Phylogeographic analysis reveals mito-nuclear discordance in Dasypterus intermedius

2020 ◽  
Vol 101 (5) ◽  
pp. 1400-1409 ◽  
Author(s):  
Sydney K Decker ◽  
Loren K Ammerman
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Sequence Data ◽  
Divergence Time ◽  
Secondary Contact ◽  
Nuclear Marker ◽  
Mitochondrial Sequence ◽  
Phylogeographic Analysis ◽  
The Family ◽  
Molecular Framework

Abstract Northern yellow bats (Dasypterus intermedius) are tree-roosting bats in the family Vespertilionidae comprised of two subspecies: D. intermedius intermedius and D. intermedius floridanus. The two subspecies are thought to be geographically separated. Due to their cryptic morphology, this hypothesis has never been tested and can benefit from being examined within a molecular framework. In this study, mitochondrial sequence data from 38 D. intermedius and nuclear sequence data from 14 D. intermedius from across their range were used to test the hypothesis that genetically defined groups correspond geographically with the two morphologically defined subspecies. Although high levels of divergence of the mitochondrial sequence (11.6%) suggest genetically distinct clusters sympatric in southern Texas, no genetic structure was recovered with the nuclear marker. Moreover, the mitochondrial sequence data recovered a paraphyletic relationship between the two subspecies of D. intermedius with the Cuban yellow bat (D. insularis), whereas no such paraphyly was recovered from analysis of the nuclear marker. Divergence time based on analyses of mitochondrial sequence for the two subspecies was approximately 5.5 Ma. The patterns observed are hypothesized to be the result of past isolation of lineages and secondary contact that is currently contributing to gene flow.

scholarly journals Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes

2014 ◽  
Author(s):  
Kimberly M Dohms ◽  
Theresa M Burg
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Sequence Data ◽  
Base Pairs ◽  
Mitochondrial Dna Control Region ◽  
Potential Barriers ◽  
Seed Crops ◽  
Wide Population

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

scholarly journals GENETIC DRIFT AND GENE FLOW IN POPULATIONS OF THE GREAT GERBILS

2018 ◽  
Vol 3 (4) ◽  
pp. 147-151
Author(s):  
V. V. Sutyagin
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Drift ◽  
Small Groups ◽  
Stochastic Matrix ◽  
Large Population ◽  
Random Fluctuation ◽  
Gene Frequencies ◽  
The Family ◽  
Different Populations

The article describes the additional evolutionary factors, apart from natural selection, which can influence the genetic structure of the  populations of the main carriers of the plague microbe – the great  gerbil. The influence of genetic drift on random fluctuation of alleles  is considered. With the help of a stochastic matrix, on the example  of the family group of gerbils consisting of four individuals, the  probabilities of the transition of allele frequencies from parents to  offspring are calculated. Based on the previously calculated size of  the neighborhood in gerbils, it is concluded that any large population  of great gerbils can be considered as small in terms of deviation of gene frequencies. In such small groups – parcels –  the drift of genes will be of great importance. In addition, the effect  of the gene flow on the genetic structure of the gerbil population on  the example of the simplest population model “continent-island” is  considered. The dynamics of changes in allelic frequencies for 100  generations has been calculated. It is shown that the allele  frequency during the 20-30 generations changes at the maximum  rate, and then slows as the equilibrium is approached. It is  concluded that different populations of gerbils should be considered  as separate historically formed structures, with different sequence of influence of external environmental factors on them.

scholarly journals A Distance Method to Reconstruct Species Trees In the Presence of Gene Flow

2014 ◽  
Author(s):  
Lingfei Cui ◽  
Laura Kubatko
Keyword(s):  
Gene Flow ◽  
Evolutionary Biology ◽  
Sequence Data ◽  
Divergence Time ◽  
Species Tree ◽  
Estimation Accuracy ◽  
Species Trees ◽  
Distance Method ◽  
Data Set ◽  
Divergence Time Estimates

One of the central tasks in evolutionary biology is to reconstruct the evolutionary relationships among species from sequence data, particularly from multilocus data. In the last ten years, many methods have been proposed to use the variance in the gene histories to estimate species trees by explicitly modeling deep coalescence. However, gene flow, another process that may produce gene history variance, has been less studied. In this paper, we propose a simple yet innovative method for species trees estimation in the presence of gene flow. Our method, called STEST (Species Tree Estimation from Speciation Times), constructs species tree estimates from pairwise speciation time or species divergence time estimates. By using methods that estimate speciation times in the presence of gene flow, (for example, M1 (Yang 2010) or SIM3s (Zhu and Yang 2012)), STEST is able to estimate species trees from data subject to gene flow. We develop two methods, called STEST (M1) and STEST (SIM3s), for this purpose. Additionally, we consider the method STEST (M0), which instead uses the M0 method (Yang 2002), a coalescent-based method that does not assume gene flow, to estimate speciation times. It is therefore devised to estimate species trees in the absence of gene flow. Our simulation studies show that STEST (M0) outperforms STEST(M1), STEST (SIM3s) and STEM in terms of estimation accuracy and outperfroms *BEAST in terms of running time when the degree of gene flow is small. STEST (M1) outperforms STEST (M0), STEST (SIM3s), STEM and *BEAST in term of estimation accuracy when the degree of gene flow is large. An empirical data set analyzed by these methods gives species tree estimates that are consistent with the previous results.

scholarly journals Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190548 ◽  
Author(s):  
Yo Y. Yamasaki ◽  
Ryo Kakioka ◽  
Hiroshi Takahashi ◽  
Atsushi Toyoda ◽  
Atsushi J. Nagano ◽  
...  
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Sequence Data ◽  
Continuous Process ◽  
Sympatric Species ◽  
Whole Genome Sequence ◽  
Secondary Contact ◽  
Pungitius Pungitius ◽  
Hybrid Male ◽  
Differential Adaptation

Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis , whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data

2021 ◽  
Author(s):  
Vanina Tonzo ◽  
AdriÀ Bellvert ◽  
Joaquín Ortego
Keyword(s):  
Gene Flow ◽  
Biological Diversity ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Secondary Contact ◽  
Lineage Sorting ◽  
Glacial Cycles ◽  
Reciprocal Monophyly ◽  
Geometric Morphometric

AbstractInferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression. In this study, we combined high throughput sequence data (ddRADseq), geometric morphometric information, and novel phylogenetic inference methods that explicitly account for gene flow to infer the evolutionary relationships and the timing and mode of diversification in a complex of Ibero-Maghrebian montane grasshoppers of the subgenus Dreuxius (genus Omocestus). Our analyses supported the phenotypic distinctiveness of most sister taxa, two events of historical introgression involving lineages at different stages of the diversification continuum, and the recent Pleistocene origin (< 1 Ma) of the complex. Phylogenetic analyses did not recover the reciprocal monophyly of taxa from Iberia and northwestern Africa, supporting overseas migration between the two continents during the Pleistocene. Collectively, these results indicate that periods of isolation and secondary contact linked to Pleistocene glacial cycles likely contributed to both allopatric speciation and post divergence gene flow in the complex. This study exemplifies how the integration of multiple lines of evidence can help to reconstruct complex histories of reticulated evolution and highlights the important role of Quaternary climatic oscillations as a diversification engine in the Ibero-Maghrebian biodiversity hotspot.

scholarly journals Limited geographic genetic structure detected in a widespread Palearctic corvid, Nucifraga caryocatactes

2014 ◽  
Author(s):  
Kimberly M Dohms ◽  
Theresa M Burg
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Sequence Data ◽  
Base Pairs ◽  
Mitochondrial Dna Control Region ◽  
Potential Barriers ◽  
Seed Crops ◽  
Wide Population

The Eurasian or spotted nutcracker (Nucifraga caryocatactes) is a widespread resident corvid found throughout the Palearctic from Central Europe to Japan. Characterized by periodic bouts of irruptive dispersal in search of Pinus seed crops, this species has potential for high levels of gene flow across its range. Previous analysis of 11 individuals did not find significant range-wide population genetic structure. We investigated population structure using 924 base pairs of mitochondrial DNA control region sequence data from 62 individuals from 12 populations distributed throughout the nutcracker’s range. We complemented this analysis by incorporating additional genetic data from previously published sequences. High levels of genetic diversity and limited population genetic structure were detected suggesting that potential barriers to dispersal do not restrict gene flow in nutcrackers.

scholarly journals Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1091-1106 ◽  
Author(s):  
Rong Lin Wang ◽  
John Wakeley ◽  
Jody Hey
Keyword(s):  
Gene Flow ◽  
Natural Selection ◽  
Sequence Data ◽  
Sexual Isolation ◽  
Secondary Contact ◽  
Drosophila Pseudoobscura ◽  
Dna Sequence Data ◽  
Principal Finding ◽  
Close Relatives ◽  
Parapatric Speciation

The divergence of Drosophila pseudoobscura and close relatives D. persimilis and D. pseudoobscura bogotana has been studied using comparative DNA sequence data from multiple nuclear loci. New data from the Hsp82 and Adh regions, in conjunction with existing data from Adh and the Period locus, are examined in the light of various models of speciation. The principal finding is that the three loci present very different histories, with Adh indicating large amounts of recent gene flow among the taxa, while little or no gene flow is apparent in the data from the other loci. The data were compared with predictions from several isolation models of divergence. These models include no gene flow, and they were found to be incompatible with the data. Instead the DNA data, taken together with other evidence, seem consistent with divergence models in which natural selection acts against gene flow at some loci more than at others. This family of models includes some sympatric and parapatric speciation models, as well as models of secondary contact and subsequent reinforcement of sexual isolation.

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