From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)

Olivieri, Gillian; Sousa, Vítor C.; Chikhi, Lounès; Radespiel, Ute

doi:10.1016/j.biocon.2008.02.025

Cited by 85 publications

(104 citation statements)

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“…They found, as expected, that bottlenecks could be detected, but, very surprisingly, they also found a significant proportion of expansion signals. This is particularly interesting since expansion signals have also been observed in real data sets from endangered species known to have rapidly decreased in the last decades due to habitat fragmentation when the method of Cornuet and Luikart (1996) was used (e.g., Cook et al 2007;Johnson et al 2008;Olivieri et al 2008). We have also found this in another set of simulations to which the Bottleneck program was applied (L. Chikhi and V. Sousa, unpublished data).…”

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“…We used the R language (R Development were interested in determining whether there was a clear bias toward either bottlenecks or expansions, not whether the quantiles were precisely estimated or whether the mean was known with high precision. This is why convergence was not as serious an issue for us as it would be with real data sets for which several independent runs would need to be performed for each data set (e.g., Okello et al 2008;Olivieri et al 2008;Sousa et al 2009a). Even in the very few cases where convergence had not been reached (based on Geweke's statistic) visual inspection of the chains suggested that the chain was close to equilibrium and the signal for either population increase or decrease was clear.…”

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confidence: 99%

“…method because it is a full-likelihood Bayesian method that is expected to use the genetic data efficiently, hence detecting bottlenecks when summary statistics-based methods are potentially unable to detect significant departures (e.g., Olivieri et al 2008;Sousa et al 2008).…”

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The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

et al. 2010

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The idea that molecular data should contain information on the recent evolutionary history of populations is rather old. However, much of the work carried out today owes to the work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e.g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality or stationarity. During the last 20 years the detection of population size changes has usually been carried out under the assumption that samples were obtained from populations that can be approximated by a Wright-Fisher model (i.e., assuming panmixia, demographic stationarity, etc.). However, natural populations are usually part of spatial networks and are interconnected through gene flow. Here we simulated genetic data at mutation and migration-drift equilibrium under an n-island and a stepping-stone model. The simulated populations were thus stationary and not subject to any population size change. We varied the level of gene flow between populations and the scaled mutation rate. We also used several sampling schemes. We then analyzed the simulated samples using the Bayesian method implemented in MSVAR, the Markov Chain Monte Carlo simulation program, to detect and quantify putative population size changes using microsatellite data. Our results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals. We also suggest an ad hoc method to counter this effect. The confounding effect of population structure and of the sampling scheme has practical implications for many conservation studies. Indeed, if population structure is creating ''spurious'' bottleneck signals, the interpretation of bottleneck signals from genetic data might be less straightforward than it would seem, and several studies may have overestimated or incorrectly detected bottlenecks in endangered species.T HE idea that molecular data should contain information on the recent evolutionary history of populations is not new and traces back to the beginning of the 20th century (e.g., Hirschfeld and Hirschfeld 1919). However, much of the work carried out today owes to the seminal work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e.g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality (Watterson 1975;Tajima 1989b) or stationarity (Nei et al. 1975;Tajima 1989a). Following this period most studies have primarily been concerned with the statistical properties of relatively simple models such as the Wright-Fisher (WF) or Moran models (Ewens 2004). During the last 20 years the detection of population size changes (e.g., Tajima 1989b;Slatkin and Hudson 1991;Rogers and Harpending 1992;Cornuet and Luikart 1996;Beaumont 1999;Garza and Williamson 2001;Storz and Beaumont 2002) has usually been carried ou...

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The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

et al. 2010

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“…submitted to different demographic histories with different time depths. Indeed, the genome retains the specific signature of major events, such as recent contractions (44,45) or ancient expansions (46). Reconstructing the demographic history of extant species may thus help to investigate how climate change and anthropogenic impact affected the dynamic of their habitat (42,47).…”

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Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region

Quéméré

Amelot

Pierson

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The impact of climate change and anthropogenic deforestation on biodiversity is of growing concern worldwide. Disentangling how past anthropogenic and natural factors contributed to current biome distribution is thus a crucial issue to understand their complex interactions on wider time scales and to improve predictions and conservation strategies. This is particularly important in biodiversity hotspots, such as Madagascar, dominated by large open habitats whose origins are increasingly debated. Although a dominant narrative argues that Madagascar was originally entirely covered by woodlands, which were destroyed by humans, a number of recent studies have suggested that past climatic fluctuations played a major role in shaping current biome distributions well before humans arrived. Here, we address the question of the origin of open habitats in the Daraina region in northern Madagascar, using a multiproxy approach combining population genetics modeling and remote-sensing analyses. We show that (i) contrary to most regions of Madagascar, the forest cover in Daraina remained remarkably stable over the past 60 y, and (ii) the golden-crowned sifaka (Propithecus tattersalli), a forest-dwelling lemur, underwent a strong population contraction before the arrival of the first humans, hence excluding an anthropogenic cause. Prehuman Holocene droughts may have led to a significant increase of grasslands and a reduction in the species' habitat. This contradicts the prevailing narrative that land cover changes are necessarily anthropogenic in Madagascar but does not preclude the later role played by humans in other regions in which recent lemur bottlenecks have been observed. habitat loss | primate | population bottleneck | coalescent

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“…In addition, landmark-based geometric morphometrics is used to quantify phenotypic variability (e.g. Hoffmann & Shirriffs, 2002;Ludoški et al, 2008;Olivieri et al, 2008;Francuski et al, 2009a, b). An investigation of wing geometry could be important assuming that wing shape is related to flight ability and thus to fitness (Kölliker-Ott et al, 2003).…”

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confidence: 99%

Genetic structure and phenotypic diversity of two northern populations of Cheilosia aff. longula (Diptera: Syrphidae) has implications for evolution and conservation

Milankov¹,

Francuski²,

Ludoški³

et al. 2010

Eur. J. Entomol.

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Abstract. The genetic structure and phenotypic diversity of two populations of Cheilosia aff. longula (Diptera: Syrphidae) in Lapland, Finland, were examined using DNA sequencing, protein electrophoresis, and geometric morphometrics. The morphological identification of the species were verified using partial sequences of mitochondrial cytochrome c oxidase subunit I (COI mtDNA), and the nuclear ribosomal internal transcribed region 2 (ITS2 rDNA), and comparing the corresponding sequences of Cheilosia aff. longula and the closely related C. longula. Two and three haplotypes of the genes COI mtDNA and ITS2 rDNA were identified in the two populations. Analysis of 12 isozyme loci showed an extremely low genetic variability in the populations originating from Utsjoki and Kevo. Discriminant analysis combined with canonical variate analysis revealed inter-population divergence in wing shape. Variation among genetically diverse individuals, both within-and among studied populations was studied, and directional (DA) and fluctuating asymmetry (FA) estimated using landmarks in the framework of geometric morphometrics. It is likely that the documented DA and FA asymmetry in both wing shape and size reflects the developmental instability of the individuals studied. By using Procrustes ANOVA the locations of particular landmarks responsible for the variation in shape were determined. The decomposition of the components of variance accorded to each landmark showed that the landmarks differed in the percentage of variation they accounted for (DA, FA and variation among individuals). In the discussion the implications of the reduced genetic diversity and asymmetry in wing traits for conservation is considered.

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From genetic diversity and structure to conservation: Genetic signature of recent population declines in three mouse lemur species (Microcebus spp.)

Cited by 85 publications

References 60 publications

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

Genetic data suggest a natural prehuman origin of open habitats in northern Madagascar and question the deforestation narrative in this region

Genetic structure and phenotypic diversity of two northern populations of Cheilosia aff. longula (Diptera: Syrphidae) has implications for evolution and conservation

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