scholarly journals Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Samantha J. Nowland ◽  
Catarina N. S. Silva ◽  
Paul C. Southgate ◽  
Jan M. Strugnell
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Population Subdivision ◽  
Data Set ◽  
Mitochondrial Coi ◽  
Rock Oyster ◽  
Snp Data ◽  
Genetic Clusters

Abstract Background The black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers. Results The mitochondrial COI data set included 273 sequences of 594 base pair length, which comprised 74 haplotypes. The SNP data set included 27,887 filtered SNPs for 272 oysters and of these 31 SNPs were identified as candidate adaptive loci. Data from the mitochondrial COI analyses, supports a broad tropical Indo-Pacific distribution of S. echinata, and showed high haplotype and nucleotide diversities (0.887–1.000 and 0.005–0.008, respectively). Mitochondrial COI analyses also revealed a ‘star-like’ haplotype network, and significant and negative neutrality tests (Tajima’s D = − 2.030, Fu’s Fs = − 25.638, P < 0.001) support a recent population expansion after a bottleneck. The SNP analyses showed significant levels of population subdivision and four genetic clusters were identified: (1) the Noumea (New Caledonia) sample location; (2) the Bowen (north Queensland, Australia) sample location, and remaining sample locations in the Northern Territory, Australia (n = 8) were differentiated into two genetic clusters. These occurred at either side of the Wessel Islands and were termed (3) ‘west’ and (4) ‘east’ clusters, and two migrant individuals were detected between them. The SNP data showed a significant positive correlation between genetic and geographic distance (Mantel test, P < 0.001, R2 = 0.798) and supported isolation by distance. Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene. Conclusions Data supports the existence of genetically distinct populations of S. echinata, suggesting that management of wild and farmed stocks should be based upon multiple management units. This research has made information on population genetic structure and connectivity available for a new aquaculture species.

scholarly journals Genomic epidemiology ofMycobacterium bovisinfection in sympatric badger and cattle populations in Northern Ireland

2021 ◽  
Author(s):  
Assel Akhmetova ◽  
Jimena Guerrero ◽  
Paul McAdam ◽  
Liliana C.M. Salvador ◽  
Joseph Crispell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spatial Distribution ◽  
Genetic Structure ◽  
Northern Ireland ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Transmission Dynamics ◽  
Data Set ◽  
Hair Samples ◽  
Disease Persistence

AbstractBackgroundBovine tuberculosis (bTB) is a costly epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra- species host transmission for disease persistence. We sequenced an exceptional data set of 619Mycobacterium bovisisolates from badgers and cattle in a 100km2bTB ‘hotspot’ in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area.ResultsGraph transmission tree methods and structured coalescent analyses indicated the majority of bacterial diversity was found in the local cattle population. Results pointed to transmission from cattle to badger being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution ofM. bovisgenetic diversity, suggesting that badger-to-badger transmission may not be a key determinant of disease persistence.SignificanceOur data were consistent with badgers playing a smaller role in the maintenance ofM. bovisinfection in this study site, compared to cattle. Comparison to other areas suggests thatM. bovistransmission dynamics are likely to be context dependent, and the role of wildlife difficult to generalise.

Population genetic structure of wild and farmed rusa deer (Cervus timorensis russa) in New-Caledonia inferred from polymorphic microsatellite loci

Genetica ◽  
2009 ◽  
Vol 137 (3) ◽  
pp. 313-323 ◽  
Author(s):  
M. de Garine-Wichatitsky ◽  
T. de Meeûs ◽  
C. Chevillon ◽  
D. Berthier ◽  
N. Barré ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
New Caledonia ◽  
Polymorphic Microsatellite

Population genetic structure and species delimitation in the Cryptanthus zonatus complex (Bromeliaceae)

2020 ◽  
Author(s):  
Débora Maria Cavalcanti Ferreira ◽  
Clarisse Palma-Silva ◽  
Jordana Néri ◽  
Maria Cláudia Melo Pacheco de Medeiros ◽  
Diego Sotero Pinangé ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Species Delimitation ◽  
Population Genetic ◽  
Species Complex ◽  
Conservation Status ◽  
Niche Modelling ◽  
Morphological Comparison ◽  
Morphological Variations ◽  
Genetic Clusters

Abstract Morphological variations of individuals and populations of plants have hampered taxonomists from understanding whether such variations are intra- or interspecific. In this research, we study Cryptanthus burle-marxii and C. zonatus, the morphological variations of which overlap, making it difficult to identify them. Both taxa are restricted to the north of the Brazilian Atlantic Forest and are included in the C. zonatus species complex. We applied different methods such as morphological comparison, population genetics using ten nuclear microsatellite markers and ecological niche modelling to study population genetic structure and species delimitation of this species complex. Our analysis revealed that the two genetic clusters were formed possibly because of the presence of a historical geographical barrier in a region called ‘depressão do Abiaí’. The two genetic clusters were concordant with the northern and southern distribution of the complex but incongruent with a morphological variation or current taxonomic delimitation. Thus, we synonymize C. burle-marxii with C. zonatus and re-evaluate its conservation status as endangered.

scholarly journals Population Genetic Structure of Clinical and Environmental Isolates of Blastomyces dermatitidis, Based on 27 Polymorphic Microsatellite Markers

2011 ◽  
Vol 77 (15) ◽  
pp. 5123-5131 ◽  
Author(s):  
Jennifer K. Meece ◽  
Jennifer L. Anderson ◽  
Matthew C. Fisher ◽  
Daniel A. Henk ◽  
Brian L. Sloss ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Microsatellite Markers ◽  
Mating Type ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Blastomyces Dermatitidis ◽  
Environmental Isolates ◽  
Data Set ◽  
Content Type ◽  
Genetic Groups

ABSTRACTBlastomyces dermatitidis, a thermally dimorphic fungus, is the etiologic agent of North American blastomycosis. Clinical presentation is varied, ranging from silent infections to fulminant respiratory disease and dissemination to skin and other sites. Exploration of the population genetic structure ofB. dermatitidiswould improve our knowledge regarding variation in virulence phenotypes, geographic distribution, and difference in host specificity. The objective of this study was to develop and test a panel of microsatellite markers to delineate the population genetic structure within a group of clinical and environmental isolates ofB. dermatitidis. We developed 27 microsatellite markers and genotypedB. dermatitidisisolates from various hosts and environmental sources (n=112). Assembly of a neighbor-joining tree of allele-sharing distance revealed two genetically distinct groups, separated by a deep node. Bayesian admixture analysis showed that two populations were statistically supported. Principal coordinate analysis also reinforced support for two genetic groups, with the primary axis explaining 61.41% of the genetic variability. Group 1 isolates average 1.8 alleles/locus, whereas group 2 isolates are highly polymorphic, averaging 8.2 alleles/locus. In this data set, alleles at three loci are unshared between the two groups and appear diagnostic. The mating type of individual isolates was determined by PCR. Both mating type-specific genes, the HMG and α-box domains, were represented in each of the genetic groups, with slightly more isolates having the HMG allele. One interpretation of this study is that the species currently designatedB. dermatitidisincludes a cryptic subspecies or perhaps a separate species.

scholarly journals Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243556
Author(s):  
Natalie Breidenbach ◽  
Oliver Gailing ◽  
Konstantin V. Krutovsky
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Ssr Markers ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Sequoia Sempervirens ◽  
Data Sets ◽  
Data Set ◽  
Coast Redwood ◽  
Natural Range

Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial timber species, especially in perspective to climate warming that makes more regions in Germany suitable for its growing. The well performing trees in colder Germany could be potential frost resistant genotypes, but their genetic properties and origin are mostly unknown. Within the natural range in southern Oregon and northern California, only two relatively weak clusters were identified, one northern and one southern, separated by the San Francisco Bay. High genetic diversity, but low differentiation was found based on the 12 nuclear SSR markers for all three data sets F, C and G. We found that investigated 147 German trees represented only 37 different genotypes. They showed genetic diversity at the level less than diversity observed within the natural range in the northern or southern cluster, but more similar to the diversity observed in the southern cluster. It was difficult to assign German trees to the original single native populations using the six cpSSR markers, but rather to either the northern or southern cluster. The high number of haplotypes found in the data sets based on six cpSSR markers and low genetic differentiation based on 12 nuclear SSRs found in this study helps us study and better understand population genetic structure of this complex polyploid tree and supports the selection of potential genotypes for German forestry.

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