Divergence and hybridization in sea turtles: inferences from genome data show evidence of ancient gene flow between species

Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of gene flow that result in a mosaic of phylogenetic signals that interact with recombinational variation. Here we tested the validity of this assumption with a recombination-aware analysis of whole genome sequences from 27 species of the cat family. We found that the prevailing phylogenetic signal within the autosomes is not always representative of speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within large, conserved X-chromosome recombination deserts that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ~40%. We conclude that standard phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic partitioning of phylogenetic signal relative to recombination rate, and its interplay with historical hybridization.

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Approximate Bayesian computation untangles signatures of contemporary and historical hybridization between two endangered species

10.1101/2021.02.24.432626 ◽

2021 ◽

Author(s):

Hannes Dittberner ◽

Aurelien Tellier ◽

Juliette de Meaux

Keyword(s):

Gene Flow ◽

Endangered Species ◽

Approximate Bayesian Computation ◽

Bayesian Computation ◽

Sympatric Population ◽

Genome Data ◽

Contemporary Gene Flow ◽

History Of ◽

Low Levels ◽

Approximate Bayesian

ABSTRACTContemporary gene flow, when resumed after a period of isolation, can have crucial consequences for endangered species, as it can both increase the supply of adaptive alleles and erode local adaptation. Determining the history of gene flow and thus the importance of contemporary hybridization, however, is notoriously difficult. Here, we focus on two endangered plant species, Arabis nemorensis and A. sagittata, which hybridize naturally in a sympatric population located on the banks of the Rhine. Using reduced genome sequencing, we determined the phylogeography of the two taxa but report only a unique sympatric population. Molecular variation in chloroplast DNA indicated that A. sagittata is the principal receiver of gene flow. Applying classical D-statistics and its derivatives to whole-genome data of 35 accessions, we detect gene flow not only in the sympatric population but also among allopatric populations. Using an Approximate Bayesian computation approach, we identify the model that best describes the history of gene flow between these taxa. This model shows that low levels of gene flow have persisted long after speciation. Around 10 000 years ago, gene flow stopped and a period of complete isolation began. Eventually, a hotspot of contemporary hybridization was formed in the unique sympatric population. Occasional sympatry may have helped protect these lineages from extinction in spite of their extremely low diversity.

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Ancient gene flow from early modern humans into Eastern Neanderthals

Nature ◽

10.1038/nature16544 ◽

2016 ◽

Vol 530 (7591) ◽

pp. 429-433 ◽

Cited By ~ 229

Author(s):

Martin Kuhlwilm ◽

Ilan Gronau ◽

Melissa J. Hubisz ◽

Cesare de Filippo ◽

Javier Prado-Martinez ◽

...

Keyword(s):

Gene Flow ◽

Early Modern ◽

Modern Humans ◽

Early Modern Humans ◽

Ancient Gene

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Complex population structure of the Atlantic puffin revealed by whole genome analyses

10.1101/2020.11.05.351874 ◽

2020 ◽

Author(s):

Oliver Kersten ◽

Bastiaan Star ◽

Deborah M. Leigh ◽

Tycho Anker-Nilssen ◽

Hallvard Strøm ◽

...

Keyword(s):

Population Structure ◽

Gene Flow ◽

Isolation By Distance ◽

Spatial Scales ◽

Secondary Contact ◽

Whole Genome ◽

Genome Data ◽

Complex Population ◽

Genome Analyses ◽

Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

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Inversions shape the divergence of Drosophila pseudoobscura and D. persimilis on multiple timescales

10.1101/842047 ◽

2019 ◽

Cited By ~ 2

Author(s):

Katharine L Korunes ◽

Carlos A Machado ◽

Mohamed AF Noor

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Sequence Data ◽

Sequence Divergence ◽

Whole Genome Sequence ◽

Drosophila Pseudoobscura ◽

Ancestral Polymorphism ◽

Chromosomal Inversions ◽

History Of ◽

Ancient Gene

AbstractBy shaping meiotic recombination, chromosomal inversions can influence genetic exchange between hybridizing species. Despite the recognized importance of inversions in evolutionary processes such as divergence and speciation, teasing apart the effects of inversions over time remains challenging. For example, are their effects on sequence divergence primarily generated through creating blocks of linkage-disequilibrium pre-speciation or through preventing gene flux after speciation? We provide a comprehensive look into the influence of chromosomal inversions on gene flow throughout the evolutionary history of a classic system: Drosophila pseudoobscura and D. persimilis. We use extensive whole-genome sequence data to report patterns of introgression and divergence with respect to chromosomal arrangements. Overall, we find evidence that inversions have contributed to divergence patterns between Drosophila pseudoobscura and D. persimilis over three distinct timescales: 1) pre-speciation segregation of ancestral polymorphism, 2) post-speciation ancient gene flow, and 3) recent gene flow. We discuss these results in terms of our understanding of evolution in this classic system and provide cautions for interpreting divergence measures in similar datasets in other systems.

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The genetic structure of the spectacled bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers

Journal of Mammalogy ◽

10.1093/jmammal/gyaa082 ◽

2020 ◽

Vol 101 (4) ◽

pp. 1072-1090

Author(s):

Manuel Ruiz-García ◽

Jessica Yanina Arias Vásquez ◽

Héctor Restrepo ◽

Carlos Herney Cáceres-Martínez ◽

Joseph Mark Shostell

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Isolation By Distance ◽

Phylogenetic Analyses ◽

Population Expansion ◽

Sudden Expansion ◽

Population Decrease ◽

Geographical Regions ◽

Show Evidence

Abstract The spectacled bear (Ursidae: Tremarctos ornatus) is an emblematic umbrella species and one of the top carnivores in the Andean mountains. It is also listed as vulnerable by IUCN and as endangered by CITES. We analyzed the genetic structure of this species in nine geographical regions representing the three Andean Cordilleras in Colombia. We sequenced six mitochondrial genes in 115 spectacled bears; a subset of these specimens (n = 61) were genotyped at seven nuclear microsatellites. We addressed three objectives: 1) determine the genetic diversity and historical demographic changes of the spectacled bear in Colombia; 2) determine phylogeographic patterns of genetic divergence among spectacled bear populations in Colombia; and 3) estimate the levels of gene flow among different regions of Colombia. Our analyses show evidence of high mitochondrial genetic diversity in spectacled bears, both in Colombia as well as in each of the nine regions, most particularly Norte de Santander, Nariño, and Antioquia-Córdoba. In addition, we detected population expansion in Colombia that occurred around 24,000 years ago, followed by a population decrease during the last 7,000 years, and a sudden expansion in the last 300 years. Phylogenetic analyses showed few well-supported clades, with some haplotypes detected in all the departments and Colombian Andean Cordilleras, and other haplotypes restricted to certain geographical areas (Antioquia, Norte de Santander, Cundinamarca, and Nariño). We detected significant genetic heterogeneity among some departments and among the three Colombian Andean Cordilleras for both mitochondrial and nuclear genes. Nevertheless, the moderate levels of gene flow estimated from FST statistics suggest that geographical barriers have not been definitive obstacles to the dispersion of the spectacled bear throughout Colombia. Despite these gene flow estimates, significant spatial autocorrelation was detected for spectacled bear in Colombia, where two kinds of spatial patterns were discovered: genetic patches of 144 km of diameter, and isolation by distance among bears separated from 578 to 800 km. The two most northern spectacled bear populations of Colombia (Norte de Santander and Antioquia) also were the two most differentiated. Their distinctiveness may qualify them as distinct Management Units (MUs) in the context of conservation policies for the spectacled bear in Colombia.

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Ancient Gene Duplication and Differential Gene Flow in Plastid Lineages: The GroEL/Cpn60 Example

Journal of Molecular Evolution ◽

10.1007/pl00006438 ◽

1999 ◽

Vol 48 (1) ◽

pp. 112-117 ◽

Cited By ~ 15

Author(s):

Jürgen Wastl ◽

Martin Fraunholz ◽

Stefan Zauner ◽

Susan Douglas ◽

Uwe-G. Maier

Keyword(s):

Gene Flow ◽

Gene Duplication ◽

Differential Gene ◽

Ancient Gene ◽

Ancient Gene Duplication

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Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq

10.1101/625848 ◽

2019 ◽

Author(s):

Maria Luisa Martin Cerezo ◽

Marek Kucka ◽

Karol Zub ◽

Yingguang Frank Chan ◽

Jarosław Bryk

Keyword(s):

Population Structure ◽

Restriction Site ◽

Population Genomics ◽

Large Degree ◽

Apodemus Flavicollis ◽

Ecological Genomics ◽

Genome Data ◽

Northern Poland ◽

Show Evidence ◽

History Of

AbstractBackgroundMice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context.ResultsHere we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST < 0.086.ConclusionOur study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

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Paracoccidioides genomes reflect high levels of species divergence and little interspecific gene flow

10.1101/2020.07.16.204636 ◽

2020 ◽

Author(s):

Heidi Mavengere ◽

Katlheen Mattox ◽

Marcus M Teixeira ◽

Victoria E. Sepúlveda ◽

Oscar M. Gomez ◽

...

Keyword(s):

Gene Flow ◽

Fungal Pathogens ◽

Fungal Species ◽

Species Boundaries ◽

Whole Genome ◽

Gene Exchange ◽

Interspecific Gene Flow ◽

Systematic Effort ◽

Species Pairs ◽

Show Evidence

ABSTRACTThe fungus Paracoccidioides spp. is a prevalent human pathogen endemic to South America. The genus is composed of five species. In this report, we use 37 whole genome sequences to study the allocation of genetic variation in Paracoccidioides. We tested three genome-wide predictions of advanced speciation, namely, that all species should be reciprocally monophyletic, that species pairs should be highly differentiated along the whole genome, and that there should be low rates of interspecific gene exchange. We find support for these three hypotheses. Species pairs with older divergences show no evidence of gene exchange, while more recently diverged species pairs show evidence of modest rates of introgression. Our results indicate that as divergence progresses, species boundaries become less porous among Paracoccidioides species. Our results suggest that species in Paracoccidioides are at different stages along the divergence continuum.IMPORTANCEParacoccidioides is the causal agent of the most frequent systemic mycosis in Latin America. Most of the inference of the evolutionary history of Paracoccidioides has used only a handful of molecular markers. In this report, we evaluate the extent of genome divergence among Paracoccidioides species and study the possibility of interspecific gene exchange. We find that all species are highly differentiated. We also find that the amount of gene flow between species is low and in some cases even completely absent in spite of geographic overlap. Our study constitutes a systematic effort to identify species boundaries in fungal pathogens, and determine the extent of gene exchange among fungal species.

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