of Ethiopia. Mountain research and development, 27 (2), 162-169.
Ellegren, H., & Galtier, N. (2016). Determinants of genetic diversity.Nature reviews genetics, 17 (7), 422.
Evans, B. J., Bliss, S. M., Mendel, S. A., & Tinsley, R. C. (2011). The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia. Molecular Ecology, 20 (20), 4216-4230.
Felsenstein, J. (1985). Phylogenies and the comparative method.The American Naturalist, 125 (1), 1-15.
Freilich, X., Anadón, J. D., Bukala, J., Calderon, O., Chakraborty, R., & Boissinot, S. (2016). Comparative Phylogeography of Ethiopian anurans: impact of the Great Rift Valley and Pleistocene climate change.BMC Evolutionary Biology, 16 (1), 206.
Friis, I., Edwards, S., Ensermu, K., & Sebsebe, D. (2001). Diversity and endemism in the flora of Ethiopia and Eritrea–what do the published flora volumes tell us. Biol. Skr, 54 , 173-193.
Frisch, W., Meschede, M., & Blakey, R. C. (2010). Plate tectonics: Continental Drift and mountain building : Springer Science & Business Media.
Gottelli, D., Marino, J., SILLERO‐ZUBIRI, C., & Funk, S. M. (2004). The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis).Molecular Ecology, 13 (8), 2275-2286.
Griffin, D. K., Robertson, L. B., Tempest, H. G., Vignal, A., Fillon, V., Crooijmans, R. P., . . . Carré, W. (2008). Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution. BMC Genomics, 9 (1), 168.
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.Systematic Biology, 59 (3), 307-321.
Habel, J. C., Borghesio, L., Newmark, W. D., Day, J. J., Lens, L., Husemann, M., & Ulrich, W. (2015). Evolution along the Great Rift Valley: phenotypic and genetic differentiation of East African white‐eyes (Aves, Zosteropidae). Ecology and Evolution, 5 (21), 4849-4862.
Hamilton, A. J., Basset, Y., Benke, K. K., Grimbacher, P. S., Miller, S. E., Novotný, V., . . . Yen, J. D. (2010). Quantifying uncertainty in estimation of tropical arthropod species richness. The American Naturalist, 176 (1), 90-95.
Hau, M., Ricklefs, R. E., Wikelski, M., Lee, K. A., & Brawn, J. D. (2010). Corticosterone, testosterone and life-history strategies of birds. Proceedings of the Royal Society B: Biological Sciences, 277 (1697), 3203-3212.
Hooper, D. M., Griffith, S. C., & Price, T. D. (2018). Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone.Molecular Ecology . doi:10.1111/mec.14874
Hubisz, M. J., Pollard, K. S., & Siepel, A. (2010). PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in bioinformatics, 12 (1), 41-51.
Hutchison, W., Fusillo, R., Pyle, D. M., Mather, T. A., Blundy, J. D., Biggs, J., . . . Barfod, D. N. (2016). A pulse of mid-Pleistocene rift volcanism in Ethiopia at the dawn of modern humans. Nature Communications, 7 (1), 1-12.
Kebede, M., Ehrich, D., Taberlet, P., Nemomissa, S., & Brochmann, C. (2007). Phylogeography and conservation genetics of a giant lobelia (Lobelia giberroa) in Ethiopian and Tropical East African mountains.Molecular Ecology, 16 (6), 1233-1243.
Kipp, F. A. (1959). Der Handflügel-Index als flugbiologisches Maß.Die Vogelwarte, 20 (2), 77-86.
Komarova, V. A., Kostin, D. S., Bryja, J., Mikula, O., Bryjová, A., Čížková, D., . . . Lavrenchenko, L. A. (2021). Complex reticulate evolution of speckled brush‐furred rats (Lophuromys) in the Ethiopian centre of endemism. Molecular Ecology, 30 (10), 2349-2365.
Largen, M., & Spawls, S. (2010). The amphibians and reptiles of Ethiopia and Eritrea : Edition Chimaira.
Leigh, J. W., & Bryant, D. (2015). popart: full‐feature software for haplotype network construction. Methods in Ecology and Evolution, 6 (9), 1110-1116.
Leroy, T., Anselmetti, A., Tilak, M. K., Bérard, S., Csukonyi, L., Gabrielli, M., . . . Nabholz, B. (2019). A bird’s white-eye view on neo-sex chromosome evolution. bioRxiv peer-reviewed and recommended by PCI Evolutionary Biology, 505610, ver. 4 . doi:10.1101/505610
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25 (14), 1754-1760.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Durbin, R. (2009). The sequence alignment/map format and SAMtools.Bioinformatics, 25 (16), 2078-2079.
Manthey, J. D., Reyes-Velasco, J., Freilich, X., & Boissinot, S. (2017). Diversification in a biodiversity hotspot: genomic variation in the river frog Amietia nutti across the Ethiopian Highlands.Biological Journal of the Linnean Society, 122 (4), 801-813.
Martin, M., Patterson, M., Garg, S., Fischer, S., Pisanti, N., Klau, G. W., . . . Marschall, T. (2016). WhatsHap: fast and accurate read-based phasing. BioRxiv DOI: 10.1101/085050 , 085050.
Mazet, O., Rodríguez, W., Grusea, S., Boitard, S., & Chikhi, L. (2016). On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?Heredity, 116 (4), 362-371.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., . . . Daly, M. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.Genome Research, 20 (9), 1297-1303.
Medina, I., Cooke, G. M., & Ord, T. J. (2018). Walk, swim or fly? Locomotor mode predicts genetic differentiation in vertebrates.Ecology Letters, 21 (5), 638-645.
Miraldo, A., Li, S., Borregaard, M. K., Flórez-Rodríguez, A., Gopalakrishnan, S., Rizvanovic, M., . . . Nogués-Bravo, D. (2016). An Anthropocene map of genetic diversity. Science, 353 (6307), 1532-1535.
Mora, C., Tittensor, D. P., Adl, S., Simpson, A. G., & Worm, B. (2011). How many species are there on Earth and in the ocean? PLoS Biology, 9 (8), e1001127.
Musher, L. J., Ferreira, M., Auerbach, A. L., McKay, J., & Cracraft, J. (2019). Why is Amazonia a ‘source’of biodiversity? Climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae). Proceedings of the Royal Society B, 286 (1900), 20182343.
Myers, N., Mittermeier, R. A., Mittermeier, C. G., Da Fonseca, G. A., & Kent, J. (2000). Biodiversity hotspots for conservation priorities.Nature, 403 (6772), 853-858.
Nadachowska-Brzyska, K., Li, C., Smeds, L., Zhang, G., & Ellegren, H. (2015). Temporal dynamics of avian populations during Pleistocene revealed by whole-genome sequences. Current Biology, 25 (10), 1375-1380.
Naka, L. N., & Brumfield, R. T. (2018). The dual role of Amazonian rivers in the generation and maintenance of avian diversity.Science Advances, 4 (8), eaar8575.
Nam, K., Mugal, C., Nabholz, B., Schielzeth, H., Wolf, J. B., Backström, N., . . . Ponting, C. P. (2010). Molecular evolution of genes in avian genomes. Genome Biology, 11 (6), R68.
O’Connell, K. A., Hamidy, A., Kurniawan, N., Smith, E. N., & Fujita, M. K. (2018). Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java. Molecular Phylogenetics and Evolution, 123 , 101-112.
Oliveros, C. H., Field, D. J., Ksepka, D. T., Barker, F. K., Aleixo, A., Andersen, M. J., . . . Braun, M. J. (2019). Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences, USA, 116 (16), 7916-7925.
Oswald, J. A., Overcast, I., Mauck III, W. M., Andersen, M. J., & Smith, B. T. (2017). Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds. Molecular Ecology, 26 (5), 1386-1400.
Pagès, H., Aboyoun, P., Gentleman, R., & DebRoy, S. (2017). Biostrings: Efficient manipulation of biological strings. R Package Version 2.0 .
Papadopoulou, A., Anastasiou, I., Keskin, B., & Vogler, A. P. (2009). Comparative phylogeography of tenebrionid beetles in the Aegean archipelago: the effect of dispersal ability and habitat preference.Molecular Ecology, 18 (11), 2503-2517.
Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20 (2), 289-290.
Peterman, W. E., Anderson, T. L., Ousterhout, B. H., Drake, D. L., Semlitsch, R. D., & Eggert, L. S. (2015). Differential dispersal shapes population structure and patterns of genetic differentiation in two sympatric pond breeding salamanders. Conservation Genetics, 16 (1), 59-69.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155 (2), 945-959.
Quinlan, A. R., & Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26 (6), 841-842.
Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009). Reconstructing Indian population history. Nature, 461 (7263), 489.
Reyes-Velasco, J., Manthey, J. D., Bourgeois, Y., Freilich, X., & Boissinot, S. (2018). Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PLoS One, 13 (2), e0190440.
Reyes‐Velasco, J., Manthey, J. D., Freilich, X., & Boissinot, S. (2018). Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia. Molecular Ecology, 27 (9), 2256-2270.
Romiguier, J., Gayral, P., Ballenghien, M., Bernard, A., Cahais, V., Chenuil, A., . . . Faivre, N. (2014). Comparative population genomics in animals uncovers the determinants of genetic diversity. Nature, 515 (7526), 261.
Sayyari, E., & Mirarab, S. (2016). Fast coalescent-based computation of local branch support from quartet frequencies. Molecular Biology and Evolution, 33 (7), 1654-1668.
Schiffels, S., & Durbin, R. (2014). Inferring human population size and separation history from multiple genome sequences. Nature Genetics, 46 (8), 919.
Sepulchre, P., Ramstein, G., Fluteau, F., Schuster, M., Tiercelin, J.-J., & Brunet, M. (2006). Tectonic uplift and Eastern Africa aridification. Science, 313 (5792), 1419-1423.
Shafer, A. B., Cullingham, C. I., Cote, S. D., & Coltman, D. W. (2010). Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Molecular Ecology, 19 (21), 4589-4621.
Silvestrini, M., Junqueira, M. G., Favarin, A. C., Guerreiro-Filho, O., Maluf, M. P., Silvarolla, M. B., & Colombo, C. A. (2007). Genetic diversity and structure of Ethiopian, Yemen and Brazilian Coffea arabica L. accessions using microsatellites markers. Genetic Resources and Crop Evolution, 54 (6), 1367-1379.
Smith, B. T., McCormack, J. E., Cuervo, A. M., Hickerson, M. J., Aleixo, A., Cadena, C. D., . . . Harvey, M. G. (2014). The drivers of tropical speciation. Nature, 515 (7527), 406.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30 (9), 1312-1313.
Sukumaran, J., & Holder, M. T. (2010). DendroPy: a Python library for phylogenetic computing. Bioinformatics, 26 (12), 1569-1571.
Tacutu, R., Thornton, D., Johnson, E., Budovsky, A., Barardo, D., Craig, T., . . . Wang, J. (2017). Human Ageing Genomic Resources: new and updated databases. Nucleic Acids Research, 46 (D1), D1083-D1090.
Taylor, B. (2020). Abyssinian Slaty-Flycatcher (Melaenornis chocolatinus ), version 1.0. In Birds of the World (J. del Hoyo, A. Elliott, J. Sargatal, D. A. Christie, and E. de Juana, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.abyslf1.01.
Taylor, P. J., Lavrenchenko, L. A., Carleton, M. D., Verheyen, E., & Oosthuizen, C. J. (2011). Specific limits and emerging diversity patterns in east African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): revision of the Otomys typus complex. Zootaxa, 3024 , 1-66.
van Balen, B., del Hoyo, J., Collar, N., & Kirwan, G. (2020). Heuglin’s White-eye (Zosterops poliogastrus ), version 1.0. In Birds of the World (S. M. Billerman, B. K. Keeney, P. G. Rodewald, and T. S. Schulenberg, Editors). Cornell Lab of Ornithology, Ithaca, NY, USA. https://doi.org/10.2173/bow.heuwhe2.01.
Wang, K., Mathieson, I., O’Connell, J., & Schiffels, S. (2020). Tracking human population structure through time from whole genome sequences. PLoS Genetics, 16 (3), e1008552.
Warren, W. C., Clayton, D. F., Ellegren, H., Arnold, A. P., Hillier, L. W., Künstner, A., . . . Fairley, S. (2010). The genome of a songbird.Nature, 464 (7289), 757.
Weeks, B. C., & Claramunt, S. (2014). Dispersal has inhibited avian diversification in Australasian archipelagoes. Proceedings of the Royal Society of London, Series B: Biological Sciences, 281 (1791), 20141257.
Willing, E.-M., Dreyer, C., & Van Oosterhout, C. (2012). Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS One, 7 (8), e42649.
Yalden, D., & Largen, M. (1992). The endemic mammals of Ethiopia.Mammal Review, 22 (3‐4), 115-150.
Zachos, F. E., & Habel, J. C. (2011). Biodiversity hotspots: distribution and protection of conservation priority areas : Springer Science & Business Media.
Zeleke, G., & Hurni, H. (2001). Implications of land use and land cover dynamics for mountain resource degradation in the Northwestern Ethiopian highlands. Mountain research and development, 21 (2), 184-192.
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19 (6), 153.