Primate DNA suggests long-term stability of an African rainforest
Article first published online: 9 OCT 2012
© 2012 The Authors. Ecology and Evolution published by Blackwell Publishing Ltd.
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Ecology and Evolution
Volume 2, Issue 11, pages 2829–2842, November 2012
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How to Cite
Ecology and Evolution 2012; 2(11): 2829–2842
- Issue published online: 8 NOV 2012
- Article first published online: 9 OCT 2012
- Manuscript Accepted: 3 SEP 2012
- Manuscript Revised: 27 AUG 2012
- Manuscript Received: 2 JUL 2012
- NSF. Grant Numbers: DEB 0717165, DEB 0845392
- 2012. Consequences of range contradictions and range shifts on molecular diversity. Mol. Biol. Evol. 29:207–218. , , , and .
- 1999. Detecting population expansion and decline using microsatellites. Genetics 153:2013–2029.
- 2010. Unified framework to evaluate panmixia and migration direction among multiple sampling locations. Genetics 185:313–326. , and .
- 2008. Thomas T. Struhsaker: recipient of the lifetime achievement award of the international primatological society. Int. J. Primatol. 29:13–18. , , , , , , et al.
- 2011. Faunal histories from Holocene ancient DNA. Trends Ecol. Evol. 26:405–413. , , , and .
- 2009. Late Quaternary vegetation history of southeast Africa: the molecular isotopic record from Lake Malawi. Palaeogeogr. Palaeoclimatol. Palaeoecol. 275:100–112. , , , and .
- 1998. The DNA revolution in population genetics. Trends Genet. 14:60–65.
- 2000. Habitat alteration and the conservation of African primates: case study of Kibale National Park, Uganda. Am. J. Primatol. 50:169–185. , and .
- 2005. Thirty years of research in Kibale National Park, Uganda, reveals a complex picture for conservation. Int. J. Primatol. 26:539–555. , , and .
- 2010a. Tropical tree community shifts: implications for wildlife conservation. Biol. Conserv. 143:366–374. , , , , , , et al.
- 2010b. Understanding long-term primate community dynamics: implications of forest change. Ecol. Appl. 20:179–191. , , , ,and .
- 1991. Gene diversity and female philopatry. Genetics 127:437–447.
- 2010. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983–995. , , , , and .
- 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014. , and .
- 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22:1185–1192. , , , and .
- 2004. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5:435–445.
- 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611–2620. , , and .
- 2011. Minimum viable populations: is there a “magic number” for conservation practitioners? Trends Ecol. Evol. 26:307–316. , , , and .
- 1995. Effective population size/adult population size ratios in wildlife: a review. Genet. Res. 66:95–107.
- 1998. How large must populations be to retain evolutionary potential? Anim. Conserv. 1:69–70. , and .
- 2001. Detection of reduction in population size using data from microsatellite loci. Mol. Ecol. 10:305–318.Direct Link:, and .
- 2009. Pleistocene megafaunal collapse, novel plant communities and enhanced fire regimes in North America. Science 326:1100–1103. , , , , and , et al.
- 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic inference. J. Hered. 88:335–342. , and .
- 1995. An evaluation of genetic distances for use with microsatellite loci. Genetics 139:463–471. , , , and .
- 1997. RST Calc: a collection of computer programs for calculating estimates of genetic differentiation from microsatellite data and determining their significance. Mol. Ecol. 6:881–885.
- 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol. 4(2):e25. , , , , , and .
- 2002. FSTAT (Version 1.2): a computer program to calculate F-statistics. J. Hered. 86:485–486.
- 2003. Assessment of the diversity of African primates. Int. J. Primatol. 24:1301–1357. , , , , , , et al.
- 1976. The significance of patterns of distribution shown by forest plants and animals in tropical Africa for the reconstruction of upper Pleistocene palaeoenvironments: a review. Pp. 63–97 in E. M. van Zinderen-Bakkered, ed. Palaeoecology of Africa and of the surrounding Island and Antarctica. Balkema, Cape Town.
- 2005. The basic coalescent. Pp. 1–32 in J. Hein, M. Schierup and C. Wiuf, eds. Gene genealogies, variation and evolution: A primer in coalescent theory. Oxford Univ. Press, New York. , , and .
- 2008. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8:289. , and .
- 2008. Mid-Holocene decline in African buffalos inferred from Bayesian coalescent-based analyses of microsatellites and mitochondrial DNA. Mol. Ecol. 17:4845–4858. , , , , and .
- 2000. Protected area planning in the tropics: Ugandaʼs national system of forest nature reserves. Conserv. Biol. 14:858–875. , , , , , , et al.
- 1996. Microsatellites, from molecules to populations and back. Trends Ecol. Evol. 11:424–429. , and .
- 1997. Vegetation dynamics in central Africa since 18,000 yr BP: pollen records from the interlacustrine highlands of Burundi, Rwanda and western Uganda. J. Biogeogr. 24:495–512. , , , , , , et al.
- 1995. Bayes factors. J. Am. Stat. Assoc. 90:773–795. , and .
- 2002. Genetic data analysis: computer program for the analysis of allelic data, Version 1.1. Free program distributed by the authors over the internet from http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php , and .
- 2000. Indicators of biodiversity for ecologically sustainable forest management. Conserv. Biol. 14:941–950. , , and .
- 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479:359–364. , , , , , , et al.
- 1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Hered. 89:238–247. , , , and .
- 1998. The critical effective size for a genetically secure population. Anim. Conserv. 1:70–72. , and .
- 2012. The hunters did it. Science 335:1452–1453.
- 2009. Primates in peril: the world's 25 most endangered primates 2008–2010. Primate Conserv. 24:1–57. , , , , , , et al.
- 1998. Did forests survive the cold in a hotspot? Nature 391:124–127.
- 2011. Parks and poverty: lessons from a decade of forest loss and economic growth around Kibale National Park, Uganda. Proc. Nat. Acad. Sci. 34:13919–13924. , , and .
- 2010. Climate predictors of late quaternary extinctions. Evolution 64:2442–2449. , , , and .
- 2004. 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. , , , , , ,
- 1994. What are the Colobines? Pp. 1–9 in A. G. Davies and J. F. Oates, eds. Colobine monkeys their ecology behavior and evolution. Cambridge Univ. Press, Cambridge. , and .
- 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol. Ecol. Notes 4:535–538. , , , and .
- 1998. Molecular evolution: a phylogenetic approach. Blackwell Publishing Ltd., Oxford, UK. , and .
- 2011. A genomic portrait of human microsatellite variation. Mol. Biol. Evol. 28:1–37. , , and .
- 2010. Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Mol. Ecol. 19:4648–4660. , , and .
- 1999. BOTTLENECK: A computer program for detecting reductions in the effective population size using allele frequency data. J. Hered. 90:502–503. , , and .
- 1996. Socioecology, population fragmentation, and patterns of genetic loss in endangered primates. Pp. 119–159 in J. C. Avise and J. L. Hamrick, eds. Conservation genetics: Case Histories from Nature. Chapman & Hall, New York.
- 2012. Quantitative global analysis of the role of climate and people in explaning late quaternary megafaunal extinctions. Proc. Nat. Acad. Sci. 109:4527–4531. , , , , and .
- 2003. Documentation for STRUCTURE software: Version 2. Available from http://pritch.bsd.uchicago.edu. , and .
- 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959. , , and .
- 2007. Tracer, version 1.4.1. Available at http://beast.bio.ed.ac.uk/Tracer. and .
- 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54:401–418. , and .
- 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
- 1998. Heterogeneity of microsatellite mutation models within and between loci, and implications for human demographic histories. Genetics 148:1269–1284. , , , , , , et al.
- 2005. The use of several microsatellite loci applied to 13 neotropical primates revealed a strong recent bottleneck event in the Woolly monkey (Lagothrix lagotricha) in Colombia. Primate Report 71:27–55.
- 2012. The aftermath of megafaunal extinction: ecosystem tranformation in Pleistocene Australia. Science 335:1483–1486. , , , , , .
- 2004. Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics 168:383–395. , , , and .
- 2010. Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus). BMC Evol. Biol. 10:105. , , , and .
- 2007. East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins. Proc. Nat. Acad. Sci. USA 104:16416–16421. , , , , , , et al.
- 2000. An economic method for the fluorescent labeling of PCR fragments. A poor man's approach to genotyping for research and high-throughput diagnostics. Nat. Biotechnol. 18:233–234.
- 2010. Parks, people and pixels: evaluating landscape effects of an East African national park on its surroundings. Trop. Conserv. Sci. 3:122–142. , , , , , , et al.
- 2008. The late Pleistocene desiccation of Lake Victoria and the origin of its endemic biota. Hydrobiologia 596:5–16. , and .
- 2002. Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56:154–166. , and .
- 1975. The Red Colobus monkey. Univ. of Chicago Press, Chicago.
- 1981a. Forest and primate conservation in East Africa. Afr. J. Ecol. 19:99–114.
- 1981b. Vocalizations, phylogeny and palaeogeography of red colobus monkeys (Colobus badius). Afr. J. Ecol. 19:265–283.
- 2005. Conservation of red colobus and their habitats. Int. J. Primatol. 26:525–538.
- 2010. The red colobus monkeys; variation demography behavior and ecology of endangered species. Oxford Univ. Press, New York.
- 1991. Mating system and reproductive success: a comparison of two African forest monkeys (Colobus badius and Cercopithecus ascanius). Behaviour 117:182–205. , and .
- 1999. A sediment-based history of medium altitude forest in central Africa: a record from Kabata Swamp, Ndale volcanic field, Uganda. J. Ecol. 87:303–315. , , and .
- 2008. Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys. J. Hum. Evol. 55:312–325.
- 2012. Genetic signatures of a demographic collapse in a large bodied forest dwelling primate (Mandrillus leucophaeus). Ecol. Evol. 3:550–561. , , , , , , et al.
- Uganda Wildlife Authority. 2011. Available at http://www.uwa.or.ug/kibale.html.
- 2008. Coalescent theory: an introduction. Roberts & Company Publishers, Greenwood Village, CO.
- 2002. Further declines of threatened primates in the Korup project area, south-west Cameroon. Oryx 36:257–265. , , and .
- 2003. Likelihood-based estimation of microsatellite mutation rates. Genetics 164:781–787. , , , , , , et al.
- 2008. Distribution patterns of land snails in Ugandan rain forests support the existence of Pleistocene forest refugia. J. Biogeogr. 35:1759–1768. , and .
- 2011. Joint inference of microsatellite mutation models, population history and genealogies using trans-dimensional MCMC. Genetics 188:151–164. , and .
- 1997. Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot.129:157. , and .