Frankham, R., Briscoe, D. A. & Ballou, J. D. Introduction to conservation genetics (Cambridge university press, 2002).
Nadachowska-Brzyska, K., Burri, R., Smeds, L. & Ellegren, H. PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers. Mol. Ecol. 25, 1058–1072 (2016).
Google Scholar
Martínez-Freiría, F., Velo-Antón, G. & Brito, J. C. Trapped by climate: Interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei. Divers. Distrib. 21, 331–344 (2015).
Google Scholar
Martínez-Freiría, F. et al. Integrative phylogeographical and ecological analysis reveals multiple pleistocene refugia for Mediterranean Daboia vipers in north-west Africa. Biol. J. Linn. Soc. 122, 366–384 (2017).
Google Scholar
Veríssimo, J. et al. Pleistocene diversification in Morocco and recent demographic expansion in the Mediterranean pond turtle Mauremys leprosa. Biol. J. Linn. Soc. 119, 943–959 (2016).
Google Scholar
Chattopadhyay, B., Garg, K. M., Gwee, C. Y., Edwards, S. V. & Rheindt, F. E. Gene flow during glacial habitat shifts facilitates character displacement in a Neotropical flycatcher radiation. BMC Evol. Biol. 17, 1–15 (2017).
Google Scholar
Garg, K. M., Chattopadhyay, B., Koane, B., Sam, K. & Rheindt, F. E. Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. BMC Evol. Biol. 20, 82 (2020).
Google Scholar
Vences, M., Wollenberg, K. C., Vieites, D. R. & Lees, D. C. Madagascar as a model region of species diversification. Trends Ecol. Evol. 24, 456–465 (2009).
Google Scholar
Goodman, S. M., Raherilalao, M. J. & Wohlhauser, S. The Terrestrial Protected Areas of Madagascar: Their History, Description and Biota (Association Vahatra in Antananarivo, The University of Chicago Press, 2018).
Douglass, K. The diversity of late holocene shellfish exploitation in Velondriake, Southwest Madagascar. J. Island Coast. Archaeol. 12, 333–359 (2016).
Yoder, A. D., Campbell, C. R., Blanco, M. B., Ganzhorn, J. U. & Goodman, S. M. Geogenetic patterns in mouse lemurs (genus Microcebus) reveal the ghosts of Madagascar’s forests past. PNAS 113, 8049–8056 (2016).
Google Scholar
Salmona, J., Heller, R., Quéméré, E. & Chikhi, L., Climate change. and human colonization triggered habitat loss and fragmentation in Madagascar. Mol. Ecol. 26, 5203–5222 (2017).
Google Scholar
Townsend, T. M., Vieites, D. R., Glaw, F. & Vences, M. Testing species-level diversification hypotheses in Madagascar: the case of microendemic Brookesia leaf Chameleons. Syst. Biol. 58, 641–656 (2009).
Google Scholar
Brown, J. L., Cameron, A., Yoder, A. D. & Vences, M. A necessarily complex model to explain the biogeography of the amphibians and reptiles of Madagascar. Nat. Commun. 5, 5046 (2014).
Schüßler, D. et al. Ecology and morphology of mouse lemurs (Microcebus spp.) in a hotspot of microendemism in northeastern Madagascar, with the description of a new species. Am. J. Primatol. 82, e23180 (2020).
Google Scholar
Chikhi, L. & Bruford, M. Mammalian population genetics and genomics. Mamm. Genome https://doi.org/10.1079/9780851999104.0539 (2005).
Olivieri, G. L., Sousa, V., Chikhi, L. & Radespiel, U. From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.). Biol. Conserv. 141, 1257–1271 (2008).
Google Scholar
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H. & Bustamante, C. D. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5, e1000695 (2009).
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).
Google Scholar
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C. & Foll, M. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).
Liu, X. & Fu, Y.-X. Exploring population size changes using SNP frequency spectra. Nat Genet. 47, 555–559 (2015).
Salmona, J., Heller, R., Lascoux, M. & Shafer, A. Inferring demographic history using genomic data. in Population Genomics 511–537 (Springer, 2017).
Beichman, A. C., Huerta-Sanchez, E. & Lohmueller, K. E. Using genomic data to infer historic population dynamics of nonmodel organisms. Annu. Rev. Ecol. Evol. Syst. 49, 433–456 (2018).
Google Scholar
Sgarlata, G. M. et al. Genetic and morphological diversity of mouse lemurs (Microcebus spp.) in northern Madagascar: The discovery of a putative new species? Am. J. Primatol. 81, e23070 (2019).
Demenocal, P. et al. Abrupt onset and termination of the African humid period:: rapid climate responses to gradual insolation forcing. Quat. Sci. Rev. 19, 347–361 (2000).
Google Scholar
Tierney, J. E. & DeMenocal, P. B. Abrupt shifts in Horn of Africa hydroclimate since the last glacial maximum. Science 342, 843–846 (2013).
Google Scholar
Los, S. O. et al. Sensitivity of a tropical montane cloud forest to climate change, present, past and future: Mt. Marsabit, N. Kenya. Quat. Sci. Rev. 218, 34–48 (2019).
Google Scholar
Ivory, S. J. & Russell, J. Climate, herbivory, and fire controls on tropical African forest for the last 60ka. Quat. Sci. Rev. 148, 101–114 (2016).
Google Scholar
Conroy, J. L., Overpeck, J. T., Cole, J. E., Shanahan, T. M. & Steinitz-Kannan, M. Holocene changes in eastern tropical Pacific climate inferred from a Galápagos lake sediment record. Quat. Sci. Rev. 27, 1166–1180 (2008).
Google Scholar
Martin-Puertas, C., Tjallingii, R., Bloemsma, M. & Brauer, A. Varved sediment responses to early Holocene climate and environmental changes in Lake Meerfelder Maar (Germany) obtained from multivariate analyses of micro X-ray fluorescence core scanning data. J. Quat. Sci. 32, 427–436 (2017).
Google Scholar
Flenley, J. R. Tropical forests under the climates of the last 30,000 years. in Potential Impacts of Climate Change on Tropical Forest Ecosystems, 37–57 (Springer, 1998).
Burrough, S. L. & Thomas, D. S. G. Central southern Africa at the time of the African humid period: a new analysis of Holocene palaeoenvironmental and palaeoclimate data. Quat. Sci. Rev. 80, 29–46 (2013).
Google Scholar
Ivory, S. J. & Russell, J. Lowland forest collapse and early human impacts at the end of the African humid period at Lake Edward, equatorial East. Afr. Quat. Res. 89, 7–20 (2018).
Google Scholar
Anderson, A. et al. New evidence of megafaunal bone damage indicates late colonization of Madagascar. PLoS ONE 13, 1–14 (2018).
Hansford, J. et al. Early Holocene human presence in Madagascar evidenced by exploitation of avian megafauna. Sci. Adv. 4, eaat6925 (2018).
Burney, D. A., Robinson, G. S. & Burney, L. P. Sporormiella and the late holocene extinctions in Madagascar. Proc. Natl Acad. Sci. USA 100, 10800–10805 (2003).
Google Scholar
Railsback, L. B. et al. Relationships between climate change, human environmental impact, and megafaunal extinction inferred from a 4000-year multi-proxy record from a stalagmite from northwestern Madagascar. Quat. Sci. Rev. 234, 106244 (2020).
Google Scholar
Dewar, R. E. et al. Stone tools and foraging in northern Madagascar challenge Holocene extinction models. PNAS 110, 12583–12588 (2013).
Google Scholar
Radimilahy, C. Mahilaka: an Archaeological Investigation of an Early Town in Northwestern Madagascar. Acta Universitatis Upsaliensis (University of Uppsala, 1998).
Liu, X. & Fu, Y.-X. Exploring population size changes using SNP frequency spectra. Nat. Genet 47, 555–559 (2015).
Google Scholar
Lapierre, M., Lambert, A. & Achaz, G. Accuracy of demographic inferences from the site frequency spectrum: the case of the yoruba population. Genetics 206, 139–449 (2017).
Google Scholar
Terhorst, J., Kamm, J. A. & Song, Y. S. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat. Genet. 49, 303–309 (2017).
Google Scholar
Patton, A. H. et al. Contemporary demographic reconstruction methods are robust to genome assembly quality: a case study in Tasmanian devils. Mol. Biol. Evol. 36, 2906–2921 (2019).
Google Scholar
Mazet, O., Rodríguez, W., Grusea, S., Boitard, S. & Chikhi, L. On the importance of being structured: Instantaneous coalescence rates and human evolution-lessons for ancestral population size inference? Heredity 116, 362–371 (2016).
Google Scholar
Orozco-terWengel, P. The devil is in the details: the effect of population structure on demographic inference. Heredity 116, 349–350 (2016).
Mazet, O., Rodríguez, W. & Chikhi, L. Demographic inference using genetic data from a single individual: separating population size variation from population structure. Theor. Popul. Biol. 104, 46–58 (2015).
Google Scholar
Chikhi, L. et al. The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: Insights into demographic inference and model choice. Heredity 120, 13–24 (2018).
Google Scholar
Simons, E. L., Godfrey, L. R., Vuillaume-Randriamanantena, M., Chatrath, P. S. & Gagnon, M. Discovery of new giant subfossil lemurs in the Ankarana Mountains of Northern Madagascar. J. Hum. Evol. 19, 311–319 (1990).
Google Scholar
Jungers, W. L., Godfrey, L. R., Simons, E. L. & Chatrath, P. S. Subfossil Indri indri from the Ankarana Massif of northern Madagascar. Am. J. Phys. Anthropol. 97, 357–366 (1995).
Google Scholar
Wilson, J. M., Stewart, P. D. & Fowler, S. V. Ankarana — a rediscovered nature reserve in northern Madagascar. Oryx 22, 163–171 (1988).
Google Scholar
Everson, K. M., Jansa, S. A., Goodman, S. M. & Olson, L. E. Montane regions shape patterns of diversification in small mammals and reptiles from Madagascar’s moist evergreen forest. J. Biogeogr. 47, 2059–2072 (2020).
Google Scholar
Douglass, K., Hixon, S., Wright, H. T., Godfrey, L. R. & Crowley, B. E. A critical review of radiocarbon dates clarifies the human settlement of Madagascar. Quat. Sci. Rev. 221, 105878 (2019).
Orozco-Terwengel, P., Andreone, F., Louis, E. & Vences, M. Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genus. Dyscophus. Mol. Ecol. 22, 6074–6090 (2013).
Google Scholar
Johnson, J. A. et al. Long-term survival despite low genetic diversity in the critically endangered Madagascar fish-eagle. Mol. Ecol. 18, 54–63 (2009).
Google Scholar
Sommer, S. Effects of habitat fragmentation and changes of dispersal behaviour after a recent population decline on the genetic variability of noncoding and coding DNA of a monogamous Malagasy rodent. Mol. Ecol. 12, 2845–2851 (2003).
Google Scholar
Craul, M. et al. Influence of forest fragmentation on an endangered large-bodied lemur in northwestern Madagascar. Biol. Conserv. 142, 2862–2871 (2009).
Google Scholar
Parga, J. A., Sauther, M. L., Cuozzo, F. P., Jacky, I. A. Y. & Lawler, R. R. Evaluating ring-tailed lemurs (Lemur catta) from southwestern Madagascar for a genetic population bottleneck. Am. J. Phys. Anthropol. 147, 21–29 (2012).
Google Scholar
Dewar, R. E. et al. Stone tools and foraging in northern Madagascar challenge Holocene extinction models. Proc. Natl Acad. Sci. USA 110, 12583–12588 (2013).
Google Scholar
Schüler, L. & Hemp, A. Atlas of pollen and spores and their parent taxa of Mt. Kilimanjaro and tropical East Africa. Quat. Int. 425, 301–386 (2016).
Google Scholar
Du Puy, D. J. & Moat, J. Vegetation mapping and classification in Madagascar (using GIS): implications and recommendations for the conservation of biodiversity. in Chorology, Taxonomy and Ecology of the floras of Africa and Madagascar, 97–117 (1998, in press).
Guillaumet, J.-L., Betsch, J.-M. & Callmander, M. W. Renaud Paulian et le programme du CNRS sur les hautes montagnes à Madagascar: étage vs domaine. Zoosystema 30, 723 (2008).
Google Scholar
Weisrock, D. W. et al. Delimiting species without nuclear monophyly in Madagascar’s mouse lemurs. PLoS ONE 5, e9883 (2010).
Google Scholar
Croudace, I. W., Rindby, A. & Rothwell, R. G. ITRAX: description and evaluation of a new multi-function X-ray core scanner. Geol. Soc. Lond. Spec. Publ. 267, 51–63 (2006).
Google Scholar
Blott, S. J. & Pye, K. GRADISTAT: a grain size distribution and statistics package for the analysis of unconsolidated sediments. Earth Surf. Process. Landforms 26, 1237–1248 (2001).
Google Scholar
Hogg, A. G. et al. SHCal13 Southern Hemisphere calibration, 0–50,000 years cal BP. Radiocarbon 55, 1889–1903 (2013).
Google Scholar
Rina Evasoa, M. et al. Sources of variation in social tolerance in mouse lemurs (Microcebus spp.). BMC Ecol. 19, 1–16 (2019).
Google Scholar
Aleixo-Pais, I. et al. The genetic structure of a mouse lemur living in a fragmented habitat in Northern Madagascar. Conserv. Genet. 20, 229–243 (2019).
Google Scholar
Radespiel, U., Jurić, M. & Zimmermann, E. Sociogenetic structures, dispersal and the risk of inbreeding in a small nocturnal lemur, the golden-brown mouse lemur (Microcebus ravelobensis). Behaviour 146, 607–628 (2009).
Google Scholar
Radespiel, U., Ehresmann, P. & Zimmermann, E. Species-specific usage of sleeping sites in two sympatric mouse lemur species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. Am. J. Primatol. 59, 139–151 (2003).
Google Scholar
Larsen, P. A. et al. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biol. 15, 1–17 (2017).
Google Scholar
Metzker, M. L. Sequencing technologies — the next generation. Nat. Rev. Genet. 11, 31 (2010).
Google Scholar
Skotte, L., Korneliussen, T. S. & Albrechtsen, A. Estimating individual admixture proportions from next generation sequencing. Data 195, 693–702 (2013).
Google Scholar
Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinforma. 15, 1–13 (2014).
Google Scholar
Korneliussen, T. S. & Moltke, I. Sequence analysis NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics 31, 4009–4011 (2015).
Google Scholar
Soraggi, S., Wiuf, C. & Albrechtsen, A. Powerful inference with the D-Statistic on low-coverage whole-genome data. G3 8, 551–566 (2017).
Google Scholar
Chikhi, L., Sousa, V. C., Luisi, P., Goossens, B. & Beaumont, M. A. 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 (2010).
Google Scholar
Kopelman, N. M., Mayzel, J., Jakobsson, M., Rosenberg, N. A. & Mayrose, I. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Mol. Ecol. Resour. 15, 1179–1191 (2015).
Google Scholar
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).
Google Scholar
Salmona, J., Heller, R., Quéméré, E. & Chikhi, L. Climate change and human colonization triggered habitat loss and fragmentation in Madagascar. Mol. Ecol. 26, 5203–5222 (2017).
Google Scholar
Schneider, N., Chikhi, L., Currat, M. & Radespiel, U. Signals of recent spatial expansions in the grey mouse lemur (Microcebus murinus). BMC Evol. Biol. 10, 105 (2010).
Radespiel, U., Lutermann, H., Schmelting, B. & Zimmermann, E. An empirical estimate of the generation time of mouse lemurs. Am. J. Primatol. 81, 1–8 (2019).
Google Scholar
Hawkins, M. T. R. et al. Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation. BMC Genomics 19, 1–15 (2018).
Google Scholar
Poelstra, J. et al. Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent. Syst. Biol. https://doi.org/10.1093/sysbio/syaa053 (2020).
Campbell, C. R. et al. Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur. Heredity 127.2, 233–244 (2021).
Google Scholar
Hudson, R. R. Generating samples under a Wright–Fisher neutral model of genetic variation. Bioinformatics 18, 337–338 (2002).
Google Scholar
Fredsted, T., Pertoldi, C., Schierup, M. H. & Kappeler, P. M. Microsatellite analyses reveal fine-scale genetic structure in grey mouse lemurs (Microcebus murinus). Mol. Ecol. 14, 2363–2372 (2005).
Google Scholar
Radespiel, U., Schulte, J., Burke, R. J. & Lehman, S. M. Molecular edge effects in the endangered golden-brown mouse lemur Microcebus ravelobensis. Oryx 53, 716–726 (2019).
Google Scholar
Radespiel, U., Lutermann, H., Schmelting, B., Bruford, M. W. & Zimmermann, E. Patterns and dynamics of sex-biased dispersal in a nocturnal primate, the grey mouse lemur, Microcebus murinus. Anim. Behav. 65, 709–719 (2003).
Google Scholar
Radespiel, U., Rakotondravony, R. & Chikhi, L. Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur, Microcebus ravelobensis. Am. J. Primatol. 70, 860–870 (2008).
Google Scholar
Schliehe-Diecks, S., Eberle, M. & Kappeler, P. M. Walk the line-dispersal movements of gray mouse lemurs (Microcebus murinus). Behav. Ecol. Sociobiol. 66, 1175–1185 (2012).
Google Scholar
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V. C. & Foll, M. Robust demographic inference from genomic and SNP data. PLoS Genet. 9, e1003905 (2013).
Beerli, P. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecol. 13, 827–836 (2004).
Google Scholar
Akaike, H. A new look at the statistical model identification. IEEE Trans. Automat. Control 19, 716–723 (1974).
Google Scholar
Bagley, R. K., Sousa, V. C., Niemiller, M. L. & Linnen, C. R. History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei). Mol. Ecol. 26, 1022–1044 (2017).
Google Scholar
Source: Ecology - nature.com