Serre, D. & Paabo, S. Evidence for gradients of human genetic diversity within and among continents. Genome Res. 14, 1679–1685 (2004).
Ohta, T. Population size and rate of evolution. J. Mol. Evol. 1, 305–314 (1972).
Slatkin, M. Gene flow and selection in a cline. Genetics 75, 733–756 (1973).
Potts, R. Variability selection in hominid evolution. Evol. Anthropol. 7, 81–96 (1998).
Potts, R. Hominin evolution in settings of strong environmental variability. Quat. Sci. Rev. 73, 1–13 (2013).
Prüfer, K. et al. The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527–531 (2012).
Hill, W. C. O. in The Nomenclature, Taxonomy and Distribution of Chimpanzees, Vol. 1 (ed. Bourne, G. H.) 22–49 (Karger, 1969).
Pruetz, J. D. & Bertolani, P. Chimpanzee (Pan troglodytes verus) behavioral responses to stresses associated with living in a savannah-mosaic environment: implications for hominin adaptations to open habitats. Paleoanthropology 2009, 252–262 (2009).
Fünfstück, T. et al. The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break. Am. J. Phys. Anthropol. 156, 181–191 (2014).
Fischer, A., Pollack, J., Thalmann, O., Nickel, B. & Paabo, S. Demographic history and genetic differentiation in apes. Curr. Biol. 16, 1133–1138 (2006).
Gonder, M. K. et al. A new west African chimpanzee subspecies? Nature 388, 337 (1997).
Becquet, C., Patterson, N., Stone, A. C., Przeworski, M. & Reich, D. E. Genetic structure of chimpanzee populations. PLoS Genet. 3, e66 (2007).
Bowden, R. et al. Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet. 8, e1002504 (2012).
Prado-Martinez, J. et al. Great ape genetic diversity and population history. Nature 499, 471–475 (2013).
de Manuel, M. et al. Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science 354, 477–481 (2016).
Langergraber, K. E. et al. Genetic and ‘cultural’ similarity in wild chimpanzees. Proc. R. Soc. B. 278, 408–416 (2010).
Garcin, Y. et al. Early anthropogenic impact on Western Central African rainforests 2,600 y ago. Proc. Natl Acad. Sci. USA 115, 3261–3266 (2018).
Vicente, M. & Schlebusch, C. M. African population history: an ancient DNA perspective. Curr. Opin. Genet. Dev. 62, 8–15 (2020).
IUCN Red List. IUCN red list of threatened species. http://www.iucnredlist.org (2020).
Wentworth, C. K. Natural bridges and glaciation. Am. J. Sci. 26, 577–584 (1933).
Maley, J. The African rainforest: main characteristics of changes in vegetation and climate from the Upper Cretaceous to the Quaternary. Proc. R. Soc. Edinb. 104B, 31–73 (1996).
Langergraber, K. E. et al. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc. Natl Acad. Sci. USA 109, 15716–15721 (2012).
Shea, B. T. & Coolidge, H. J. Craniometric differentiation and systematics in the genus Pan. J. Hum. Evol. 13, 671–685 (1988).
Albrecht, G. H. & Miller, J. M. A. in Geographic Variation in Primates (eds Kimbel, W. H. & Martin, L. B.) 123–161 (Springer Science & Business Media, 2013).
Shea, B. T., Leigh, S. R. & Groves, C. P. in Multivariate Craniometric Variation in Chimpanzees (eds Kimbel, W. H. & Martin, L. B.) 265–296 (Springer Science & Business Media, 2013).
Kühl, H. S. et al. Chimpanzee accumulative stonethrowing. Sci. Rep. 6, 22219 (2016).
Wright, S. Isolation by distance. Genetics 28, 114–138 (1943).
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
Pritchard, J. K., Wen, X. & Falush, D. Documentation for structure version 2.3 software: version 2.3. 1–39. http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf (2009).
Meirmans, P. G. The trouble with isolation by distance. Mol. Ecol. 21, 2839–2846 (2012).
Perez, M. F. et al. Assessing population structure in the face of isolation by distance: are we neglecting the problem? Divers. Distrib. 24, 1883–1889 (2018).
Thalib, L., Kitching, R. L. & Bhatti, M. I. Principal component analysis for grouped data – a case study. Environmetrics 10, 565–574 (1999).
Fischer, A. et al. Bonobos fall within the genomic variation of chimpanzees. PLoS ONE 6, e21605 (2011).
Frantz, A. C., Cellina, S., Krier, A., Schley, L. & Burke, T. Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? J. Appl. Ecol. 46, 493–505 (2009).
Kalinowski, S. T. The computer program STRUCTURE does not reliably identify the main genetic clusters within species: simulations and implications for human population structure. Heredity 106, 625–632 (2010).
Schwartz, M. K. & McKelvey, K. S. Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv. Genet. 10, 441–452 (2008).
Meirmans, P. G. Seven common mistakes in population genetics and how to avoid them. Mol. Ecol. 24, 3223–3231 (2015).
Arandjelovic M, et al. Pan African Programme—The cultured chimpanzee. Guidelines for research and data collection. http://panafrican.eva.mpg.de/english/approaches_and_methods.php (2014).
Arandjelovic, M. & Vigilant, L. Non-invasive genetic censusing and monitoring of primate populations. Am. J. Primatol. 80, e22743 (2018).
Arthofer, W., Heussler, C., Krapf, P., Schlick-Steiner, B. C. & Steiner, F. M. Identifying the minimum number of microsatellite loci needed to assess population genetic structure: a case study in fly culturing. Fly 12, 13–22 (2018).
Wenburg, J. K., Bentzen, P. & Foote, C. J. Microsatellite analysis of genetic population structure in an endangered salmonid: the coastal cutthroat trout (Oncorhyncus clarki clarki). Mol. Ecol. 7, 733–749 (1998).
Guo, X.-Z. et al. Phylogeography and populationgenetics of Schizothorax o’connori: strong subdivision in the Yarlung Tsangpo River inferred from mtDNA and microsatellite markers. Sci. Rep. 6, 29821 (2016).
Kleinhans, C. & Willows-Munro, S. Low genetic diversity andshallow population structure inthe endangered vulture, Gyps copotheres. Sci. Rep. 9, 5536 (2019).
Bonato, L. et al. Diversity among peripheral populations: genetic and evolutionary differentiation of Salamandra atraat the southern edge of the Alps. J. Zool. Syst. Evol. Res. 56, 533–548 (2018).
Balkenhol, N. et al. A multi-method approach for analyzing hierarchical genetic structures: a case study with cougars Puma concolor. Ecography 37, 552–563 (2014).
Kobayashi, T. & Sota, T. Contrasting effects of habitat discontinuity on three closely related fungivorous beetle species with diverging host‐use patterns and dispersal ability. Ecol. Evol. 9, 2475–2486 (2019).
Rousset, F. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145, 1219–1228 (1997).
Valdes, A. M., Slatkin, M. & Freimer, N. B. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133, 737–749 (1993).
Goldstein, D. B., Ruiz Linares, A., Cavalli-Sforza, L. L. & Feldman, M. W. An evaluation of genetic distances for use with microsatellite loci. Genetics 139, 463–471 (1995).
Calabrese, P. P., Durrett, R. T. & Aquadro, C. F. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics 159, 839–852 (2001).
Petkova, D., Novembre, J. & Stephens, M. Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48, 94–100 (2015).
Rich, A. M., Wasserman, M. D., Hunt, K. D. & Kaestle, F. A. Chimpanzee (Pan troglodytes schweinfurthii) population spans multiple protected areas in the Albertine Rift. Folia. Primatol. 91, 595–609 (2020).
Baldwin, P. J., McGrew, W. C. & Tutin, C. E. G. Wide-ranging chimpanzees at Mt. Assirik, Senegal. Int. J. Primatol. 3, 367–385 (1982).
Lemoine, S. et al. Group dominance increases territory size and reduces neighbour pressure in wild chimpanzees. R. Soc. Open Sci. 7, 200577 (2020).
Newton-Fisher, N. E. The home range of the Sonso community of chimpanzees from the Budongo Forest, Uganda. Afr. J. Ecol. 41, 150–156 (2003).
Allendorf, F. W. Genetic drift and the loss of alleles versus heterozygosity. Zoo. Biol. 5, 181–190 (1986).
Barratt, C. D., et al. Late Quaternary habitat suitability models for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP). Preprint at BioRxiv https://www.biorxiv.org/content/10.1101/2020.05.15.066662v1 (2019).
Bertola, L. D. et al. Phylogeographic patterns in Africa and high resolution delineation of genetic clades in the lion (Panthera leo). Sci. Rep. 6, 30807 (2016).
Marchesi, P., Marchesi, N., Fruth, B. & Boesch, C. Census and distribution of chimpanzees in Côte D’Ivoire. Primates 36, 591–607 (1995).
Sommer, V., Adanu, J., Faucher, I. & Fowler, A. Nigerian chimpanzees (Pan troglodytes vellerosus) at Gashaka: two years of habituation efforts. Folia Primatol. 75, 295–316 (2004).
Chancellor, R. L., Langergraber, K. E., Ramirez, S., Rundus, A. S. & Vigilant, L. Genetic sampling of unhabituated chimpanzees (Pan troglodytes schweinfurthii) in Gishwati Forest Reserve, an isolated forest fragment in western Rwanda. Int. J. Primatol. 33, 479–488 (2012).
Piel, A. K. et al. Population status of chimpanzees in the Masito-Ugalla Ecosystem, Tanzania. Am. J. Primatol. 77, 1027–1035 (2015).
Wessling, E. G. et al. Seasonal variation in physiology challenges the notion of chimpanzees as a forest-adapted species. Front. Ecol. Evol. 6, 1–21 (2018).
Whiten, A. et al. Cultures in chimpanzees. Nature 399, 682–685 (1999).
Kühl, H. S. et al. Human impact erodes chimpanzee behavioral diversity. Science 363, 1453–1455 (2019).
Luncz, L. V., Mundry, R. & Boesch, C. Evidence for cultural differences between neighboring chimpanzee communities. Curr. Biol. 22, 922–926 (2012).
Boesch, C., Marchesi, P., Marchesi, N., Fruth, B. & Joulian, F. Is nut cracking in wild chimpanzees a cultural behaviour? J. Hum. Evol. 26, 325–338 (1994).
Kalan, A. K. et al. Environmental variability supports chimpanzee behavioural diversity. Nat. Commun. 11, 4451 (2020).
Hockings, K. J. in Chimpanzees of Bossou and Nimba, 221–219 (Springer Science & Business Media, 2011).
McCarthy, M. S., Lester, J. D. & Stanford, C. B. Chimpanzees (Pan troglodytes) flexibly use introduced species for nesting and bark feeding in a human-dominated habitat. Int. J. Primatol. 38, 321–337 (2016).
McLennan, M. R. et al. Surviving at the extreme: chimpanzee ranging is not restricted in a deforested human‐dominated landscape in Uganda. Afr. J. Ecol. 8, e57872 (2020).
Junker, J. et al. Recent decline in suitable environmental conditions for African great apes. Divers. Distrib. 18, 1077–1091 (2012).
Kühl, H. S. et al. The Critically Endangered western chimpanzee declines by 80%. Am. J. Primatol. 79, e22681 (2017).
Walsh, P. D., Breuer, T., Sanz, C., Morgan, D. B. & Doran-Sheehy, D. M. Potential for Ebola transmission between gorilla and chimpanzee social groups. Am. Nat. 169, 684–689 (2007).
Baden, A. L. et al. Anthropogenic pressures drive population genetic structuring across a critically endangered lemur species range. Sci. Rep. 9, 16276 (2019).
Nsubuga, A. M. et al. Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Mol. Ecol. 13, 2089–2094 (2004).
Arandjelovic, M. et al. Two-step multiplex polymerase chain reaction improves the speed and accuracy of genotyping using DNA from noninvasive and museum samples. Mol. Ecol. Resour. 9, 28–36 (2009).
Kalinowski, S. T., Taper, M. L. & Marshall, T. C. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099–1106 (2007).
Waits, L. P., Luikart, G. & Taberlet, P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol. Ecol. 10, 249–256 (2001).
Meirmans, P. G. & Hedrick, P. W. Assessing population structure: FST and related measures. Mol. Ecol. Resour. 11, 5–18 (2010).
Mondol, S. et al. New evidence for hybrid zones of forest and savanna elephants in Central and West Africa. Mol. Ecol. 24, 6134–6147 (2015).
Source: Ecology - nature.com
