Inferring population history with<i>DIY ABC</i>: a user-friendly approach to approximate Bayesian computation

Cornuet, Jean‐Marie; Santos, Filipe Martins; Beaumont, Mark A.; Robert, Christian P.; Marin, Jean‐Michel; Balding, David J.; Guillemaud, Thomas; Estoup, Arnaud

doi:10.1093/bioinformatics/btn514

Cited by 639 publications

(930 citation statements)

References 37 publications

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“…For each question, we modeled two or more scenarios and then compared these against each other in order to quantify their relative probabilities. We used the program DIYABC to conduct these analyses (Cornuet et al., 2008, 2014) and used the following summary statistics to conduct our analyses: one‐sample statistics—number of haplotypes and number of segregating sites, two‐sample statistics—number of haplotypes.…”

Section: Methodsmentioning

confidence: 99%

Influence of invasion history on rapid morphological divergence across island populations of an exotic bird

Valentin

Lockwood

Mathys

et al. 2018

Ecology and Evolution

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There is increasing evidence that exotic populations may rapidly differentiate from those in their native range and that differences also arise among populations within the exotic range. Using morphological and DNA‐based analyses, we document the extent of trait divergence among native North American and exotic Hawaiian populations of northern cardinal (Cardinalis cardinalis). Furthermore, using a combination of historical records and DNA‐based analyses, we evaluate the role of founder effects in producing observed trait differences. We measured and compared key morphological traits across northern cardinal populations in the native and exotic ranges to assess whether trait divergence across the Hawaiian Islands, where this species was introduced between 1929 and 1931, reflected observed variation across native phylogeographic clades in its native North America. We used and added to prior phylogenetic analyses based on a mitochondrial locus to identify the most likely native source clade(s) for the Hawaiian cardinal populations. We then used Approximate Bayesian Computation (ABC) to evaluate the role of founder effects in producing the observed differences in body size and bill morphology across native and exotic populations. We found cardinal populations on the Hawaiian Islands had morphological traits that diverged substantially across islands and overlapped the trait space of all measured native North American clades. The phylogeographic analysis identified the eastern North American clade (C. cardinalis cardinalis) as the most likely and sole native source for all the Hawaiian cardinal populations. The ABC analyses supported written accounts of the cardinal's introduction that indicate the original 300 cardinals shipped to Hawaii were simultaneously and evenly released across Hawaii, Kauai, and Oahu. Populations on each island likely experienced bottlenecks followed by expansion, with cardinals from the island of Hawaii eventually colonizing Maui unaided. Overall, our results suggest that founder effects had limited impact on morphological trait divergence of exotic cardinal populations in the Hawaiian archipelago, which instead reflect postintroduction events.

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Section: Methodsmentioning

confidence: 99%

Influence of invasion history on rapid morphological divergence across island populations of an exotic bird

Valentin

Lockwood

Mathys

et al. 2018

Ecology and Evolution

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“…Competing hypotheses about the introduction history of L. serriola in the two non-native groups were compared within an approximate Bayesian computing (ABC) framework using the software DIYABC [25,26]. The 14 scenarios (see electronic supplementary material, table S2) considered all four possible combinations of Europe and/or Asia as putative source regions, plus five scenarios in which at least one non-native group arose through admixture between Asia and Europe.…”

Section: (C) Statistical Analyses (I) Inferring Invasion Historymentioning

confidence: 99%

“…The observed and simulated datasets were summarized and compared using a set of nine statistics. These were: for each region, the mean number of alleles, mean gene diversity, mean allele size variance and mean M index (the ratio of the number of alleles to the range in allele sizes) across loci; and for each pair of regions, the mean number of alleles, gene diversity and allele size variance across loci, pairwise F ST and the mean index of classification [25]. The total number of summary statistics was 52.…”

Section: (C) Statistical Analyses (I) Inferring Invasion Historymentioning

confidence: 99%

Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant

Alexander

2013

Proc. R. Soc. B.

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A topic of great current interest is the capacity of populations to adapt genetically to rapidly changing climates, for example by evolving the timing of life-history events, but this is challenging to address experimentally. I use a plant invasion as a model system to tackle this question by combining molecular markers, a common garden experiment and climatic niche modelling. This approach reveals that non-native Lactuca serriola originates primarily from Europe, a climatic subset of its native range, with low rates of admixture from Asia. It has rapidly refilled its climatic niche in the new range, associated with the evolution of flowering phenology to produce clines along climate gradients that mirror those across the native range. Consequently, some non-native plants have evolved development times and grow under climates more extreme than those found in Europe, but not among populations from the native range as a whole. This suggests that many plant populations can adapt rapidly to changed climatic conditions that are already within the climatic niche space occupied by the species elsewhere in its range, but that evolution to conditions outside of this range is more difficult. These findings can also help to explain the prevalence of niche conservatism among non-native species.

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“…We inferred effective population sizes of the STRUCTURE clusters based on an SSR data set using ABC as implemented in DIYABC v. 1.0.4.37 (Cornuet et al 2008(Cornuet et al , 2010, available from http://www1.montpellier.inra.fr/CBGP/ diyabc/. Beaumont et al (2002) provide a full description of the ABC method.…”

Section: Approximate Bayesian Computation (Abc) Analysismentioning

confidence: 99%

The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation

et al. 2017

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reflects its extreme isolation. This factor, coupled with inbreeding and genetic drift, are major threats to JW. A neighbor-joining tree based on mtDNA haplotypes shows that JW clusters among samples representing the Central subgroup that is known from central Germany but that has not yet been identified in Poland. Findings presented here improve our understanding of the spread and diversification of the common hamster. We offer the following hypotheses to explain the observed pattern of mtDNA haplotype distribution: JW could be a byproduct of postglacial migrations or back-migrations from eastern refugia to the western part of Europe, or/and be a result of population and habitat fragmentation. We recommend translocation of individuals as an effective management strategy, both at the level of Central phylogeographic group and at the species level, to overcome the negative consequences of inbreeding and geographical isolation of the JW population.

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Inferring population history withDIY ABC: a user-friendly approach to approximate Bayesian computation

Cited by 639 publications

References 37 publications

Influence of invasion history on rapid morphological divergence across island populations of an exotic bird

Influence of invasion history on rapid morphological divergence across island populations of an exotic bird

Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant

The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation

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