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.

scholarly journals Analysis of Genome-Wide Differentiation between Native and Introduced Populations of the Cupped Oysters Crassostrea gigas and Crassostrea angulata

2018 ◽  
Vol 10 (9) ◽  
pp. 2518-2534 ◽  
Author(s):  
Pierre-Alexandre Gagnaire ◽  
Jean-Baptiste Lamy ◽  
Florence Cornette ◽  
Serge Heurtebise ◽  
Lionel Dégremont ◽  
...  
Keyword(s):  
Crassostrea Gigas ◽  
Introduced Populations ◽  
Genome Wide ◽  
Crassostrea Angulata

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.

scholarly journals Genomic divergence in allopatric Northern Cardinals of the North American warm deserts is associated with behavioral differentiation

2018 ◽  
Author(s):  
Kaiya L. Provost ◽  
William M. Mauck ◽  
Brian Tilston Smith
Keyword(s):  
Gene Flow ◽  
Sonoran Desert ◽  
Demographic History ◽  
Isolation With Migration ◽  
Song Recognition ◽  
Behavioral Isolation ◽  
The North ◽  
Genome Wide ◽  
Behavioral Differentiation ◽  
Northern Cardinals

ABSTRACTBiogeographic barriers are thought to be important in initiating speciation through geographic isolation, but they rarely indiscriminately and completely reduce gene flow across the entire community. Understanding which species’ attributes regulate a barrier could help elucidate how speciation is initiated. Here, we investigated the association of behavioral isolation on population differentiation in Northern Cardinals (Cardinalis cardinalis) distributed across the Cochise Filter Barrier, a region of transitional habitat which separates the Sonoran and Chihuahuan deserts. Using genome-wide markers, we modeled demographic history by fitting the data to isolation and isolation-with-migration models. The best-fit model indicated that desert populations diverged in the mid-Pleistocene and there has been historically low, unidirectional gene flow into the Sonoran Desert. We then tested song recognition using reciprocal call-broadcast experiments to compare song recognition between deserts, controlling for song dialect changes within deserts. We found that male Northern Cardinals in both deserts were most aggressive to local songs and failed to recognize across-barrier songs. A correlation of genomic differentiation despite historic introgression and strong song discrimination is consistent with a model where speciation is initiated across a barrier and maintained by behavioral isolation.

scholarly journals Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

2020 ◽  
Author(s):  
S.G. Olvera-Vazquez ◽  
C. Remoue ◽  
A. Venon ◽  
A. Rousselet ◽  
O. Grandcolas ◽  
...  
Keyword(s):  
Gene Flow ◽  
North America ◽  
Genetic Differentiation ◽  
North Africa ◽  
Large Scale ◽  
Demographic History ◽  
High Genetic Diversity ◽  
The North ◽  
The Us ◽  
History Of

With frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may be involved or affected by colonization, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its endosymbiotic bacterial community. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe, and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the Moroccan and the North American that are likely the result of recent colonization events. Coalescent-based inferences releaved high levels of gene flow among populations during the colonization, but did not allow determining the sequence of colonization of Europe, America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. Finally, we found that D. plantaginea rarely hosts any other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play any role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

Regional population structuring and conservation units in the platypus (Ornithorhynchus anatinus)

2013 ◽  
Vol 61 (5) ◽  
pp. 378 ◽  
Author(s):  
Stephen H. Kolomyjec ◽  
Tom R. Grant ◽  
Christopher N. Johnson ◽  
David Blair
Keyword(s):  
Gene Flow ◽  
Genetic Differentiation ◽  
Large Scale ◽  
Wide Distribution ◽  
Conservation Units ◽  
Genetic Structuring ◽  
The North ◽  
Contemporary Gene Flow ◽  
Ornithorhynchus Anatinus ◽  
Southern Island

The platypus (Ornithorhynchus anatinus) has a wide distribution in Australia, encompassing the southern island of Tasmania and a broad latitudinal range of the mainland from the temperate south to the tropical north. We used 12 microsatellite markers from 235 individuals sampled from 13 river systems to examine patterns of genetic differentiation and gene flow throughout the species’ range. Using a Bayesian approach we identified three large-scale groupings that correspond closely to geographically distinct regions of the species’ distribution: the tropical northern mainland, the subtropical and temperate southern mainland, and Tasmania. Six additional clusters were found within the regional groups, three in the northern, two in the southern mainland regions, and the last in Tasmania. These clusters coincided with major river drainages. Genetic differentiation was generally high, with pairwise Fst values ranging from 0.065 to 0.368 for regions and 0.037 to 0.479 for clusters. We found no evidence of contemporary gene flow among the three clusters in the north, but some migration may occur between the larger clusters in the south. Due to the high genetic structuring and lack of gene flow between these three regional populations of the platypus we recommend their treatment as evolutionarily significant units (ESUs) within the platypus species. We have also detailed several smaller management units (MUs) existing within our study area based on subregional clusters and geographically significant features.

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.

Review of the genetics, dispersal and recruitment of crown-of-thorns starfish (Acanthaster planci)

1992 ◽  
Vol 43 (3) ◽  
pp. 597 ◽  
Author(s):  
JAH Benzie
Keyword(s):  
Gene Flow ◽  
Indian Ocean ◽  
Genetic Differentiation ◽  
Primary Source ◽  
Acanthaster Planci ◽  
Genetic Structuring ◽  
West Pacific ◽  
North West ◽  
The Pacific ◽  
Western Australian

The lack of genetic structuring reported for Acanthaster planci (L.) from major biogeographical zones (i.e. Indian Ocean versus Pacific) may reflect a lack of data rather than confirmation of a recent and rapid dispersal of the species worldwide. The low level of genetic variation among A. planci populations throughout the Pacific is evidence of high levels of gene flow throughout this region. However, gene flow among widely separated reef complexes (average number of migrants per generation, N/em, approximately 2) is an order of magnitude less than that occurring within highly connected reef systems like the Ryukyus and the Great Barrier Reef (GBR) (Nem approximately 20). The genetic similarity between North-west Pacific and Australian populations is likely to reflect gene flow to each place from the central Indo-West Pacific region. Populations peripheral to the species' main distribution show greater genetic differentiation, probably as a result of founder effect. Some, like the Hawaiian and western Australian populations, show reduced genetic diversity, implying colonization by a very small number of individuals or a recent severe bottleneck in population size. Western Australian populations appear to have been derived from eastern Australian populations in the Pacific rather than Indian Ocean sources. On the GBR, genetic differentiation is low among populations that are undergoing outbreaks but there is significant differentiation among populations that are not involved in outbreaks; this suggests that a single primary source is the origin of outbreaks on the GBR. The development of distinctive DNA markers may also allow the detailed tracking of dispersal routes of A. planci and of recruitment within reefs.

Genetic variation and population structure of western Mediterranean and northern Atlantic Stenella coeruleoalba populations inferred from microsatellite data

2007 ◽  
Vol 87 (1) ◽  
pp. 265-269 ◽  
Author(s):  
Vincent J.R. Bourret ◽  
Matthias R.J.M. Macé ◽  
Brigitte Crouau-Roy
Keyword(s):  
Genetic Differentiation ◽  
North Atlantic Ocean ◽  
Western Mediterranean ◽  
Mediterranean Population ◽  
Stenella Coeruleoalba ◽  
The North ◽  
Western Mediterranean Sea ◽  
The Pacific ◽  
Hardy Weinberg Equilibrium ◽  
The Mediterranean

The patterns of genetic differentiation and levels of genetic diversity among striped dolphin (Stenella coeruleoalba) populations from the North Atlantic Ocean (N=45 individuals) and the central and western Mediterranean Sea (N=78) were investigated using five polymorphic microsatellite loci. A North Pacific sample (N=14) was added as an out-group. Two of the markers were tetranucleotide repeats tested for the first time in this species. The Mediterranean, Atlantic and Pacific samples displayed a mean number of alleles per locus of 11.2, 13.4, and 9.6 respectively, suggesting a high but variable polymorphism across loci. The Mediterranean sample displayed particular characteristics: (i) the lowest allelic richness and expected heterozygosity (HeMediterranean=0.76, while HeAtlantic=0.83 and HePacific=0.85); (ii) a significant departure from Hardy–Weinberg equilibrium (P<0.001; FIS=0.050); and (iii) a significant linkage disequilibrium between two pairs of loci. These last two features, present neither in the Atlantic sample nor in the Pacific one, suggest that the western Mediterranean population might possibly be further subdivided. Significant genetic differentiation was detected between the Mediterranean and Pacific populations, and between the Mediterranean and Atlantic populations. However, pairwise Wright's FST was not significantly different from zero between the two geographically isolated Atlantic and Pacific populations.

scholarly journals Mitochondrial DNA Suggests High Gene Flow in Ancient Murrelets

The Condor ◽  
2002 ◽  
Vol 104 (1) ◽  
pp. 84-91 ◽  
Author(s):  
Rebecca L. Pearce ◽  
Jesse J. Wood ◽  
Yuri Artukhin ◽  
Timothy P. Birt ◽  
Martin Damus ◽  
...  
Keyword(s):  
British Columbia ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
North Pacific ◽  
Mitochondrial Control Region ◽  
Female Population ◽  
The North ◽  
Effective Female Population Size ◽  
High Gene ◽  
The North Pacific

Abstract Ancient Murrelets (Synthliboramphus antiquus) are subarctic seabirds that breed on islands from British Columbia through Alaska to China. In this study, we used sequence variation in the mitochondrial control region and cytochrome b gene to estimate the extent of genetic differentiation and gene flow among populations both within British Columbia and across the North Pacific. Results suggest that genetic differentiation is low and female-mediated gene flow is high among colonies within British Columbia, in agreement with banding studies. Surprisingly, genetic differentiation appears to be low and gene flow high between British Columbia and Asia. The effective female population size appears to be stable, but the species may have undergone a range expansion. These results suggest that Ancient Murrelets from throughout the North Pacific may represent a single management unit for conservation. El ADN Mitocondrial Sugiere Alto Flujo Génico en Synthliboramphus antiquus Resumen. Synthliboramphus antiquus es una especie de ave marina subártica que se reproduce en islas desde British Columbia a través de Alaska hasta China. En este estudio estimamos el grado de diferenciación genética y de flujo génico entre poblaciones localizadas dentro de British Columbia y a través del Pacífico Norte. Nos basamos en la variación en secuencias de la región control y el gen citocromo b del ADN mitocondrial. Los resultados sugieren baja diferenciación genética y alto flujo génico mediado por las hembras entre las colonias de British Columbia, lo que es consistente con estudios de aves anilladas. Sorprendentemente, la diferenciación genética parece ser baja y el flujo génico alto entre British Columbia y Asia. El tamaño efectivo de la población de hembras parece estar estable, pero la especie podría haber expandido su rango de distribución. Estos resultados sugieren que los S. antiquus de todo el Pacífico Norte pueden representar una sola unidad de manejo en términos de conservación.

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