Interspecific cytoplasmic gene flow in the absence of nuclear gene flow: evidence from Drosophila.

Abstract The genetic structure of green turtle (Chelonia mydas) rookeries located around the Australian coast was assessed by (1) comparing the structure found within and among geographic regions, (2) comparing microsatellite loci vs. restriction fragment length polymorphism analyses of anonymous single copy nuclear DNA (ascnDNA) loci, and (3) comparing the structure found at nuclear DNA markers to that of previously analyzed mitochondrial (mtDNA) control region sequences. Significant genetic structure was observed over all regions at both sets of nuclear markers, though the microsatellite data provided greater resolution in identifying significant genetic differences in pairwise tests between regions. Inferences about population structure and migration rates from the microsatellite data varied depending on whether statistics were based on the stepwise mutation or infinite allele model, with the latter being more congruent with geography. Estimated rates of gene flow were generally higher than expected for nuclear DNA (nDNA) in comparison to mtDNA, and this difference was most pronounced in comparisons between the northern and southern Great Barrier Reef (GBR). The genetic data combined with results from physical tagging studies indicate that the lack of nuclear gene divergence through the GBR is likely due to the migration of sGBR turtles through the courtship area of the nGBR population, rather than male-biased dispersal. This example highlights the value of combining comparative studies of molecular variation with ecological data to infer population processes.

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Genic differentiation and origin of Robertsonian populations of the house mouse (Mus musculus domesticus Rutty)

Genetics Research ◽

10.1017/s0016672300027841 ◽

1989 ◽

Vol 53 (1) ◽

pp. 29-44 ◽

Cited By ~ 54

Author(s):

Janice Britton-Davidian ◽

Joseph H. Nadeau ◽

Henri Croset ◽

Louis Thaler

Keyword(s):

Gene Flow ◽

House Mouse ◽

Mus Musculus ◽

Western Europe ◽

Chromosomal Rearrangements ◽

Nuclear Gene ◽

Electrophoretic Analysis ◽

Mus Musculus Domesticus ◽

Effective Population ◽

Chromosomal Races

SummaryThis paper examines the relation between chromosomal and nuclear-gene divergence in 28 wild populations of the house mouse semi-species, Mus musculus domesticus, in Western Europe and North Africa. Besides describing the karyotypes of 15 of these populations and comparing them to those of 13 populations for which such information was already known, it reports the results of an electrophoretic survey of proteins encoded by 34 nuclear loci in all 28 populations. Karyotypic variation in this taxon involves only centric (or Robertsonian) fusions which often differ in arm combination and number between chromosomal races. The electrophoretic analysis showed that the amount of genic variation within Robertsonian (Rb) populations was similar to that for all-acrocentric populations, i.e. bearing the standard karyotype. Moreover, divergence between the two types of populations was extremely low. These results imply that centric fusions in mice have not modified either the level or the nature of genic variability. The genetic similarity between Rb and all-acrocentric populations is not attributed to the persistence of gene flow, since multiple fusions cause marked reproductive isolation. Rather, we attribute this extreme similarity to the very recent origin of chromosomal races in Europe. Furthermore, genic diversity measures suggest that geographically separated Rb populations have in situ and independent origins. Thus, Rb translocations are probably not unique events, but originated repeatedly. Two models are presented to explain how the rapid fixation of a series of chromosomal rearrangements can occur in a population without lowering variability in the nuclear genes. The first model assumes that chromosomal mutation rates are between 10−3 and 10−4 and that populations underwent a series of transient bottlenecks in which the effective population size did not fall below 35. In the second model, genic variability is restored following severe bottlenecks, through gene flow and recombination.

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Geographic distribution and seasonal variation of mitochondrial DNA haplotypes in the aphid Rhopalosiphum padi (Hemiptera: Aphididae)

Bulletin of Entomological Research ◽

10.1017/s0007485300027309 ◽

1997 ◽

Vol 87 (2) ◽

pp. 161-167 ◽

Cited By ~ 34

Author(s):

D. Martinez-Torres ◽

A. Moya ◽

P.D.N. Hebert ◽

J.-C. Simon

Keyword(s):

Mitochondrial Dna ◽

Seasonal Variation ◽

Gene Flow ◽

Temperature Regime ◽

Rhopalosiphum Padi ◽

Nuclear Gene ◽

Selective Advantage ◽

Nuclear Markers ◽

Host Alternation ◽

Dna Diversity

AbstractThis study examines the spatial and seasonal patterning of mitochondrial DNA diversity in French populations of the bird cherry-oat aphid, Rhopalosiphum padi (Linnaeus), on both its primary and secondary hosts. Our results confirm the presence of two major mitochondrial lineages that are generally associated with the breeding system variation (cyclic and obligate parthenogenesis) shown by this species. The strength of this relationship varies regionally, being most evident in the south and west. Cyclically parthenogenetic populations show no significant regional or seasonal genetic divergence reflecting high levels of gene flow, possibly promoted by their obligate host-alternation. However, obligately parthenogenetic populations show a north-south cline in the distribution of the dominant haplotypes. This pattern might result from a selective advantage of some obligately parthenogenetic lineages under cold temperature regime. Alternatively, this cline might be established by a gradient in the intensity of nuclear gene flow between cyclically and obligately parthenogenetic populations mediated by androcyclic males. The discrimination between these possible explanations will require extending analysis to include hypervariable nuclear markers.

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Population differentiation and nuclear gene flow in the Dominican anole (Anolis oculatus)

Molecular Ecology ◽

10.1046/j.1365-294x.2002.01564.x ◽

2002 ◽

Vol 11 (9) ◽

pp. 1679-1688 ◽

Cited By ~ 34

Author(s):

Andrew G. Stenson ◽

Anita Malhotra ◽

Roger S. Thorpe

Keyword(s):

Gene Flow ◽

Population Differentiation ◽

Nuclear Gene

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Phylogenetic, population genetic, and morphological analyses reveal evidence for one species of Eastern Indigo Snake (Drymarchon couperi)

10.1101/318766 ◽

2018 ◽

Cited By ~ 1

Author(s):

Brian Folt ◽

Javan Bauder ◽

Stephen Spear ◽

Dirk Stevenson ◽

Michelle Hoffman ◽

...

Keyword(s):

Gene Flow ◽

Species Delimitation ◽

Nuclear Dna ◽

Sequence Data ◽

Phylogenetic Reconstruction ◽

Nuclear Gene ◽

Large Species ◽

High Dispersal ◽

Contemporary Gene Flow ◽

Eastern Indigo Snake

AbstractAccurate species delimitation and description are necessary to guide effective conservation management of imperiled species. The Eastern Indigo Snake (Drymarchon couperi) is a large species in North America that is federally-protected as Threatened under the Endangered Species Act. Recently, two associated studies hypothesized that Drymarchon couperi is two species. Here, we use diverse approaches to test the two-species hypothesis for D. couperi. Our analyses reveal that (1) phylogenetic reconstruction in previous studies was based entirely on variance of mitochondrial DNA sequence data, (2) microsatellite data demonstrate significant population admixture and nuclear gene flow between mitochondrial lineages, and (3) morphological analyses recover a single diagnosable species. Our results are inconsistent with the two-species hypothesis, thus we reject it and formally place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA may be driven by high dispersal of males relative to females. We caution against species delimitation exercises when one or few loci are used without evaluation of contemporary gene flow, particularly species with strong sex-biased dispersal (e.g., squamates) and/or when results have implications for ongoing conservation efforts.

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PERCHED AT THE MITO-NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD

Evolution ◽

10.1111/evo.12107 ◽

2013 ◽

Vol 67 (12) ◽

pp. 3412-3428 ◽

Cited By ~ 74

Author(s):

Alexandra Pavlova ◽

J. Nevil Amos ◽

Leo Joseph ◽

Kate Loynes ◽

Jeremy J. Austin ◽

...

Keyword(s):

Gene Flow ◽

Nuclear Gene ◽

The Face

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Spatiotemporal segregation among summer stocks of beluga (Delphinapterus leucas) despite nuclear gene flow: implication for the endangered belugas in eastern Hudson Bay (Canada)

Conservation Genetics ◽

10.1007/s10592-011-0294-x ◽

2011 ◽

Vol 13 (2) ◽

pp. 419-433 ◽

Cited By ~ 21

Author(s):

Julie Turgeon ◽

Pierre Duchesne ◽

Gabriel J. Colbeck ◽

Lianne D. Postma ◽

Mike O. Hammill

Keyword(s):

Gene Flow ◽

Nuclear Gene ◽

Delphinapterus Leucas ◽

Hudson Bay

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Erratum — Beyond mtDNA: nuclear gene flow suggests taxonomic oversplitting in the little brown bat (Myotis lucifugus)

Canadian Journal of Zoology ◽

10.1139/z08-100 ◽

2008 ◽

Vol 86 (9) ◽

pp. 1083-1083 ◽

Cited By ~ 2

Author(s):

C. L. Lausen ◽

I. Delisle ◽

R. M.R. Barclay ◽

C. Strobeck

Keyword(s):

Gene Flow ◽

Nuclear Gene ◽

Myotis Lucifugus ◽

Little Brown Bat

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First microsatellite markers for the pine catkin sawfly Xyela concava (Hymenoptera, Xyelidae) and their application in phylogeography and population genetics

PeerJ ◽

10.7717/peerj.8010 ◽

2019 ◽

Vol 7 ◽

pp. e8010

Author(s):

Dustin Kulanek ◽

Stephan M. Blank ◽

Katja Kramp

Keyword(s):

Population Genetics ◽

Gene Flow ◽

Nuclear Gene ◽

Gene Region ◽

Model Organisms ◽

Dispersal Ability ◽

Atpase Subunit ◽

High Gene Flow ◽

High Gene ◽

Genetic Structures

Microsatellites are widely used as powerful markers in population genetics because of their ability to access recent genetic variation and to resolve subtle population genetic structures. However, their development, especially for non-model organisms with no available genome-wide sequence data has been difficult and time-consuming. Here, a commercial high-throughput sequencing approach (HTS) was used for the very first identification of microsatellite motifs in the genome of Xyela concava and the design of primer pairs flanking those motifs. Sixteen of those primer pairs were selected and implemented successfully to answer questions on the phylogeography and population genetics of X. concava. The markers were characterized in three geographically distinct populations of X. concava and tested for cross-species amplification in two additional Xyela and one Pleroneura species (Xyelidae). All markers showed substantial polymorphism as well as revealing subtle genetic structures among the three genotyped populations. We also analyzed a fragment of the nuclear gene region of sodium/potassium-transporting ATPase subunit alpha (NaK) and a partial mitochondrial gene region coding for cytochrome oxidase subunit I (COI) to demonstrate different genetic resolutions and sex-biased patterns of these markers, and their potential for combined use in future studies on the phylogeography and population genetics of X. concava. Although a limited number of populations was analyzed, we nevertheless obtained new insights on the latter two topics. The microsatellites revealed a generally high gene flow between the populations, but also suggested a deep historical segregation into two genetic lineages. This deep genetic segregation was confirmed by NaK. While the high gene flow was unexpected, because of assumed restricted dispersal ability of X. concava and the discontinuous distribution of the host trees between the populations, the segregation of two lineages is comprehensible and could be explained by different refuge areas of the hosts during glacial times. The COI results showed a discordant strong genetic structure between all populations, which might be explained by the smaller effective population size of the mitochondrial genome. However, given the frequent evidence of a similar nature in recent studies on sawflies, we also consider and discuss mitochondrial introgression on population level as an alternative explanation.

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Mitochondrial and nuclear genetic relationships of deer (Odocoileus spp.) in western North America

Canadian Journal of Zoology ◽

10.1139/z91-179 ◽

1991 ◽

Vol 69 (5) ◽

pp. 1270-1279 ◽

Cited By ~ 21

Author(s):

Matthew A. Cronin

Keyword(s):

Gene Flow ◽

North America ◽

Genetic Relationships ◽

Mitochondrial Gene ◽

Mule Deer ◽

Introgressive Hybridization ◽

Nuclear Gene ◽

Allele Frequencies ◽

Western North America ◽

Mtdna Sequence

Odocoileus hemionus (mule deer and black-tailed deer) and Odocoileus virginanus (white-tailed deer) are sympatric in western North America and are characterized by distinct morphology, behavior, and allozyme allele frequencies. However, there is discordance among nuclear and mitochondrial genetic relationships, as mule deer (O. h. hemionus) and white-tailed deer have similar mitochondrial DNA (mtDNA) which is very different from that of black-tailed deer (O. h. columbianus, O. h. sitkensis). I expanded previous studies to clarify the genetic relationships of these groups by determining mtDNA haplotype and allozyme genotypes for 667 deer from several locations in northwestern North America. Different mtDNA haplotypes in mule deer, black-tailed deer, and white-tailed deer indicate that mitochondrial gene flow is restricted. Allozyme allele frequencies indicate that there is also restriction of nuclear gene flow between O. virginianus and O. hemionus, and to a lesser extent between mule deer and black-tailed deer. There is a low level of introgressive hybridization of mtDNA from mule deer and black-tailed deer into white-tailed deer populations and considerable interbreeding of mule deer and black-tailed deer in a contact zone. The discordance of mitochondrial and nuclear genomes is apparent only if mtDNA sequence divergences, and not haplotype frequencies, are considered.

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