scholarly journals Phylogeny and phylogeography of Atlantic oyster species: evolutionary history, limited genetic connectivity and isolation by distance

2011 ◽  
Vol 426 ◽  
pp. 197-212 ◽  
Author(s):  
C Lazoski ◽  
J Gusmão ◽  
P Boudry ◽  
AM Solé-Cava
Keyword(s):  
Evolutionary History ◽  
Isolation By Distance ◽  
Genetic Connectivity ◽  
Oyster Species

scholarly journals Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽  
2021 ◽  
Author(s):  
Yael S. Rodger ◽  
Alexandra Pavlova ◽  
Steve Sinclair ◽  
Melinda Pickup ◽  
Paul Sunnucks
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Evolutionary History ◽  
Livestock Grazing ◽  
Genetic Connectivity ◽  
Evolutionary Divergence ◽  
Common Component ◽  
A Genome ◽  
Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

scholarly journals Phylogeography of the California Thrasher (Toxostoma Redivivum) Based on Nested-Clade Analysis of Mitochondrial-DNA Variation

The Auk ◽  
2003 ◽  
Vol 120 (2) ◽  
pp. 346-361
Author(s):  
Erik A. Sgariglia ◽  
Kevin J. Burns
Keyword(s):  
Mitochondrial Dna ◽  
Range Expansion ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Nested Clade Analysis ◽  
Dna Variation ◽  
History Of ◽  
Past Fragmentation ◽  
Intraspecific Relationships ◽  
Geologic Data

Abstract Distribution of genealogical lineages within a species is likely the result of a complicated series of ecological and historical events. Nested-clade analysis is specifically designed as an objective phylogeographic approach for inferring evolutionary processes on a spatial and temporal scale for small subclades within a larger set of intraspecific relationships. Here, we use nested-clade analysis as well as other phylogeographic methods to investigate the evolutionary history of California Thrasher (Toxostoma redivivum) populations. Inferences resulting from nested clade analysis suggest a history that includes past fragmentation, range expansion, and isolation-by-distance. Along with root information, those inferences enable the construction of a biogeographic scenario for this species involving general southern ancestry, an early north–south division, northward range expansion, and a southward back-expansion into an already populated southern region. Isolation-by-distance is also identified, particularly in southern California, indicating that gene flow between localities does occur but is restricted. Many conclusions drawn from this study are concordant with geologic data as well as phylogeographic scenarios drawn for other codistributed California taxa.

scholarly journals Evaluation of the minimum sampling design for population genomic and microsatellite studies. An analysis based on wild maize

2020 ◽  
Author(s):  
Jonás A. Aguirre-Liguori ◽  
Javier A. Luna-Sánchez ◽  
Jaime Gasca-Pineda ◽  
Luis E. Eguiarte
Keyword(s):  
Evolutionary History ◽  
Isolation By Distance ◽  
Molecular Ecology ◽  
Population Genomic ◽  
History Of ◽  
Outlier Tests ◽  
Landscape Genetic ◽  
Genomic Regions ◽  
Computational Resources ◽  
Number Of Individuals

ABSTRACTMassive parallel sequencing is revolutionizing the field of molecular ecology by allowing to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the needed economic and computational resources generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two extensive genomic and one large microsatellite datasets consisting of empirical data. We generated different subsampling designs by changing the number of loci, individuals, populations and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST) and landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the genomic and microsatellite datasets. For the genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For all datasets we found that increasing the number of population sampled is important to obtain precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.

scholarly journals Population genetic structure of New Zealand blue cod (Parapercis colias) based on mitochondrial and microsatellite DNA markers

2021 ◽  
Author(s):  
◽  
Clare Louise Gebbie
Keyword(s):  
New Zealand ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Population Genetic ◽  
Current Knowledge ◽  
Isolation By Distance ◽  
Genetic Connectivity ◽  
Microsatellite Dna Markers

<p>Parapercis colias (blue cod) is an endemic temperate reef fish that supports an important commercial and recreational fishery in New Zealand. However, concerns have been raised about localized stock depletion, and multiple lines of evidence have suggested P. colias may form several biologically distinct populations within the New Zealand Exclusive Economic Zone. Mark and recapture studies along with otolith and stable isotope studies have indicated that individuals are sedentary with very limited movement beyond the scale of 10-20km. The primary goal of this research was to advance the current knowledge of P. colias population genetic structure. This information can be incorporated into stock assessment models with the aim of improving the management of the P. colias fishery. This study made use of 454 pyrosequencing technology to isolate and develop the first set of microsatellite DNA markers for P. colias. These seven microsatellite loci, along with mitochondrial control region sequences, were used to determine the levels of genetic variation and differentiation between sites around the New Zealand coastline, including the Chatham Islands.  Significant differentiation was observed between the Chatham Islands and mainland New Zealand sample sites, indicating that these two regions form distinct populations. Interpretation of the results for the mainland sites was more complex. Mitochondrial sequence data detected no significant pairwise differentiation between mainland sites, although a pattern of isolation-by-distance was observed. However, evidence for genetic differentiation among mainland sites was weak based on the microsatellite DNA analysis. Although pairwise Gѕт levels were significant in some sites, this was not reflected in principal component analysis or Bayesian structure analysis. It is likely that through long range dispersal, migration is at or above the threshold for genetic connectivity, but below a level necessary for demographic connectivity. This is indicated by both the genetic structure reported here, along with previous studies showing limited dispersal of P. colias.</p>

scholarly journals Temporally dynamic habitat suitability predicts genetic relatedness among caribou

2014 ◽  
Vol 281 (1792) ◽  
pp. 20140502 ◽  
Author(s):  
Glenn Yannic ◽  
Loïc Pellissier ◽  
Maël Le Corre ◽  
Christian Dussault ◽  
Louis Bernatchez ◽  
...  
Keyword(s):  
Habitat Selection ◽  
Habitat Use ◽  
Genetic Relatedness ◽  
Landscape Heterogeneity ◽  
Isolation By Distance ◽  
Temporal Variations ◽  
Genetic Connectivity ◽  
Landscape Permeability ◽  
Conservation Implications ◽  
Distance Model

Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.

scholarly journals Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

2019 ◽  
Vol 125 (1) ◽  
pp. 105-117 ◽  
Author(s):  
Yixuan Kou ◽  
Li Zhang ◽  
Dengmei Fan ◽  
Shanmei Cheng ◽  
Dezhu Li ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Divergence ◽  
Evolutionary History ◽  
Isolation By Distance ◽  
Demographic History ◽  
East China ◽  
Population Divergence ◽  
Isolation By Environment ◽  
Late Neogene ◽  
History Of

Abstract Background and Aims Many monotypic gymnosperm lineages in south-east China paradoxically remain in relict status despite long evolutionary histories and ample opportunities for allopatric speciation, but this paradox has received little attention and has yet to be resolved. Here, we address this issue by investigating the evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae). Methods DNA sequences from two chloroplast regions and 14 nuclear loci were obtained for 134 samples. The demographic history was inferred and the contribution of isolation by environment (IBE) in patterning genetic divergence was compared with that of isolation by distance (IBD). Key Results Three genetic clusters were identified. Approximate Bayesian computation analyses showed that the three clusters diverged in the late Pliocene (~3.68 Ma) and two admixture events were detected. Asymmetric gene flow and similar population divergence times (~ 3.74 Ma) were characterized using the isolation with migration model. Neither IBD nor IBE contributed significantly to genetic divergence, and the contribution of IBE was much smaller than that of IBD. Conclusions These results suggest that several monotypic relict gymnosperm lineages like P. chienii in south-east China did not remain in situ and undiversified for millions of years. On the contrary, they have been evolving and the extant populations have become established more recently, having insufficient time to speciate. Our findings provide a new perspective for understanding the formation and evolution of the relict gymnosperm flora of China as well as of the Sino-Japanese Flora.

Landscape structure and climatic variation determine Atlantic salmon genetic connectivity in the Northwest Atlantic

2014 ◽  
Vol 71 (2) ◽  
pp. 246-258 ◽  
Author(s):  
Ian R. Bradbury ◽  
Lorraine C. Hamilton ◽  
Martha J. Robertson ◽  
Chuck E. Bourgeois ◽  
Atef Mansour ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Spatial Structure ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Spatial Diversity ◽  
Genetic Connectivity ◽  
Stepwise Multiple Regression ◽  
Adaptive Divergence ◽  
Management And Conservation

The identification of landscape or climatic correlates of genetic connectivity can reveal the processes that regulate spatial diversity and inform the management and conservation of exploited or endangered species. Increasingly, the role of local adaptation in regulating spatial structure is gaining recognition, though disentangling its influence from that of dispersal and genetic drift remains challenging. We examined genetic connectivity using 15 microsatellite loci in 3546 Atlantic salmon (Salmo salar) from 47 locations in Newfoundland and Labrador. Cluster analysis revealed regional associations, but examples of unexpectedly high divergence over small spatial scales (<50 km) or low divergence over large scales (>500 km) were common with little evidence of isolation by distance (R2 = 0.04). We evaluated the hypothesis that spatial structure is less influenced by straying and more by adaptation and (or) drift using sample-associated data on 22 landscape and climate variables and both stepwise multiple regression and redundancy analysis. Landscape variables explained ∼40% of the variation in spatial structure with freshwater habitat area as the largest determinant. Linkages were also observed with water chemistry and winter severity, supporting hypotheses of adaptive divergence. Overall, the results suggest Atlantic salmon populations are structured by extensive genetic drift and low rates of effective straying and demonstrate how a landscape genetics approach can inform wildlife management and conservation.

scholarly journals High genetic connectivity in a gastropod with long-lived planktonic larvae

2019 ◽  
Vol 86 (1) ◽  
pp. 42-55 ◽  
Author(s):  
Fabio Crocetta ◽  
Luigi Caputi ◽  
Sofia Paz-Sedano ◽  
Valentina Tanduo ◽  
Angelo Vazzana ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Gross Anatomy ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Extrinsic Factors ◽  
Dna Sequence Data ◽  
Pelagic Larvae

Abstract Genetic connectivity plays a crucial role in shaping the geographic structure of species. Our aim in this study was to explore the pattern of genetic connectivity in Bursa scrobilator, an iconic marine caenogastropod with long-lived pelagic larvae. Our study was based on the analysis of DNA sequence data for the 658-bp barcoding fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. This is the largest DNA sequence dataset assembled to date for B. scrobilator. These data confirm that the two recently described subspecies B. scrobilator scrobilator (Linnaeus, 1758), from the Mediterranean and Macaronesia, and B. s. coriacea (Reeve, 1844), from West Africa, constitute two evolutionarily significant units (ESUs). We found that for the nominal subspecies, the variation in morphology (shell, radula and gross anatomy) and DNA sequences was not geographically structured, and this agrees with what we would expect in a species with high connectivity at the larval stage. The divergence between the two subspecies cannot be easily explained by isolation by distance, and we would argue that one or more extrinsic factors may have played a role in isolating the two ESUs and maintaining that isolation.

Evolutionary history of the calcareous sponge Clathrina aurea: genetic connectivity in the Western Atlantic and intriguing occurrence in the Eastern Pacific

2021 ◽  
Vol 168 (8) ◽  
Author(s):  
Báslavi Cóndor-Luján ◽  
Pedro Leocorny ◽  
André Padua ◽  
Fernanda Azevedo ◽  
Victor Corrêa Seixas ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Eastern Pacific ◽  
Genetic Connectivity ◽  
Western Atlantic ◽  
Calcareous Sponge ◽  
History Of
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