scholarly journals Genome-wide sampling suggests island divergence accompanied by cryptic epigenetic plasticity in Canada lynx

2018 ◽  
Author(s):  
J.B. Johnson ◽  
D.L. Murray ◽  
A.B.A. Shafer
Keyword(s):  
Dna Methylation ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Markers ◽  
Phenotypic Variation ◽  
Lynx Canadensis ◽  
Functional Plasticity ◽  
Canada Lynx ◽  
Last Glaciation ◽  
Genome Wide

ABSTRACTDetermining the molecular signatures of adaptive differentiation is a fundamental component of evolutionary biology. A key challenge remains for identifying such signatures in wild organisms, particularly between populations of highly mobile species that undergo substantial gene flow. The Canada lynx (Lynx canadensis) is one species where mainland populations appear largely undifferentiated at traditional genetic markers, despite inhabiting diverse environments and displaying phenotypic variation. Here, we used high-throughput sequencing to investigate both neutral genetic structure and epigenetic differentiation across the distributional range of Canada lynx. Using a customized bioinformatics pipeline we scored both neutral SNPs and methylated nucleotides across the lynx genome. Newfoundland lynx were identified as the most differentiated population at neutral genetic markers, with diffusion approximations of allele frequencies indicating that divergence from the panmictic mainland occurred at the end of the last glaciation, with minimal contemporary admixture. In contrast, epigenetic structure revealed hidden levels of differentiation across the range coincident with environmental determinants including winter conditions, particularly in the peripheral Newfoundland and Alaskan populations. Several biological pathways related to morphology were differentially methylated between populations, with Newfoundland being disproportionately methylated for genes that could explain the observed island dwarfism. Our results indicate that epigenetic modifications, specifically DNA methylation, are powerful markers to investigate population differentiation and functional plasticity in wild and non-model systems.SIGNIFICANCEPopulations experiencing high rates of gene flow often appear undifferentiated at neutral genetic markers, despite often extensive environmental and phenotypic variation. We examined genome-wide genetic differentiation and DNA methylation between three interconnected regions and one insular population of Canada lynx (Lynx canadensis) to determine if epigenetic modifications characterized climatic associations and functional molecular plasticity. Demographic approximations indicated divergence of Newfoundland during the last glaciation, while cryptic epigenetic structure identified putatively functional differentiation that might explain island dwarfism. Our study suggests that DNA methylation is a useful marker for differentiating wild populations, particularly when faced with functional plasticity and low genetic differentiation.

scholarly journals A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0240743
Author(s):  
Maurice Marcel Sandeu ◽  
Charles Mulamba ◽  
Gareth D. Weedall ◽  
Charles S. Wondji
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Insecticide Resistance ◽  
Pyrethroid Resistance ◽  
Anopheles Funestus ◽  
Metabolic Resistance ◽  
Transcription Analysis ◽  
Genome Wide

Background Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya. Methods Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation. Results Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley. Conclusion The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

New insights on the genetic basis of Portuguese grapevine and on grapevine domestication

Genome ◽  
2009 ◽  
Vol 52 (9) ◽  
pp. 790-800 ◽  
Author(s):  
M. S. Lopes ◽  
D. Mendonça ◽  
M. Rodrigues dos Santos ◽  
J. E. Eiras-Dias ◽  
A. da Câmara Machado
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Vitis Vinifera ◽  
Ssr Markers ◽  
Genetic Basis ◽  
Genetic Resource ◽  
Putative Parent ◽  
Last Glaciation ◽  
Wild Grapevine ◽  
Nuclear Ssr

As the ancestor of cultivated grape, Vitis vinifera subsp. sylvestris represents a unique, invaluable genetic resource for the improvement of cultivated grapevines. Recently, five populations of wild grapevines were identified in Portugal. Sixty vines were characterized with 11 nuclear SSR markers and further compared with 70 genotypes of Portuguese Vitis vinifera subsp. sativa. The obtained data demonstrate moderate genetic differentiation between wild grapevine populations and moderate to high genetic differentiation between wild and cultivated grapevines. However, the identification of high degrees of similarity between wild and cultivated grapes (up to 87%) and a putative parent–progeny relationship between wild and cultivated grapes with 17 additional SSR markers is indicative of gene flow between local wild grapevine populations and Portuguese domesticated vines. Also, the ancestry of some Azorean cultivars was ascertained. The obtained data further support the hypothesis of several domestication centres, with Portugal, Spain, and Italy playing a particular role after the last glaciation, giving rise to many of the Western European cultivars.

scholarly journals Testing concordance and conflict in spatial replication of landscape genetics inferences

2021 ◽  
Author(s):  
Van Wishingrad ◽  
Robert C Thomson
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Markers ◽  
Sierra Nevada ◽  
Landscape Genetics ◽  
Species Range ◽  
Genetic Connectivity ◽  
Small Subset ◽  
Mountain Range ◽  
Spatial Replication

The field of landscape genetics relates habitat features and genetic information to infer dispersal and genetic connectivity between populations or individuals distributed across a landscape. Such studies usually focus on a small portion of a species range, and the degree to which these geographically restricted results can be extrapolated to different areas of a species range remains poorly understood. Studies that have focused on spatial replication in landscape genetics processes either evaluate a small number of sites, are informed by a small set of genetic markers, analyze only a small subset of environmental variables, or implement models that do not fully explore parameter space. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range, using thousands of ddRAD genetic markers distributed across the genome, implemented in the landscape genetics program ResistanceGA. Across study areas, we found a great deal of consistency in the variables impacting genetic connectivity, but also noted site-specific differences in the factors in each study area. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Vegetation type was found to substantially affect gene flow only in the southernmost Sequoia site, likely due to a higher proportion of desert habitat here, thereby fragmenting habitats that have lower costs to dispersal. The effect of roads also varied between sites and may be related to differences in road usage and amount of traffic in each area. Across study areas, canyons were always substantially implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity across landscapes. We emphasize that spatial data layers are complex and multidimensional, and a careful consideration of associations between variables is vital to form sound conclusions about the critical factors affecting dispersal and genetic connectivity across space.

scholarly journals Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings

2020 ◽  
Vol 10 (3) ◽  
pp. 1019-1028 ◽  
Author(s):  
Luke Browne ◽  
Alayna Mead ◽  
Courtney Horn ◽  
Kevin Chang ◽  
Zeynep A. Celikkol ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Phenotypic Variation ◽  
Foliar Application ◽  
Substantial Reduction ◽  
Dna Demethylation ◽  
Soil Microbiome ◽  
Relative Reduction ◽  
Tree Seedlings ◽  
Genome Wide

Epigenetic modifications such as DNA methylation, where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence plant response to changing environments. One way to test this impact is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. In this study, we treated 5-month-old seedlings of the tree, Quercus lobata, with foliar application of 5-Azacytidine to test whether a reduction in genome-wide methylation would cause differential gene expression and change phenotypic development. First, we demonstrate that demethylation treatment led to 3–6% absolute reductions and 6.7–43.2% relative reductions in genome-wide methylation across CG, CHG, and CHH sequence contexts, with CHH showing the strongest relative reduction. Seedlings treated with 5-Azacytidine showed a substantial reduction in new growth, which was less than half that of control seedlings. We tested whether this result could be due to impact of the treatment on the soil microbiome and found minimal differences in the soil microbiome between two groups, although with limited sample size. We found no significant differences in leaf fluctuating asymmetry (i.e., deviations from bilateral symmetry), which has been found in other studies. Nonetheless, treated seedlings showed differential expression of a total of 23 genes. Overall, this study provides initial evidence that DNA methylation is involved in gene expression and phenotypic variation in seedlings and suggests that removal of DNA methylation affects plant development.

scholarly journals Selection and drift influence genetic differentiation of insular Canada lynx (Lynx canadensis ) on Newfoundland and Cape Breton Island

2017 ◽  
Vol 7 (9) ◽  
pp. 3281-3294 ◽  
Author(s):  
Melanie B. Prentice ◽  
Jeff Bowman ◽  
Kamal Khidas ◽  
Erin L. Koen ◽  
Jeffrey R. Row ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Lynx Lynx ◽  
Lynx Canadensis ◽  
Cape Breton Island ◽  
Canada Lynx ◽  
Cape Breton

scholarly journals Global drivers of diversification in a marine species complex

2019 ◽  
Author(s):  
Catarina N.S. Silva ◽  
Nicholas P. Murphy ◽  
James J. Bell ◽  
Bridget S. Green ◽  
Guy Duhamel ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Continental Shelf ◽  
Demographic History ◽  
Significant Proportion ◽  
Secondary Contact ◽  
Larval Duration ◽  
Genome Wide ◽  
Extant Species ◽  
Species Pairs

AbstractInvestigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence before speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all extant rock lobster species (Jasus spp.), a complex with long larval duration, that has populated continental shelf and seamount habitats around the globe at approximately 40°S. Genetic differentiation patterns revealed the effects of the environment and geographic isolation. Species associated with the same habitat structure (either continental shelf or seamount/island) shared a common ancestry, even though the habitats were not adjacent. Differences in benthic temperature explained a significant proportion (41.3%) of the genetic differentiation. The Eastern Pacific species pair of J. caveorum and J. frontalis retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa and seamounts in the Indian and Atlantic oceans included events of introgression after secondary contact. Parameters estimated for time in isolation and gene flow were congruent with genetic differentiation metrics suggesting that the observed differentiation patterns are the product of migration and genetic drift. Our results reveal important effects of habitat and demographic processes on the divergence of species within the genus Jasus providing the first empirical study of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.

Isolation of peripheral populations of Canada lynx (Lynx canadensis)

2015 ◽  
Vol 93 (7) ◽  
pp. 521-530 ◽  
Author(s):  
E.L. Koen ◽  
J. Bowman ◽  
P.J. Wilson
Keyword(s):  
Gene Flow ◽  
Peripheral Populations ◽  
Lynx Lynx ◽  
Lynx Canadensis ◽  
Isolated Populations ◽  
Eastern Canada ◽  
Canada Lynx ◽  
Animal Populations ◽  
The Usa ◽  
St Lawrence River

Landscape barriers to gene flow, such as rivers, can affect animal populations by limiting the potential for rescue of these isolated populations. We tested the riverine barrier hypothesis, predicting that the St. Lawrence River in eastern Canada would cause genetic divergence of Canada lynx (Lynx canadensis Kerr, 1792) populations by restricting dispersal and gene flow. We sampled 558 lynx from eastern Canada and genotyped these at 14 microsatellite loci. We found three genetic clusters, defined by the St. Lawrence River and the Strait of Belle Isle, a waterway separating Newfoundland from mainland Canada. However, these waterways were not absolute barriers, as we found 24 individuals that appeared to have crossed them. Peripheral populations of lynx are threatened in parts of Canada and the USA, and it is thought that these populations are maintained by immigration from the core. Our findings suggest that in eastern North America, rescue might be less likely because the St. Lawrence River restricts dispersal. We found that ice cover was often sufficient to allow lynx to walk across the ice in winter. If lynx used ice bridges in winter, then climate warming could cause a reduction in the extent and longevity of river and sea ice, further isolating these peripheral lynx populations.

scholarly journals Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli )

2017 ◽  
Vol 4 (3) ◽  
pp. 170057 ◽  
Author(s):  
Carrie L. Branch ◽  
Joshua P. Jahner ◽  
Dovid Y. Kozlovsky ◽  
Thomas L. Parchman ◽  
Vladimir V. Pravosudov
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Local Adaptation ◽  
Sierra Nevada ◽  
Phenotypic Variation ◽  
Population Genetic ◽  
Indirect Evidence ◽  
High Elevation ◽  
Elevational Gradients ◽  
Mountain Chickadees

Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation ( F ST , Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.

scholarly journals Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata

2018 ◽  
Author(s):  
Pierre-Alexandre Gagnaire ◽  
Jean-Baptiste Lamy ◽  
Florence Cornette ◽  
Serge Heurtebise ◽  
Lionel Dégremont ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Crassostrea Gigas ◽  
The North ◽  
Introduced Populations ◽  
Genome Wide ◽  
Crassostrea Angulata ◽  
The Pacific ◽  
Demographic Inference ◽  
Native And Introduced Ranges

AbstractThe Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and C. angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and morphologic similarity. In particular, whether ecological and/or intrinsic isolating mechanisms participate to species divergence remains unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation maintains under new environmental and demographic conditions. We generated a pseudo-chromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

Sign in / Sign up

Export Citation Format

Share Document