scholarly journals Estimating the temporal and spatial extent of gene flow among sympatric lizard populations (genus Sceloporus) in the southern Mexican highlands

2014 ◽  
Author(s):  
Jared A Grummer ◽  
Martha L. Calderón ◽  
Adrián Nieto Montes-de Oca ◽  
Eric N Smith ◽  
Fausto Méndez-de la Cruz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Ancestral Population ◽  
Secondary Contact ◽  
Sympatric Populations ◽  
Interspecific Gene Flow ◽  
Ancestral Gene ◽  
Mixed Support ◽  
Coalescent Simulations ◽  
Range Overlap ◽  
Analytical Approaches

Interspecific gene flow is pervasive throughout the tree of life. Although detecting gene flow between populations has been facilitated by new analytical approaches, determining the timing and geography of hybridization has remained difficult, particularly for historical gene flow. A geographically explicit phylogenetic approach is needed to determine the ancestral population overlap. In this study, we performed population genetic analyses, species delimitation, simulations, and a recently developed approach of species tree diffusion to infer the phylogeographic history, timing and geographic extent of gene flow in lizards of the Sceloporus spinosus group. The two species in this group, S. spinosus and S. horridus, are distributed in eastern and western portions of Mexico, respectively, but populations of these species are sympatric in the southern Mexican highlands. We generated data consisting of three mitochondrial genes and eight nuclear loci for 148 and 68 individuals, respectively. We delimited six lineages in this group, but found strong evidence of mito-nuclear discordance in sympatric populations of S. spinosus and S. horridus owing to mitochondrial introgression. We used coalescent simulations to differentiate ancestral gene flow from secondary contact, but found mixed support for these two models. Bayesian phylogeography indicated more than 60% range overlap between ancestral S. spinosus and S. horridus populations since the time of their divergence. Isolation-migration analyses, however, revealed near-zero levels of gene flow between these ancestral populations. Interpreting results from both simulations and empirical data indicate that despite a long history of sympatry among these two species, gene flow in this group has only recently occurred.

scholarly journals Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

2020 ◽  
Author(s):  
Athene Giesen ◽  
Wolf U. Blanckenhorn ◽  
Martin A. Schäfer ◽  
Kentaro K. Shimizu ◽  
Rie Shimizu-Inatsugi ◽  
...  
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Species Boundaries ◽  
Adaptive Divergence ◽  
Sympatric Populations ◽  
Interspecific Gene Flow ◽  
Natural Systems ◽  
Sequence Identity ◽  
Interspecific Differences ◽  
Genome Wide

ABSTRACTInterspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but can also initiate reinforcement of reproductive isolation trough natural and sexual selection. The extent of interspecific gene flow and its consequences for the initiation and maintenance of species barriers in natural systems remain poorly understood, however. To assess genome-wide patterns of gene flow between the two closely related European dung fly species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae), we tested for historical gene flow with the aid of ABBA-BABA test using whole-genome resequencing data from pooled DNA of male specimens originating from natural and laboratory populations. We contrasted genome-wide variation in DNA sequence differences between samples from sympatric populations of the two species in France and Switzerland with that of interspecific differences between pairs of samples involving allopatric populations from Estonia and Italy. In the French Cevennes, we detected a relative excess of DNA sequence identity, suggesting interspecific gene flow in sympatry. In contrast, at two sites in Switzerland, we observed a relative depletion of DNA sequence identity compatible with reinforcement of species boundaries in sympatry. Our results suggest that the species boundaries between S. cynipsea and S. neocynipsea in Europe depend on the eco-geographic context.

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 Can secondary contact following range expansion be distinguished from barriers to gene flow?

2016 ◽  
Author(s):  
Johanna Bertl ◽  
Harald Ringbauer ◽  
Michael G. B. Blum
Keyword(s):  
Gene Flow ◽  
Range Expansion ◽  
Isolation By Distance ◽  
Molecular Data ◽  
Secondary Contact ◽  
Evolutionary Scenario ◽  
Coalescent Simulations ◽  
Distance Model ◽  
Northward Expansion ◽  
Spatio Temporal

AbstractSecondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of Linkage Disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index Ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.

scholarly journals Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros

2020 ◽  
Vol 37 (11) ◽  
pp. 3105-3117 ◽  
Author(s):  
Yoshan Moodley ◽  
Michael V Westbury ◽  
Isa-Rita M Russo ◽  
Shyam Gopalakrishnan ◽  
Andrinajoro Rakotoarivelo ◽  
...  
Keyword(s):  
Gene Flow ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Early Pleistocene ◽  
Secondary Contact ◽  
Feeding Strategies ◽  
Ecological Specialization ◽  
Ancestral Gene ◽  
Black And White ◽  
White Rhinoceros

Abstract Africa’s black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa’s Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.

scholarly journals Complex introgression history of the erato-sara clade of Heliconius butterflies

2021 ◽  
Author(s):  
Yuttapong Thawornwattana ◽  
Fernando A. Seixas ◽  
Ziheng Yang ◽  
James Mallet
Keyword(s):  
Gene Flow ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Hybrid Origin ◽  
Ancestral Population ◽  
Ancestral Gene ◽  
Species Phylogeny ◽  
Full Likelihood ◽  
History Of

AbstractIntrogression plays a key role in adaptive evolution and species diversification in many groups of species including Heliconius butterflies. However, frequent hybridization and subsequent gene flow between species makes estimation of the species phylogeny challenging. Here, we infer species phylogeny and introgression events from whole-genome sequence data of six members of the erato-sara clade of Heliconius using a multispecies coalescent model with introgression (MSci) and an isolation-with-migration (IM) model. These approaches probabilistically capture the genealogical heterogeneity across the genome due to introgression and incomplete lineage sorting in a full likelihood framework. We detect robust signals of introgression across the genome, and estimate the direction, timing and magnitude of each introgression event. The results clarify several processes of speciation and introgression in the erato-sara group. In particular, we confirm ancestral gene flow between the sara clade and an ancestral population of H. telesiphe, a hybrid origin of H. hecalesia, and gene flow between the sister species H. erato and H. himera. The ability to confidently infer the presence, timing and magnitude of introgression events using genomic sequence data is helpful for understanding speciation in the presence of gene flow and will be useful for understanding the adaptive consequences of introgressed regions of the genome. Our analysis serves to highlight the power of full likelihood methods under the MSci model to the history of species divergence and cross-species introgression from genome-scale data.

scholarly journals Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

2021 ◽  
Author(s):  
Athene Giesen ◽  
Wolf Blanckenhorn ◽  
Martin Schäfer ◽  
Kentaro K. Shimizu ◽  
Rie Shimizu-Inatsugi ◽  
...  
Keyword(s):  
Gene Flow ◽  
Dna Sequence ◽  
Species Boundaries ◽  
Adaptive Divergence ◽  
Sympatric Populations ◽  
Interspecific Gene Flow ◽  
Natural Systems ◽  
Sequence Identity ◽  
Interspecific Differences ◽  
Genome Wide

Interspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but can also initiate reinforcement of reproductive isolation trough natural and sexual selection. The extent of interspecific gene flow and its consequences for the initiation and maintenance of species barriers in natural systems remain poorly understood, however. To assess genome-wide patterns of gene flow between the two closely related European dung fly species Sepsis cynipsea and Sepsis neocynipsea (Diptera: Sepsidae), we tested for historical gene flow with the aid of ABBA-BABA test using whole-genome resequencing data from pooled DNA of male specimens originating from natural and laboratory populations. We contrasted genome-wide variation in DNA sequence differences between samples from sympatric populations of the two species in France and Switzerland with that of interspecific differences between pairs of samples involving allopatric populations from Estonia and Italy. In the French Cevennes, we detected a relative excess of DNA sequence identity, suggesting interspecific gene flow in sympatry. In contrast, at two sites in Switzerland, we observed a relative depletion of DNA sequence identity compatible with reinforcement of species boundaries in sympatry. Our results suggest that the species boundaries between S. cynipsea and S. neocynipsea in Europe depend on the eco-geographic context.

scholarly journals Maintaining their genetic distance; limited gene flow between widely hybridising species of Geum with contrasting mating systems

2017 ◽  
Author(s):  
Crispin Y. Jordan ◽  
Konrad Lohse ◽  
Frances Turner ◽  
Marian Thomson ◽  
Karim Gharbi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Mating System ◽  
Draft Genome ◽  
Sympatric Populations ◽  
Species Classification ◽  
Interspecific Gene Flow ◽  
System Transition ◽  
Tentative Evidence ◽  
Limited Gene Flow

AbstractMating system transition from outcrossing to selfing frequently gives rise to sister lineages with contrasting outcrossing rates. The evolutionary fate of such lineages depends on the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, two sister species derived by mating system transition, which frequently hybridise. A draft genome was generated for G. urbanum and used to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the two species diverged 2-3 Mya, and that long term gene flow between them has been very low (M=0.04). G. rivale showed greater genetic diversity in sympatry than allopatry, but genetic divergence between species was no lower in sympatry than allopatry, providing little evidence for recent introgression. Clustering of genotypes revealed that, apart from four early generation hybrids, individuals in sympatric populations fell into two genetically distinct groups with <1% admixture that corresponded exactly to their morphological species classification. Although our data suggest limited gene flow, we observed joint segregation of two putatively introgressed SNPs in G. urbanum populations that was associated with significant morphological variation; this provides tentative evidence for rare introduction of novel genetic diversity by interspecific gene flow. Our results indicate that despite frequent hybridisation, genetic exchange between G. rivale and G. urbanum has been very limited throughout their evolutionary history.

scholarly journals Can secondary contact following range expansion be distinguished from barriers to gene flow?

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5325 ◽  
Author(s):  
Johanna Bertl ◽  
Harald Ringbauer ◽  
Michael G.B. Blum
Keyword(s):  
Gene Flow ◽  
Range Expansion ◽  
Isolation By Distance ◽  
Molecular Data ◽  
Secondary Contact ◽  
Evolutionary Scenario ◽  
Coalescent Simulations ◽  
Distance Model ◽  
Northward Expansion ◽  
Spatio Temporal

Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.

Interspecific gene flow and an intermediate molecular profile of Dyckia julianae (Bromeliaceae), an endemic species from southern Brazil

2019 ◽  
Vol 192 (4) ◽  
pp. 675-690 ◽  
Author(s):  
Luiza D Hirsch ◽  
Camila M Zanella ◽  
Camila Aguiar-Melo ◽  
Laís M S Costa ◽  
Fernanda Bered
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
The Other ◽  
Hybrid Origin ◽  
Molecular Profile ◽  
Southern Brazil ◽  
Sympatric Populations ◽  
Interspecific Gene Flow ◽  
Viable Seeds ◽  
Origin Hypothesis

Abstract When related species are distributed in sympatric populations, hybridization may occur. Likewise, one or more of these species may have arisen through historical hybridization between taxa. Here, we aim to elucidate the occurrence of hybridization among three Dyckia spp. (Bromeliaceae) from southern Brazil. We used seven nuclear and six plastid microsatellite loci to assess patterns of genetic diversity, population structure and hybridization in the three species. Furthermore, we performed manual crosses between species to test compatibility and fertility. The results showed that Dyckia julianae has an intermediate molecular profile, low gene flow occurs between Dyckia hebdingii and Dyckia choristaminea and higher gene flow occurs between D. julianae and the other two species. Plastid microsatellites identified 12 haplotypes that are shared among the species. The manual crosses between D. julianae and the other two species produced viable seeds, but no crosses between D. hebdingii and D. choristaminea generated fruits. Our data suggest that the reproductive barrier between D. julianae and the other two species is permeable. Further investigation into the hybrid origin hypothesis of D. julianae should be undertaken, as well as the mechanisms involved in reproductive isolation between D. hebdingii and D. choristaminea.

scholarly journals Gene duplicates cause hybrid lethality between sympatric species of Mimulus

2017 ◽  
Author(s):  
Matthew P. Zuellig ◽  
Andrea L. Sweigart
Keyword(s):  
Gene Flow ◽  
Critical Role ◽  
Sympatric Species ◽  
Mimulus Guttatus ◽  
Sympatric Populations ◽  
Genetic Incompatibility ◽  
Interspecific Gene Flow ◽  
Evolutionary Forces ◽  
Photosynthetic Gene ◽  
Functional Copy

AbstractHybrid incompatibilities play a critical role in the evolution and maintenance of species. We have discovered a simple genetic incompatibility that causes lethality in hybrids between two closely related species of yellow monkeyflower (Mimulus guttatus and M. nasutus). This hybrid incompatibility, which causes one sixteenth of F2 hybrid seedlings to lack chlorophyll and die shortly after germination, occurs between sympatric populations that are connected by ongoing interspecific gene flow. Using complimentary genetic mapping and gene expression analyses, we show that lethality occurs in hybrids that lack a functional copy of the critical photosynthetic gene pTAC14. In M. guttatus, this gene was duplicated, but the ancestral copy is no longer expressed. In M. nasutus, the duplication is missing altogether. As a result, hybrids die when they are homozygous for the nonfunctional M. guttatus copy and missing the duplicate from M. nasutus, apparently due to misregulated transcription of key photosynthetic genes. Our study indicates that neutral evolutionary processes may play an important role in the evolution of hybrid incompatibilities and opens the door to direct investigations of their contribution to reproductive isolation among naturally hybridizing species.Author SummaryHybrid incompatibilities play an important role in speciation, because they act to limit gene flow between species. Identifying the genes that underlie these barriers sheds light on the evolutionary forces and genetic mechanisms that give rise to new species. We identified a reproductive barrier that causes lethality in the F2 offspring of sympatric species of yellow monkeyflower (Mimulus guttatus and M. nasutus). We show that lethality occurs in hybrids that lack a functional copy of the critical photosynthetic gene pTAC14. This gene was duplicated in M. guttatus, but the ancestral copy subsequently lost function. In M. nasutus, no duplication occurred. As a consequence, F2 hybrids that are homozygous for non-functional M. guttatus copies at one locus and missing M. nasutus duplicates at the other locus completely lack functional pTAC14 and die. Our data indicate that non-functionalization of ancestral pTAC14 in M. guttatus occurred via neutral evolutionary change. These results suggest that neutral evolutionary forces may play an important role in speciation.

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