Inferring Demographic History Using Genomic Data

Salmona, Jordi; Heller, Rasmus; Lascoux, Martin; Shafer, Aaron B. A.

doi:10.1007/13836_2017_1

Cited by 18 publications

(20 citation statements)

References 133 publications

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“…Species diversity can be viewed as an imprint left by past events on the present-day genetic polymorphism of populations. Therefore, using genetic diversity for the inference of species population history can provide evidence for past demographic events linked to changes in species environmental conditions (Salmona et al, 2017). Several methods have been developed to take advantage of the patterns of genetic variation observed in contemporary populations to investigate species demographic history (Hey & Machado, 2003;Gutenkunst et al, 2009;Beaumont, 2010;Liu & Fu, 2015).…”

Section: Introductionmentioning

confidence: 99%

Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

et al. 2019

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Summary Past climatic fluctuations have played a major role in shaping the current plant biodiversity. Although harbouring an exceptional biota, oceanic islands have received little attention in studies on species demographic history and past vegetation patterns. We investigated the impact of past climatic changes on the effective population size of a tree (Coffea mauritiana) that is endemic to Reunion Island, located in the south‐western Indian Ocean (SWIO). Demographic changes were inferred using summary statistics calculated from genomic data. Using ecological niche modelling and the current distribution of genetic diversity, the paleodistribution of the species was also assessed. A reduction in the effective population size of C. mauritiana during the last glaciation maximum was inferred. The distribution of the species was reduced on the western side of the island, due to low rainfall. It appeared that a major reduction in rainfall and a slight temperature decrease prevailed in the SWIO. Our findings indicated that analyses on the current patterns of intraspecific genetic variations can efficiently contribute to past climatic changes characterisation in remote islands. Identifying area with higher resilience in oceanic islands could provide guidance in forest management and conservation faced to the global climate change.

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Section: Introductionmentioning

confidence: 99%

Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

et al. 2019

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“…7a). The and 800 (Nebot ~ U [1,800]) while the bottleneck start and end times tbotstart and tbotend were drawn from uniform distributions ranging between ten and 70 (tbotstart ~U [10,70]) and one and 30 (tbotend ~ U [1,30]) generations ago respectively. Hence, the bottleneck time priors encompassed the last four centuries for all species, as their estimated generation times vary between approximately 7 and 19 years (Supplementary Table 1).…”

Section: Demographic Modelsmentioning

confidence: 99%

“…Unravelling the demographic histories of species is a fundamental goal of population biology and has tremendous implications for understanding the genetic variability observed today 1,2 . Of particular interest are sharp reductions in the effective population size (Ne) known as population bottlenecks 3,4 , which may negatively impact the viability and adaptive evolutionary potential of species through a variety of stochastic demographic processes and the loss of genetic diversity [5][6][7][8] .…”

Section: Introductionmentioning

confidence: 99%

Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history

Stoffel

Humble

Acevedo‐Whitehouse

et al. 2018

Preprint

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A central paradigm in conservation biology is that population bottlenecks reduce genetic diversity and negatively impact population viability and adaptive potential. In an era of unprecedented biodiversity loss and climate change, understanding both the determinants and consequences of bottlenecks in wild populations is therefore an increasingly important challenge. However, as most studies have focused on single species, the multitude of potential drivers and the consequences of bottlenecks remain elusive. Here, we used a comparative approach by integrating genetic data from over 11,000 individuals of 30 pinniped species with demographic, ecological and life history data to elucidate the consequences of large-scale commercial exploitation by 18 th and 19 th century sealers. We show that around one third of these species exhibit strong genetic signatures of recent population declines, with estimated bottleneck effective population sizes reflecting just a few tens of surviving individuals in the most extreme cases. Bottleneck strength was strongly associated with both breeding habitat and mating system variation, and together with global abundance explained a large proportion of the variation in genetic diversity across species. Overall, there was no relationship between bottleneck intensity and IUCN status, although three of the four most heavily bottlenecked species are currently endangered. Our study reveals an unforeseen interplay between anthropogenic exploitation, ecology, life history and demographic declines, sheds new light on the determinants of genetic diversity, and is consistent with the notion that both genetic and demographic factors influence population viability.

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“…However, assessing the relative and confounding effects of complex landscape dynamics (forest loss, fragmentation, barriers emergence, etc.) on population dynamics, is notoriously challenging (Nater et al ., 2015; Salmona et al ., 2017a,b; Beichman et al ., 2018).…”

Section: Introductionmentioning

confidence: 99%

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree

Salmona

Dresen

Ranaivoson

et al. 2020

Preprint

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Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exception in areas like the Loky-Manambato region (North) raises questions. This region also harbors a rich and endemic flora, whose evolutionary origin remains poorly understood.We assessed the genetic diversity of an endangered micro-endemic Malagasy olive species (Noronhia spinifolia) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR).Extremely high genetic diversity was revealed in the three genomic compartments (chloroplast h = 0.99, mitochondrial h = 0.85, and nuclear HO = 0.07-0.20). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is best explained by the current forest cover (R2 = 0.90), highlighting a long-standing forest fragmentation in the region. Our results further suggest a predominant role of forestdwelling organisms in mediating pollen and seed dispersals.This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.

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Inferring Demographic History Using Genomic Data

Cited by 18 publications

References 133 publications

Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

Recent demographic histories and genetic diversity across pinnipeds are shaped by anthropogenic interactions and mediated by ecology and life-history

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree

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