Contrasts between the phylogeographic patterns of chloroplast and nuclear DNA highlight a role for pollen-mediated gene flow in preventing population divergence in an East Asian temperate tree

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

Journal of Heredity ◽

10.1093/jhered/esx006 ◽

2017 ◽

Vol 108 (3) ◽

pp. 288-298 ◽

Cited By ~ 3

Author(s):

María José Sanín ◽

Patricia Zapata ◽

Jean-Christophe Pintaud ◽

Gloria Galeano ◽

Adriana Bohórquez ◽

...

Keyword(s):

Gene Flow ◽

Population Divergence ◽

Blind Alley

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

Molecular Ecology ◽

10.1111/mec.15523 ◽

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

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Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0342 ◽

2014 ◽

Vol 369 (1648) ◽

pp. 20130342 ◽

Cited By ~ 24

Author(s):

Alexander S. T. Papadopulos ◽

Maria Kaye ◽

Céline Devaux ◽

Helen Hipperson ◽

Jackie Lighten ◽

...

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Plant Species ◽

Environmental Gradients ◽

Isolation By Distance ◽

Model Averaging ◽

Dispersal Limitation ◽

Population Divergence ◽

Environmental Pressures ◽

Isolation By Environment

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.

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ADAPTIVE POPULATION DIVERGENCE IN CRYPTIC COLOR-PATTERN FOLLOWING A REDUCTION IN GENE FLOW

Evolution ◽

10.1111/j.1558-5646.2009.00671.x ◽

2009 ◽

Vol 63 (7) ◽

pp. 1902-1912 ◽

Cited By ~ 55

Author(s):

Patrik Nosil

Keyword(s):

Gene Flow ◽

Color Pattern ◽

Population Divergence

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Genetic studies of human diversity in East Asia

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2007.2028 ◽

2007 ◽

Vol 362 (1482) ◽

pp. 987-996 ◽

Cited By ~ 50

Author(s):

Feng Zhang ◽

Bing Su ◽

Ya-ping Zhang ◽

Li Jin

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

East Asia ◽

Pacific Islands ◽

East Asian ◽

Human Populations ◽

Genetic Studies ◽

The North ◽

Asian Populations ◽

Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

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Lack of specialization in trophic morphology between genetically differentiated dwarf and normal forms of lake whitefish (Coregonus clupeaformis Mitchill) in Lac de l'Est, Quebec

Canadian Journal of Zoology ◽

10.1139/z96-226 ◽

1996 ◽

Vol 74 (11) ◽

pp. 1989-1998 ◽

Cited By ~ 31

Author(s):

Angelo Chouinard ◽

Dany Pigeon ◽

Louis Bernatchez

Keyword(s):

Gene Flow ◽

Trophic Ecology ◽

Early Stage ◽

Population Divergence ◽

Gene Pools ◽

Coregonus Clupeaformis ◽

Lake Whitefish ◽

Apparent Lack ◽

Enzyme Loci ◽

Trophic Niches

We recently observed a bimodal distribution in size of sexually maturing lake whitefish (Coregonus clupeaformis Mitchill) in Lac de L'Est, Quebec. The objective of this study was to test the hypothesis that these two spawning size classes represent genetically distinct ecotypes, potentially adapted in morphology for occupying different trophic niches. This was accomplished by quantifying the extent of genetic (mitochondrial DNA (mtDNA) and enzyme loci) and morphological differences. Significant differences in haplotype and allele frequency distributions confirmed the hypothesis that whitefish maturing at small (dwarf) and normal sizes are structured into two distinct gene pools. However, low Fst values at mtDNA and enzyme loci, coupled with the apparent lack of spatial and temporal spawning segregation, suggest that reproductive isolation is incomplete and that gene flow is still occurring between the two forms. Patterns of mtDNA diversity favoured the origin of genetically distinct dwarf and normal-size lake whitefish forms in Lac de l'Est through sympatric divergence. However, a lack of differences in morphological traits potentially related to trophic ecology did not support the hypothesis that the two forms represent ecotypes which are morphologically specialized in trophic niches. This study established that sympatric dwarf and normal-size spawning groups of lake whitefish in Lac de l'Est represent two genetically distinct populations despite the potential for gene flow between them. This, coupled with their low level of morphological diversification, suggests that they represent an early stage of population divergence, and therefore makes them of particular interest for understanding the gene–environment processes involved in the early steps of speciation events.

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Quantitating and Dating Recent Gene Flow between European and East Asian Populations

Scientific Reports ◽

10.1038/srep09500 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 19

Author(s):

Pengfei Qin ◽

Ying Zhou ◽

Haiyi Lou ◽

Dongsheng Lu ◽

Xiong Yang ◽

...

Keyword(s):

Gene Flow ◽

East Asian ◽

Recent Gene Flow ◽

Asian Populations

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Comparative systematics and phylogeography of Quercus Section Cerris in western Eurasia: inferences from plastid and nuclear DNA variation

10.7287/peerj.preprints.26995v1 ◽

2018 ◽

Author(s):

Marco Cosimo Simeone ◽

Simone Cardoni ◽

Roberta Piredda ◽

Francesca Imperatori ◽

Michael Avishai ◽

...

Keyword(s):

Nuclear Dna ◽

East Asian ◽

Northeast Asia ◽

Hybrid Origin ◽

Dna Variation ◽

Early Oligocene ◽

Eurasian Lineage ◽

Taxonomic Framework ◽

Chloroplast Haplotypes ◽

Western Eurasia

Oaks (Quercus) comprise more than 400 species worldwide and centres of diversity for most sections lie in the Americas and East/Southeast Asia. The only exception is the Eurasian Sect. Cerris that comprises 15 species, a dozen of which are confined to western Eurasia. This section has not been comprehensively studied using molecular tools. Here, we assess species diversity and reconstruct a first comprehensive taxonomic scheme of western Eurasian members of Sect. Cerris using plastid (trnH-psbA) and nuclear (5S-IGS) DNA variation with a dense intra-specific and geographic sampling. Chloroplast haplotypes primarily reflected geographic patterns of species coevolution within Sect. Cerris and its sister section Ilex. We identified two widespread and ancestral haplotypes, and less common, locally restricted, derived variants. Signatures shared with Mediterranean species of Sect. Ilex, but not with the East Asian Cerris siblings, suggest that the western Eurasian lineage came into contact with Ilex only after the first (early Oligocene) members of Sect. Cerris in Northeast Asia had begun to radiate and move westwards. Nuclear 5S-IGS diversification patterns were more efficient for establishing a molecular-taxonomic framework and to reveal hybridization and reticulation processes. Four main evolutionary lineages were identified. The first lineage comprises Q. libani, Q. trojana and Q. afares and appears to be closest to the root of Sect. Cerris. These taxa are morphologically most similar to the East Asian species of Cerris, and to both Oligocene and Miocene fossils of East Asia and Miocene fossils of western Eurasia. The second lineage is mainly composed of the widespread Q. cerris and the narrow endemic species Q. castaneifolia, Q. look, and Q. euboica. The third lineage comprises three Near East species (Q. brantii, Q. ithaburensis and Q. macrolepis), well adapted to continental climates with cold winters. The forth lineage appears the most derived and comprises Q. suber, the cork oak, and Q. crenata. Quercus cerris and Q. trojana displayed exceptional levels of variation; Q. macrolepis and Q. euboica, previously treated as subspecies of Q. ithaburensis and Q. trojana, likely deserve an independent species status. A trend towards inter-specific crosses was detected in several taxa; however, we found no clear evidence of a hybrid origin of Q. afares and Q. crenata, as currently assumed. Phylogeographic inferences on the origin and diversification of Quercus Sect. Cerris are provided to fill an important gap in the knowledge of oak diversity and evolution.

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