The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes
Abstract: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 usuall… Show more
“…We provide here additional empirical evidence of contrasting results between tests and model‐based studies of demographic history. The MSVAR analysis can lead to false inferences of population decline in cases of strong departures from a stepwise mutation model (SMM; Girod et al., 2011; Faurby & Pertoldi, 2012) or in case of underlying genetic structure (Chikhi et al., 2010). Concerning departures from SMM, the inference of demographic decline was coherent along all our loci which present different levels of variability and distributions of allele sizes.…”
Section: Discussionmentioning
confidence: 99%
“…Concerning departures from SMM, the inference of demographic decline was coherent along all our loci which present different levels of variability and distributions of allele sizes. Regarding genetic structure, the analysis at the deme level inside regions gave similar results to pooled samples, but the analysis of a single deme can lead to spurious inference of decline as well (Chikhi et al., 2010). A decline, though less strong, was also inferred for a pool of individuals scattered along different demes as suggested by Chikhi et al.…”
Section: Discussionmentioning
confidence: 99%
“…A decline, though less strong, was also inferred for a pool of individuals scattered along different demes as suggested by Chikhi et al. (2010). These observations suggest that E. cavolini populations were indeed impacted by a demographic decline, but the estimates of the magnitude of this decline may be biased by population structure.…”
Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.
“…We provide here additional empirical evidence of contrasting results between tests and model‐based studies of demographic history. The MSVAR analysis can lead to false inferences of population decline in cases of strong departures from a stepwise mutation model (SMM; Girod et al., 2011; Faurby & Pertoldi, 2012) or in case of underlying genetic structure (Chikhi et al., 2010). Concerning departures from SMM, the inference of demographic decline was coherent along all our loci which present different levels of variability and distributions of allele sizes.…”
Section: Discussionmentioning
confidence: 99%
“…Concerning departures from SMM, the inference of demographic decline was coherent along all our loci which present different levels of variability and distributions of allele sizes. Regarding genetic structure, the analysis at the deme level inside regions gave similar results to pooled samples, but the analysis of a single deme can lead to spurious inference of decline as well (Chikhi et al., 2010). A decline, though less strong, was also inferred for a pool of individuals scattered along different demes as suggested by Chikhi et al.…”
Section: Discussionmentioning
confidence: 99%
“…A decline, though less strong, was also inferred for a pool of individuals scattered along different demes as suggested by Chikhi et al. (2010). These observations suggest that E. cavolini populations were indeed impacted by a demographic decline, but the estimates of the magnitude of this decline may be biased by population structure.…”
Understanding the factors explaining the observed patterns of genetic diversity is an important question in evolutionary biology. We provide the first data on the genetic structure of a Mediterranean octocoral, the yellow gorgonian Eunicella cavolini, along with insights into the demographic history of this species. We sampled populations in four areas of the Mediterranean Sea: continental France, Algeria, Turkey, and the Balearic and Corsica islands. Along French coasts, three sites were sampled at two depths (20 and 40 m). We demonstrated a high genetic structure in this species (overall FST = 0.13), and most pairwise differentiation tests were significant. We did not detect any difference between depths at the same site. Clustering analyses revealed four differentiated groups corresponding to the main geographical areas. The levels of allelic richness and heterozygosity were significantly different between regions, with highest diversity in Algeria and lowest levels in Turkey. The highest levels of private allelic richness were observed in Algeria followed by Turkey. Such contrasted patterns of genetic diversity were not observed in other Mediterranean octocorals and could be the result of different evolutionary histories. We also provide new empirical evidence of contrasting results between tests and model‐based studies of demographic history. Our results have important consequences for the management of this species.
“…Whether the recent population size decline (over last few hundreds of years) apparent in most mitochondrial lineages is a true signal potentially correlated with increasing human population sizes along the lake shore or simply a methodological artifact (Chikhi et al, 2010;Heller et al, 2013) remains unclear. It is also interesting to note that the TCS-1 haplotypes assigned to the pink haplotype cluster are not exclusive to the very northern part of the lake.…”
In Lake Tanganyika, lake level fluctuations were shown to have had a major impact on the evolution of littoral species. Many species are subdivided into arrays of populations, geographical races and sister species, each colonizing a particular section of the shore. Their often limited dispersal abilities promoted geographic isolation and, on the long run, allopatric speciation. With more than 120 distinct populations, the genus Tropheus represents the most spectacular and best-studied example of this phenomenon. The present study aims at the fine-scale reconstruction of the spread of two mitochondrial Tropheus-lineages in the very north of the lake, where two species, T. sp. 'black' and T. brichardi, occur. Using mtDNA sequences and AFLP-data, we analyzed samples from 21 localities and found a highly complex conglomerate of introgressed populations formed by the repeated contact of two lineages. Our data suggest repeated cross-lake dispersal of T. sp. 'black' haplotypes along the ridge between the West and East Ubwari Fault, supporting an additional persisting lowstand-lake in the Bujumbura subbasin at the very north of the lake and highlighting once more the impact of lake level fluctuations on the genetic structure and evolution of stenotopic rockdwelling cichlid species.
“…To avoid overrepresentation of populations [26], the dataset was standardized by random pruning to approximately 50 samples per island, excluding islands with fewer than 20 samples. For San Cristóbal, 124 samples were used, with 50 each for LO and PP, plus 24 specimens from the previously unsampled East coast.…”
The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes-are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within-island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50 000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island-ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.
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