scholarly journals Low‐coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

2020 ◽  
Vol 29 (19) ◽  
pp. 3649-3666
Author(s):  
Lisa Cooper ◽  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
James M. Cook ◽  
Konrad Lohse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rain Forest ◽  
Genomic Data ◽  
Population Divergence ◽  
Fig Wasp ◽  
History Of ◽  
Low Coverage

scholarly journals Low coverage genomic data resolve the population divergence and gene flow history of an Australian rain forest fig wasp

2020 ◽  
Author(s):  
Lisa Cooper ◽  
Lynsey Bunnefeld ◽  
Jack Hearn ◽  
James M Cook ◽  
Konrad Lohse ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rain Forest ◽  
Sequence Data ◽  
Dry Forest ◽  
Whole Genome Sequence ◽  
Model Organisms ◽  
Eastern Coast ◽  
Population Divergence ◽  
Fig Wasp ◽  
History Of

AbstractPopulation divergence and gene flow are key processes in evolution and ecology. Model-based analysis of genome-wide datasets allows discrimination between alternative scenarios for these processes even in non-model taxa. We used two complementary approaches (one based on the blockwise site frequency spectrum (bSFS), the second on the Pairwise Sequentially Markovian Coalescent (PSMC)) to infer the divergence history of a fig wasp, Pleistodontes nigriventris. Pleistodontes nigriventris and its fig tree mutualist Ficus watkinsiana are restricted to rain forest patches along the eastern coast of Australia, and are separated into northern and southern populations by two dry forest corridors (the Burdekin and St. Lawrence Gaps). We generated whole genome sequence data for two haploid males per population and used the bSFS approach to infer the timing of divergence between northern and southern populations of P. nigriventris, and to discriminate between alternative isolation with migration (IM) and instantaneous admixture (ADM) models of post divergence gene flow. Pleistodontes nigriventris has low genetic diversity (π = 0.0008), to our knowledge one of the lowest estimates reported for a sexually reproducing arthropod. We find strongest support for an ADM model in which the two populations diverged ca. 196kya in the late Pleistocene, with almost 25% of northern lineages introduced from the south during an admixture event ca. 57kya. This divergence history is highly concordant with individual population demographies inferred from each pair of haploid males using PSMC. Our analysis illustrates the inferences possible with genome-level data for small population samples of tiny, non-model organisms and adds to a growing body of knowledge on the population structure of Australian rain forest taxa.

scholarly journals Phylogeographic Inference Using Approximate Likelihoods

2015 ◽  
Author(s):  
Brian C O'Meara ◽  
Nathan D Jackson ◽  
Ariadna E Morales-Garcia ◽  
Bryan C Carstens
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
A Priori ◽  
Evolutionary Process ◽  
Population Divergence ◽  
Parameter Estimates ◽  
Single Model ◽  
History Of ◽  
Tree Methods

The demographic history of most species is complex, with multiple evolutionary processes combining to shape the observed patterns of genetic diversity. To infer this history, the discipline of phylogeography has (to date) used models that simplify the historical demography of the focal organism, for example by assuming or ignoring ongoing gene flow between populations or by requiring a priori specification of divergence history. Since no single model incorporates every possible evolutionary process, researchers rely on intuition to choose the models that they use to analyze their data. Here, we develop an approach to circumvent this reliance on intuition. PHRAPL allows users to calculate the probability of a large number of demographic histories given their data, enabling them to identify the optimal model and produce accurate parameter estimates for a given system. Using PHRAPL, we reanalyze data from 19 recent phylogeographic investigations. Results indicate that the optimal models for most datasets parameterize both gene flow and population divergence, and suggest that species tree methods (which do not consider gene flow) are overly simplistic for most phylogeographic systems. These results highlight the importance of phylogeographic model selection, and reinforce the role of phylogeography as a bridge between population genetics and phylogenetics.

scholarly journals Extensive Interspecific Gene Flow Shaped Complex Evolutionary History and Underestimated Species Diversity in Rapidly Radiated Dolphins

2021 ◽  
Author(s):  
Weijian Guo ◽  
Di Sun ◽  
Yang Cao ◽  
Linlin Xiao ◽  
Xin Huang ◽  
...  
Keyword(s):  
Gene Flow ◽  
Bayesian Methods ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Genomic Data ◽  
Sliding Window ◽  
Interspecific Gene Flow ◽  
History Of ◽  
Relationship Of

AbstractRecently diverged taxa are often characterized by high rates of hybridization, which can complicate phylogenetic reconstruction. For this reason, the phylogenetic relationships and evolutionary history of dolphins are still not very well resolved; the question of whether the genera Tursiops and Stenella are monophyletic is especially controversial. Here, we performed re-sequencing of six dolphin genomes and combined them with eight previously published dolphin SRA datasets and six whole-genome datasets to investigate the phylogenetic relationships of dolphins and test the monophyly hypothesis of Tursiops and Stenella. Phylogenetic reconstruction with the maximum likelihood and Bayesian methods of concatenated loci, as well as with coalescence analyses of sliding window trees, produced a concordant and well-supported tree. Our studies support the non-monophyletic status of Tursiops and Stenella because the species referred these genera do not form exclusive monophyletic clades. This suggests that the current taxonomy of both genera might not reflect their evolutionary history and may underestimate their diversity. A four-taxon D-statistic (ABBA-BABA) test, five-taxon DFOIL test, and tree-based PhyloNet analyses all showed extensive gene flow across dolphin species, which could explain the instability in resolving phylogenetic relationship of oceanic dolphins with different and limited markers. This study could be a good case to demonstrate how genomic data can reveal complex speciation and phylogeny in rapidly radiating animal groups.

scholarly journals Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Gang Wang ◽  
Xingtan Zhang ◽  
Edward Allen Herre ◽  
Doyle McKey ◽  
Carlos A. Machado ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genomic Data ◽  
Host Switching ◽  
Fig Wasp ◽  
Chloroplast Genomes ◽  
Dominant Feature ◽  
Pollination Mutualism ◽  
History Of ◽  
Coevolutionary History

AbstractFicus (figs) and their agaonid wasp pollinators present an ecologically important mutualism that also provides a rich comparative system for studying functional co-diversification throughout its coevolutionary history (~75 million years). We obtained entire nuclear, mitochondrial, and chloroplast genomes for 15 species representing all major clades of Ficus. Multiple analyses of these genomic data suggest that hybridization events have occurred throughout Ficus evolutionary history. Furthermore, cophylogenetic reconciliation analyses detect significant incongruence among all nuclear, chloroplast, and mitochondrial-based phylogenies, none of which correspond with any published phylogenies of the associated pollinator wasps. These findings are most consistent with frequent host-switching by the pollinators, leading to fig hybridization, even between distantly related clades. Here, we suggest that these pollinator host-switches and fig hybridization events are a dominant feature of fig/wasp coevolutionary history, and by generating novel genomic combinations in the figs have likely contributed to the remarkable diversity exhibited by this mutualism.

scholarly journals Mitochondrial-nuclear interactions maintain geographic separation of deeply diverged mitochondrial lineages in the face of nuclear gene flow

2016 ◽  
Author(s):  
Hernán E. Morales ◽  
Alexandra Pavlova ◽  
Nevil Amos ◽  
Richard Major ◽  
Andrzej Kilian ◽  
...  
Keyword(s):  
Gene Flow ◽  
Nuclear Gene ◽  
Population Divergence ◽  
Direct Role ◽  
Genome Wide ◽  
Mitochondrial Functions ◽  
The Face ◽  
History Of ◽  
Nuclear Differentiation ◽  
Geographic Separation

AbstractMetabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could play a direct role in population divergence. We studied the evolution of mitonuclear interactions in a widespread passerine that experienced population divergence followed by bi-directional mitochondrial introgression into different nuclear backgrounds. Using >60,000 SNPs, we quantified patterns of nuclear genetic differentiation between populations that occupy different climates and harbour deeply divergent mitolineages despite ongoing nuclear gene flow. Analyses were performed independently for two sampling transects intersecting mitochondrial divergence in different nuclear backgrounds. In both transects, low genome-wide nuclear differentiation was accompanied by strong differentiation at a ~15.4 Mb region of chromosome 1A. This region is enriched for genes performing mitochondrial functions. Molecular signatures of selective sweeps in this region alongside those in the mitochondrial genome suggest a history of adaptive mitonuclear co-introgression. The chromosome 1A region has elevated linkage disequilibrium, suggesting that selection on genomic architecture may favour low recombination among nuclear-encoded genes with mitochondrial functions. In this system, mitonuclear interactions appear to maintain the geographic separation of two mitolineages in the face of nuclear gene flow, supporting mitonuclear co-evolution as an important vehicle for climatic adaptation and population divergence.

scholarly journals Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 489
Author(s):  
Bartosz Łabiszak ◽  
Witold Wachowiak
Keyword(s):  
Gene Flow ◽  
Reticulate Evolution ◽  
Modeling Framework ◽  
Closely Related Species ◽  
Interspecific Gene Flow ◽  
Nucleotide Sequence Variation ◽  
History Of ◽  
Best Fitting ◽  
Species Integrity

Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from the Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found a great overlap of neutral variation within the P. mugo complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best-fitting model revealed P. mugo and P. uncinata as sister species with basal P. uliginosa and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of P. mugo complex to P. sylvestris than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide a genetic framework to study species integrity maintained by selection and local adaptation.

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

scholarly journals Up and Down the Blind Alley: Population Divergence with Scant Gene Flow in an Endangered Tropical Lineage of Andean Palms (Ceroxylon quindiuense Clade: Ceroxyloideae)

2017 ◽  
Vol 108 (3) ◽  
pp. 288-298 ◽  
Author(s):  
María José Sanín ◽  
Patricia Zapata ◽  
Jean-Christophe Pintaud ◽  
Gloria Galeano ◽  
Adriana Bohórquez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Divergence ◽  
Blind Alley

scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

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