Population genomics of Monadenia (Gastropoda: Stylommatophora: Xanthonychidae) land snails reveals structuring but gene-flow across distinct species and morphotypes

Despite the global biodiversity of terrestrial gastropods and their ecological and economic importance, the genomic basis of ecological adaptation and speciation in land snail taxa is still largely unknown. Here, we combined whole-genome re-sequencing with population genomics to evaluate the historical demography and the speciation process of two closely related species of land snails from western Europe, Candidula unifasciata and C. rugosiuscula . Historical demographic analysis indicated fluctuations in the size of ancestral populations, probably driven by Pleistocene climatic fluctuations. Although the current population distributions of both species do not overlap, our approximate Bayesian computation model selection approach on several speciation scenarios suggested that gene flow has occurred throughout the divergence process until recently. Positively selected genes diverging early in the process were associated with intragenomic and cyto-nuclear incompatibilities, respectively, potentially fostering reproductive isolation as well as ecological divergence. Our results suggested that the speciation between species entails complex processes involving both gene flow and ecological speciation, and that further research based on whole-genome data can provide valuable understanding on species divergence. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

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Population genomics reveals high gene flow in grass rockfish ( Sebastes rastrelliger )

Marine Genomics ◽

10.1016/j.margen.2017.01.004 ◽

2017 ◽

Vol 33 ◽

pp. 57-63 ◽

Cited By ~ 9

Author(s):

Edith Martinez ◽

Vincent Buonaccorsi ◽

John R. Hyde ◽

Andres Aguilar

Keyword(s):

Gene Flow ◽

Population Genomics ◽

High Gene Flow ◽

High Gene

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Spatial population genomics of a recent mosquito invasion

10.1101/2020.11.30.405191 ◽

2020 ◽

Author(s):

Thomas L Schmidt ◽

T. Swan ◽

Jessica Chung ◽

Stephan Karl ◽

Samuel Demok ◽

...

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Isolation By Distance ◽

Spatial Genetic Structure ◽

Nucleotide Polymorphisms ◽

Discrete Events ◽

Long Distance ◽

Population Genomic ◽

Asian Tiger ◽

Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

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Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes

10.1101/713081 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jacob S. Berv ◽

Leonardo Campagna ◽

Teresa J. Feo ◽

Ivandy Castro-Astor ◽

Camila C. Ribas ◽

...

Keyword(s):

Gene Flow ◽

Distinct Species ◽

Passerine Bird ◽

Biological Species ◽

Genetic Connectivity ◽

Population Isolation ◽

Continental Scale ◽

The Andes ◽

Areas Of Endemism ◽

History Of

AbstractThe complex landscape history of the Neotropics has generated opportunities for population isolation and subsequent diversification that place this region among the most species-rich in the world. Detailed phylogeographic studies are required to uncover the biogeographic histories of Neotropical taxa, to identify evolutionary correlates of diversity, and to reveal patterns of genetic connectivity, disjunction, and potential differentiation among lineages from different areas of endemism. The White-crowned Manakin (Pseudopipra pipra) is a small suboscine passerine bird that is broadly distributed through the subtropical rainforests of Central America, the lower montane cloud forests of the Andes from Colombia to central Peru, the lowlands of Amazonia and the Guianas, and the Atlantic forest of southeast Brazil. Pseudopipra is currently recognized as a single, polytypic biological species. We studied the effect of the Neotropical landscape on genetic and phenotypic differentiation within this species using genomic data derived from double digest restriction site associated DNA sequencing (ddRAD), and mitochondrial DNA. Most of the genetic breakpoints we identify among populations coincide with physical barriers to gene flow previously associated with avian areas of endemism. The phylogenetic relationships among these populations imply a novel pattern of Andean origination for this group, with subsequent diversification into the Amazonian lowlands. Our analysis of genomic admixture and gene flow establishes a complex history of introgression between some western Amazonian populations. These reticulate processes confound our application of standard concatenated and coalescent phylogenetic methods and raise the question of whether a lineage in the western Napo area of endemism should be considered a hybrid species. Lastly, analysis of variation in vocal and plumage phenotypes in the context of our phylogeny supports the hypothesis that Pseudopipra is a species-complex composed of at least 8, and perhaps up to 17 distinct species which have arisen in the last ∼2.5 Ma.

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Speciation in the presence of gene flow: population genomics of closely related and diverging Eucalyptus species

Heredity ◽

10.1038/s41437-018-0073-2 ◽

2018 ◽

Vol 121 (2) ◽

pp. 126-141 ◽

Cited By ~ 15

Author(s):

Susan Rutherford ◽

Maurizio Rossetto ◽

Jason G. Bragg ◽

Hannah McPherson ◽

Doug Benson ◽

...

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Eucalyptus Species

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Gene flow analysis demonstrates that Phytophthora fragariae var. rubi constitutes a distinct species, Phytophthora rubi comb. nov.

Mycologia ◽

10.1080/15572536.2007.11832581 ◽

2007 ◽

Vol 99 (2) ◽

pp. 222-226 ◽

Cited By ~ 7

Author(s):

Willem A. Man in ’t Veld

Keyword(s):

Gene Flow ◽

Flow Analysis ◽

Distinct Species ◽

Phytophthora Fragariae

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Population genomics data supports introgression between western Iberian Squalius freshwater fish species

10.1101/585687 ◽

2019 ◽

Author(s):

Sofia L. Mendes ◽

Maria M. Coelho ◽

Vitor C. Sousa

Keyword(s):

Gene Flow ◽

Freshwater Fish ◽

Population Genomics ◽

Genotyping By Sequencing ◽

Population Divergence ◽

Freshwater Species ◽

Genomic Approach ◽

Demographic Modelling ◽

Paraphyletic Group ◽

First Time

AbstractIn freshwater fish, processes of population divergence and speciation are often linked to the geomorphology of rivers and lakes that isolate populations. However, current geographical isolation does not necessarily imply total absence of gene flow during the divergence process. Here, we focused on four species of the genus Squalius in Portuguese rivers: S. carolitertii, S. pyrenaicus, S. aradensis and S. torgalensis. Previous studies based on eight nuclear and mitochondrial markers revealed incongruent patterns, with nuclear loci suggesting that S. pyrenaicus was a paraphyletic group since its northern populations were genetically closer to S. carolitertii than to its southern populations. For the first time, we successfully applied a genomic approach to the study of the relationship between these species, using a Genotyping by Sequencing (GBS) approach. Our results revealed a species tree with two main lineages: (i) S. carolitertii and S. pyrenaicus; (ii) S. torgalensis and S. aradensis. Regarding S. carolitertii and S. pyrenaicus, we found evidence for past introgression between the two in the northern part of S. pyrenaicus distribution. This introgression reconciles previous mitochondrial and nuclear incongruent results and explains the apparent paraphyly of S. pyrenaicus. Our demographic modelling estimates are consistent across models, suggesting that the northern populations of S. pyrenaicus received a contribution of approximately 90% from S. carolitertii and 10% from southern S. pyrenaicus. This illustrates that even in freshwater species currently allopatric, we are able to detect past gene flow events in present-day genomes, suggesting speciation is more complex than simply allopatric.

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Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2020.1960 ◽

2020 ◽

Vol 287 (1938) ◽

pp. 20201960

Author(s):

Matheus E. Bianconi ◽

Luke T. Dunning ◽

Emma V. Curran ◽

Oriane Hidalgo ◽

Robyn F. Powell ◽

...

Keyword(s):

Gene Flow ◽

Population Genomics ◽

Nuclear Genome ◽

Its Region ◽

Grass Species ◽

Region Of Origin ◽

Ploidy Levels ◽

Lower Elevation ◽

Limited Dispersal ◽

Genome Analyses

C 4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C 4 and non-C 4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata . We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C 4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C 4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C 4 physiology away from its region of origin.

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Population genomics of Cryptosporidium hominis across five continents identifies two subspecies that have diverged and recombined during 500 years of evolution

10.1101/2021.09.09.459610 ◽

2021 ◽

Author(s):

Swapnil Tichkule ◽

Simone M. Cacciò ◽

Guy Robinson ◽

Rachel M. Chalmers ◽

Ivo Mueller ◽

...

Keyword(s):

Gene Flow ◽

Low Income ◽

Population Genomics ◽

Balancing Selection ◽

Public Health Problem ◽

High Income ◽

Secondary Contact ◽

Middle Income ◽

Middle Income Countries ◽

Low And Middle Income

AbstractCryptosporidium is a significant public health problem and one of the primary causes of diarrhoea in humans, particularly in very young children living in low- and middle-income countries. While the zoonotic Cryptosporidium parvum and anthroponotic C. hominis species collectively account for most cases globally, the latter is predominant in low- and middle-income countries. Here, we present a comprehensive whole genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two highly diverged lineages with a distinct biology and demography that have diverged circa 500 years ago. We consider these lineages as two subspecies, and provisionally propose the names C. hominis hominis (clade 1) and C. hominis aquapotentis (clade 2 or gp60 subtype IbA10G2). C. h. hominis is mostly found in low-income countries in Africa and Asia, and it appears to have recently undergone population contraction. In marked contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America and Oceania, and we reveal a signature of population expansion. Moreover, we detected genomic regions of introgression representing gene flow after a secondary contact between the subspecies from low- and high-income countries. We demonstrate that this gene flow resulted in genomic island of high diversity and divergence, and that this diversity at potential virulence genes is maintained by balancing selection, suggesting that they are involved in a coevolutionary arms race.

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