SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal

Currat, Mathias; Arenas, Miguel; Quilodrán, Claudio S.; Excoffier, Laurent; Ray, Nicolas

doi:10.1093/bioinformatics/btz311

Cited by 44 publications

(55 citation statements)

References 53 publications

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“…We simulated biological invasions with various levels of interbreeding between two closely related taxa by using the program SPLATCHE3 (Currat et al, 2019). SPLATCHE3 is a spatially explicit program that allows the simulation of neutral genetic diversity.…”

Section: Simulation Frameworkmentioning

confidence: 99%

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

2020

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The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.

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Section: Simulation Frameworkmentioning

confidence: 99%

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

2020

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“…An alternative scenario would involve the recolonization of Brittany by shoals composed of a mixture of the two shad's species with unequal abundance similarly to the Ocean sampling where most of the individuals are from one species and one or a few individuals belong to the other species. Previous studies had also found sympatric occurrence of both species at sea (Taverny, 1991 Highly polymorphic (Jolly et al, 2012;Martin et al, 2015) or genomewide (Catchen et al, 2013) neutral markers and spatially explicit simulation-based approach (Currat, Arenas, Quilodran, Excoffier, & Ray, 2019) should be able to shed new light on the demographic aspect of hybridization during this recent northern shad recolonization event.…”

Section: Similar Observation Was Made Inmentioning

confidence: 94%

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

Taillebois¹,

Sabatino

Manicki³

et al. 2019

Evolutionary Applications

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Hybridization dynamics between co‐occurring species in environments where human‐mediated changes take place are important to quantify for furthering our understanding of human impacts on species evolution and for informing management. The allis shad Alosa alosa (Linnaeus, 1758) and twaite shad Alosa fallax (Lacépède, 1803), two clupeids sister species, have been severely impacted by human activities across Europe. The shrinkage of A. alosa distribution range along with the decline of the remaining populations' abundance threatens its persistence. The main objective was to evaluate the extent of hybridization and introgression between those interacting species. We developed a set of 77 species‐specific SNP loci that allowed a better resolution than morphological traits as they enabled the detection of hybrids up to the third generation. Variable rates of contemporary hybridization and introgression patterns were detected in 12 studied sites across the French Atlantic coast. Mitochondrial markers revealed a cyto‐nuclear discordance almost invariably involving A. alosa individuals with an A. fallax mitochondrial DNA and provided evidence of historical asymmetric introgression. Overall, contemporary and historical introgression revealed by nuclear and mitochondrial markers strongly suggests that a transfer of genes occurs from A. fallax toward A. alosa genome since at least four generations. Moreover, the outcomes of introgression greatly depend on the catchments where local processes are thought to occur. Undoubtedly, interspecific interaction and gene flow should not be overlooked when considering the management of those species.

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“…Spatially explicit computer simulations. We performed spatially explicit computer simulations with the evolutionary framework SPLATCHE3 34 . Information about the applied evolutionary models and landscape is presented in the Supplementary Material.…”

Section: Sample Collection and Ethical Statementsmentioning

confidence: 99%

The Early Peopling of the Philippines based on mtDNA

Arenas

Gorostiza

Baquero

et al. 2020

Sci Rep

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The Philippines constitutes an important geographic region in the expansion of modern humans despite it was frecuently ignored in human evolutionary analyses of the SEA and Oceania. Here we explored the expansion of modern humans towards the Philippines and we found that this expansion was rapid, presenting LDD events, and following diverse migration routes that geography and existing technology could allow. We believe that the rapid expansion an explosive population growth could be favored by optimal environmental conditions present in the region at the time of the expansion.

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SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal

Cited by 44 publications

References 53 publications

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

The Spatial Signature of Introgression After a Biological Invasion With Hybridization

Variable outcomes of hybridization between declining Alosa alosa and Alosa fallax

The Early Peopling of the Philippines based on mtDNA

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