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 Premating barriers in young sympatric snail species

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arina L. Maltseva ◽  
Marina A. Varfolomeeva ◽  
Arseniy A. Lobov ◽  
Polina O. Tikanova ◽  
Egor A. Repkin ◽  
...  
Keyword(s):  
Gene Flow ◽  
Snail Species ◽  
Sympatric Populations ◽  
Gastropod Species ◽  
Shell Size ◽  
Closely Related Species ◽  
Partial Canonical Correspondence Analysis ◽  
In The Wild ◽  
Isolation Index

AbstractSympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.

scholarly journals Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence

2019 ◽  
Vol 37 (3) ◽  
pp. 668-682 ◽  
Author(s):  
Fanny E Hartmann ◽  
Ricardo C Rodríguez de la Vega ◽  
Pierre Gladieux ◽  
Wen-Juan Ma ◽  
Michael E Hood ◽  
...  
Keyword(s):  
Gene Flow ◽  
Mating Type ◽  
Sex Chromosomes ◽  
Smut Fungi ◽  
Effective Population ◽  
Closely Related Species ◽  
Fungal Mating ◽  
Anther Smut ◽  
Genomic Regions

Abstract Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.

scholarly journals Modeling the Multiple Facets of Speciation-with-Gene-Flow Towards Inferring the Divergence History of Lake Whitefish Species Pairs (Coregonus Clupeaformis)

2016 ◽  
Author(s):  
Clément Rougeux ◽  
Louis Bernatchez ◽  
Pierre-Alexandre Gagnaire
Keyword(s):  
Gene Flow ◽  
Genomic Variation ◽  
Secondary Contact ◽  
Lake Whitefish ◽  
Lineage Sorting ◽  
Effective Population ◽  
Modeling Framework ◽  
Species Pairs ◽  
History Of ◽  
And Migration

AbstractParallel divergence patterns across replicated species pairs occurring in similar environmental contrasts may arise through distinct evolutionary scenarios. Deciphering whether such parallelism actually reflects repeated parallel divergence driven by divergent selection or a single divergence event with subsequent gene flow needs to be ascertained. Reconstructing historical gene flow is therefore of fundamental interest to understand how demography and selection jointly shaped genomic divergence during speciation. Here, we use an extended modeling framework to explore the multiple facets of speciation-with-gene-flow with demo-genetic divergence models that capture both temporal and genomic variation in effective population size and migration rate. We investigate the divergence history of five sympatric Lake Whitefish limnetic (dwarf) and benthic (normal) species pairs characterized by variable degrees of ecological divergence and reproductive isolation. Genome-wide SNPs were used to document the extent of genetic differentiation in each species pair, and 26 divergence models were fitted and compared to the unfolded joint allele frequency spectrum of each pair. We found evidence that a recent (circa 3000-4000 generations) asymmetrical secondary contact between expanding post-glacial populations has accompanied Whitefish diversification. Our results suggest that heterogeneous genomic differentiation patterns have emerged through the combined effects of linked selection generating variable rates of lineage sorting across the genome during geographical isolation, and heterogeneous introgression eroding divergence at different rates across the genome upon secondary contact. This study thus provides a new retrospective insight into the historical demographic and selective processes that shaped a continuum of divergence associated with ecological speciation.

scholarly journals Speciation in the face of gene flow within the toothed whale superfamily Delphinoidea

2020 ◽  
Author(s):  
Michael V Westbury ◽  
Andrea A. Cabrera ◽  
Alba Rey-Iglesia ◽  
Binia De Cahsan ◽  
Stefanie Hartmann ◽  
...  
Keyword(s):  
Gene Flow ◽  
Marine Species ◽  
Interspecific Gene Flow ◽  
Ancestral Gene ◽  
Multifaceted Approach ◽  
Ecological Barriers ◽  
The Face ◽  
Toothed Whale ◽  
Bifurcation Process

AbstractUnderstanding speciation is a central aspect in Biology. The formation of new species was once thought to be a simple bifurcation process. However, recent advances in genomic resources now provide the opportunity to investigate the role of post-divergence gene flow in the speciation process. The diversification of lineages in the presence of gene flow appears almost paradoxical. However, with enough time and in the presence of incomplete physical and/or ecological barriers to gene flow, speciation can and does occur. Speciation without complete isolation seems especially likely to occur in highly mobile, wide ranging marine species, such as cetaceans, which face limited geographic barriers. The toothed whale superfamily Delphinoidea represents a good example to further explore speciation in the presence of interspecific gene flow. Delphinoidea consists of three families (Delphinidae, Phocoenidae, and Monodontidae) and within all three families, contemporary interspecific hybrids have been reported. Here, we utilise publicly available genomes from nine species, representing all three families, to investigate signs of post-divergence gene flow across their genomes, and to address the speciation processes that led to the diversity seen today within Delphinoidea. We use a multifaceted approach including: (i) phylogenetics, (ii) the distribution of shared derived alleles, and (iii) demography-based. We find that the divergence and evolution of lineages in Delphinoidea did not follow a simple bifurcating pattern, but were much more complex. Our results indicate multiple, long-lasting ancestral gene flow events both within and among families, which continued for millions of years after initial divergence.

scholarly journals Interspecific gene flow and maintenance of species integrity in oaks

2014 ◽  
Vol 0 (0) ◽  
pp. 1 ◽  
Author(s):  
Oliver Gailing ◽  
Alexandru Lucian Curtu
Keyword(s):  
Gene Flow ◽  
Interspecific Gene Flow ◽  
Species Integrity

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 Rampant genome-wide admixture across the Heliconius radiation

2021 ◽  
Author(s):  
Krzysztof M Kozak ◽  
Mathieu Joron ◽  
W Owen McMillan ◽  
Chris D Jiggins
Keyword(s):  
Gene Flow ◽  
Phylogenetic Networks ◽  
Adaptive Traits ◽  
Closely Related Species ◽  
Interspecific Gene Flow ◽  
Genomic Representation ◽  
Genome Wide ◽  
Wing Patterns ◽  
New Evidence ◽  
Complete Genomic

Abstract How frequent is gene flow between species? The pattern of evolution is typically portrayed as a phylogenetic tree, yet gene flow between good species may be an important mechanism in diversification, spreading adaptive traits and leading to a complex pattern of phylogenetic incongruence. This process has thus far been studied mainly among a few closely related species, or in geographically restricted areas such as islands, but not on the scale of a continental radiation. Using a nearly complete genomic representation of 47 species in the genus, we demonstrate that admixture has played a role throughout the evolution of the charismatic Neotropical butterflies Heliconius. Modeling of phylogenetic networks based on the exome uncovers up to 13 instances of interspecific gene flow. Admixture is detected among the relatives of H. erato, as well as between the ancient lineages leading to modern clades. Interspecific gene flow played a role throughout the evolution of the genus, although the process has been most frequent in the clade of H. melpomene and relatives. We identify H. hecalesia and relatives as putative hybrids, including new evidence for introgression at the loci controlling the mimetic wing patterns. Models accounting for interspecific gene flow yield a more complete picture of the radiation as a network, which will improve our ability to study trait evolution in a realistic comparative framework.

scholarly journals Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity

2019 ◽  
Author(s):  
Rowan J. Schley ◽  
R. Toby Pennington ◽  
Oscar Alejandro Pérez-Escobar ◽  
Andrew J. Helmstetter ◽  
Manuel de la Estrella ◽  
...  
Keyword(s):  
Gene Flow ◽  
Incomplete Lineage Sorting ◽  
Gene Tree ◽  
Reticulate Evolution ◽  
Specific Gene ◽  
Lineage Sorting ◽  
Closely Related Species ◽  
Genome Wide ◽  
High Degree ◽  
Prevailing View

AbstractHybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of species undergoing inter-specific gene flow. However, hybridization in Amazonia’s megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by introgression, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ∼19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species which co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and a persistence of hybridization over time. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization’s rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.

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