GADMA2: more efficient and flexible demographic inference from genetic data

Noskova, Ekaterina; Abramov, Nikita; Iliutkin, Stanislav; Sidorin, Anton; Dobrynin, Pavel; Ulyantsev, Vladimir

doi:10.1101/2022.06.14.496083

Cited by 10 publications

(12 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To quantify the extent of temporal change in genetic diversity and migration rates among populations, we next fit a series of demographic models to the three‐dimensional site frequency spectrum (SFS) of eastern California ( P. s. nevadensis ), Bay Area ( P. s. alaudinus ), and Newport Bay ( P. s. beldingi ) birds in GADMA2 (Noskova et al., 2023). We ran separate analyses for a historic dataset and a modern dataset of these three populations.…”

Section: Methodsmentioning

confidence: 99%

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Benham,

Walsh,

Bowie

2024

Global Change Biology

View full text Add to dashboard Cite

Combating the current biodiversity crisis requires the accurate documentation of population responses to human‐induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial–temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater‐adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.

show abstract

Section: Methodsmentioning

confidence: 99%

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Benham,

Walsh,

Bowie

2024

Global Change Biology

View full text Add to dashboard Cite

show abstract

“…The parameters in the demographic model were inferred using GADMA ver. 2 ( 80 ), which employs a genetic algorithm to optimize parameter values. As an engine in the inference we used Moments ( 81 ), which fits the observed joint MAF spectrum to simulated data using ordinary differential equations.…”

Section: Methodsmentioning

confidence: 99%

Evolution of hybrid inviability associated with chromosome fusions

Boman,

Näsvall,

Vila

et al. 2023

Preprint

View full text Add to dashboard Cite

Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. However, less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we used crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. By contrasting allele frequencies between F2hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities, we show that candidate loci for hybrid inviability mainly are situated in fast-evolving regions with reduced recombination rates, especially in regions where chromosome fusions have occurred. Our results show that the extensive variation in chromosome numbers observed across the tree of life can be involved in speciation by being hotspots for the early evolution of postzygotic reproductive isolation.

show abstract

“…To test for the presence of gene flow exceeding potential thresholds for homogenizing population structure, we estimated a model accounting for divergence times, effective population sizes, and migration rates between current and ancestral lineages. We optimized a three‐population demographic model based on the site‐frequency spectrum (SFS) using the genetic algorithm “GADMA” (Noskova et al., 2020, 2023) based on the “moments” engine (Jouganous et al., 2017). We first down projected the VCF file from ipyrad to a three‐dimensional SFS of [27,9,21] allele counts from (28,8,20) diploid individuals from the NTA, COH, and CHR lineages (see Section 3) using “easySFS” (https://github.com/isaacovercast/easySFS; Gutenkunst et al., 2009).…”

Section: Methodsmentioning

confidence: 99%

Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype

Pyron,

Kakkera,

Beamer

et al. 2023

Molecular Ecology

View full text Add to dashboard Cite

Numerous mechanisms can drive speciation, including isolation by adaptation, distance, and environment. These forces can promote genetic and phenotypic differentiation of local populations, the formation of phylogeographic lineages, and ultimately, completed speciation. However, conceptually similar mechanisms may also result in stabilizing rather than diversifying selection, leading to lineage integration and the long‐term persistence of population structure within genetically cohesive species. Processes that drive the formation and maintenance of geographic genetic diversity while facilitating high rates of migration and limiting phenotypic differentiation may thereby result in population genetic structure that is not accompanied by reproductive isolation. We suggest that this framework can be applied more broadly to address the classic dilemma of “structure” versus “species” when evaluating phylogeographic diversity, unifying population genetics, species delimitation, and the underlying study of speciation. We demonstrate one such instance in the Seepage Salamander (Desmognathus aeneus) from the southeastern United States. Recent studies estimated up to 6.3% mitochondrial divergence and four phylogenomic lineages with broad admixture across geographic hybrid zones, which could potentially represent distinct species supported by our species‐delimitation analyses. However, while limited dispersal promotes substantial isolation by distance, microhabitat specificity appears to yield stabilizing selection on a single, uniform, ecologically mediated phenotype. As a result, climatic cycles promote recurrent contact between lineages and repeated instances of high migration through time. Subsequent hybridization is apparently not counteracted by adaptive differentiation limiting introgression, leaving a single unified species with deeply divergent phylogeographic lineages that nonetheless do not appear to represent incipient species.

show abstract

GADMA2: more efficient and flexible demographic inference from genetic data

Cited by 10 publications

References 60 publications

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Evolution of hybrid inviability associated with chromosome fusions

Discerning structure versus speciation in phylogeographic analysis of Seepage Salamanders (Desmognathus aeneus) using demography, environment, geography, and phenotype

Contact Info

Product

Resources

About