scholarly journals Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ryo Orita ◽  
Yukio Nagano ◽  
Yoshio Kawamura ◽  
Kei Kimura ◽  
Genta Kobayashi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Snp Markers ◽  
Genetic Population Structure ◽  
Ariake Bay ◽  
Genetic Population ◽  
Sinonovacula Constricta ◽  
Razor Clam ◽  
High Level

AbstractThe razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

scholarly journals Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

2020 ◽  
Author(s):  
Ryo Orita ◽  
Yukio Nagano ◽  
Yoshio Kawamura ◽  
Kei Kimura ◽  
Genta Kobayashi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Snp Markers ◽  
Genetic Population Structure ◽  
Ariake Bay ◽  
Genetic Population ◽  
Sinonovacula Constricta ◽  
Razor Clam ◽  
High Level

AbstractThe razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, the two genetically distinct populations need to be available as fishery resources, while taking into account their conservation and hybridization status.

Genetic population structure and connectivity in a commercially exploited and wide-ranging deepwater shark, the leafscale gulper (Centrophorus squamosus)

2012 ◽  
Vol 63 (6) ◽  
pp. 505 ◽  
Author(s):  
A. Veríssimo ◽  
J. R. McDowell ◽  
J. E. Graves
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
New Zealand ◽  
Indian Ocean ◽  
Genetic Homogeneity ◽  
Genetic Population Structure ◽  
Maturity Stage ◽  
Genetic Population ◽  
The Indian Ocean ◽  
Nuclear Loci

The leafscale gulper (Centrophorus squamosus) is a wide-ranging deepwater benthopelagic shark threatened by commercial fisheries in parts of its range. Despite concerns about resource sustainability, little is known about the population structure and connectivity between critical habitats of the leafscale gulper. This study investigates the genetic population structure and the migration patterns of C. squamosus using nuclear microsatellites and mitochondrial NADH dehydrogenase subunit 2 (ND2) gene sequences. Genetic diversity was estimated and compared among sample collections from off Ireland, Portugal, the Azores, South Africa and New Zealand. The null hypothesis of genetic homogeneity among all collections was not rejected by the nuclear loci (FST (the overall genetic differentiation among sample collections) = –0.002, P = 0.88), but we found long-term genetic divergence between New Zealand and the remaining collections at the mtDNA ND2 (FCT (genetic differentation among groups of sample collections) = 0.366, P = 0.000). Migration rate estimates indicated limited female dispersal across the Indian Ocean whereas males showed less restricted dispersal. Our results are consistent with a single genetic stock of C. squamosus and the existence of sex-biased dispersal across the Indian Ocean. Widespread genetic homogeneity at nuclear loci minimizes the loss of unique adaptive genetic diversity in the event of localised depletion. However, high local fishing mortality may have far reaching impacts given the marked sex- and maturity-stage-based habitat partitioning previously reported for C. squamosus.

scholarly journals Genetic population structure of the blue sea star Linckia laevigata in the Visayas (Philippines)

2015 ◽  
pp. 1-7 ◽  
Author(s):  
Diana Sr Alcazar ◽  
Marc Kochzius
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Comparative Analysis ◽  
Marine Invertebrates ◽  
Genetic Population Structure ◽  
Sea Star ◽  
Genetic Population ◽  
Gene Coi ◽  
Linckia Laevigata

Coral reef associated marine invertebrates, such as the blue sea starLinckia laevigata, have a life history with two phases: sedentary adults and planktonic larvae. On the one hand it is hypothesised that the long pelagic larval duration facilitates large distance dispersal. On the other hand, complex oceanographic and geographic characteristics of the Visayan seascape could cause isolation of populations. The study aims to investigate the genetic diversity, genetic population structure and gene flow inL. laevigatato reveal connectivity among populations in the Visayas. The analysis is based on partial sequences (626 bp in length) of the mitochondrial cytochrome oxidase I gene (COI) from 124 individuals collected from five localities in the Visayas. A comparative analysis of these populations with populations from the Indo-Malay Archipelago (IMA) published previously is also presented. Genetic diversity was high (h = 0.98, π = 1.6%) and comparable with preceding studies. Analyses of molecular variance (AMOVA) revealed a lack of spatial population differentiation among sample sites in the Visayas (ΦST-value = 0.009;P > 0.05). The lack of genetic population structure indicates high gene flow among populations ofL. laevigatain the Visayas. Comparative analysis with data from the previous study indicates high connectivity of the Visayas with the central part of the IMA.

scholarly journals Genetic assessment reveals inbreeding, possible hybridization and low levels of genetic structure in a declining goose population

2021 ◽  
Author(s):  
Johanna Honka ◽  
Serena Baini ◽  
Jeremy Searle ◽  
Laura Kvist ◽  
Jouni Aspi
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Incomplete Lineage Sorting ◽  
Extinction Risk ◽  
Genetic Population Structure ◽  
Natal Philopatry ◽  
Genetic Structuring ◽  
Genetic Population ◽  
Bean Goose

The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase the extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (A. brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.

scholarly journals Genetic Diversity and Population Structure Revealed by SSR Markers on Endemic Species Osmanthus serrulatus Rehder from Southwestern Sichuan Basin, China

Forests ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1365
Author(s):  
Lin Chen ◽  
Tingting Pan ◽  
Huirong Qian ◽  
Min Zhang ◽  
Guodong Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Sichuan Basin ◽  
Polymorphic Information Content ◽  
Population Decline ◽  
Natural Populations ◽  
Genetic Population ◽  
Endangered Status ◽  
High Level

Osmanthus serrulatus Rehder (Oleaceae) is an endemic spring-flowering species in China. It is narrowly distributed in the southwestern Sichuan Basin, and is facing the unprecedented threat of extinction due to problems associated with natural regeneration, habitat fragmentation and persistent and serious human interference. Here, the genetic diversity and population structure of 262 individuals from ten natural populations were analyzed using 18 microsatellites (SSR) markers. In total, 465 alleles were detected across 262 individuals, with a high polymorphic information content (PIC = 0.893). A high level of genetic diversity was inferred from the genetic diversity parameters (He = 0.694, I = 1.492 and PPL = 98.33%). AMOVA showed that a 21.55% genetic variation existed among populations and the mean pairwise Fst (0.215) indicated moderate genetic population differentiation. The ten populations were basically divided into three groups, including two obviously independent groups. Our results indicate that multiple factors were responsible for the complicated genetic relationship and endangered status of O. serrulatus. The concentrated distribution seems to be the key factor causing endangerment, and poor regeneration, human-induced habitat loss and fragmentation seem to be the primary factors in the population decline and further genetic diversity loss. These findings will assist in future conservation management and the scientific breeding of O. serrulatus.

scholarly journals PSVIII-23 High-density SNP marker based genetic diversity and population structure study of reindeer populations

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 265-266
Author(s):  
Veronika R Kharzinova ◽  
Arsen V Dotsev ◽  
Anastasiya Solovieva ◽  
Klaus Wimmers ◽  
Henry Reyer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Structure Study ◽  
Snp Markers ◽  
Negative Effects ◽  
Russian Science ◽  
Data Set ◽  
Northern Territories ◽  
High Level ◽  
Wild Reindeer

Abstract Wild reindeer populations form the basis of the traditional activities of indigenous peoples of the northern territories of Siberia, the main part of which is concentrated in two large regions: Taimyr and Northern Yakutia. Currently, there is a sharp decline in the number of wild reindeer, which leads to a loss of the genetic diversity necessary for survival in the changing habitat conditions. To infer the population structure and genome-wide diversity of wild reindeer, the Taymyr (TAI, n = 33) and Yakut populations including Tundra Leno-Olenek (LNO, n = 20), the Island (ISL, n = 6), the Sundrun (SUN, n = 6) and the Taiga (TGA, n = 5) were genotyped with the Illumina Bovine HD BeadChip. Data set consisting of 8801 polymorphic SNP markers was used to calculate population genetic parameters in PLINK 1.9, SplitsTree 4.14.6. software, R packages “diveRsity” and “StAMMP.” We detected the similar level of observed heterozygosity across the TAI, ISL, SUN and LNO: 0.187, 0.188, 0.184, and 0.189 respectively. Meanwhile, allelic richness was slightly higher in Taimyr population compared to the Yakut groups. The lowest level of genetic diversity was recorded in the Taiga reindeer (Ho=0.168; Ar = 1.476). All populations showed heterozygotes deficiency (uFIS 95%, CI > 0) with higher uFIS values in TGA (0.079). MDS analysis revealed the high level of genetic similarity of TAI, ISL and LNO and placed SUN in close proximity to them. The first and the second MDS components (2.36% and 2.15% of the genetic variability) clearly divided the Taiga reindeer, the genetic apartness of which was also confirmed by the results of the Neighbour-Net tree analysis. Information obtained here, might be helpful for further effective use and maintenance of the reindeer populations as well as for overcoming the negative effects of decreasing their number. The study was supported by Russian Science Foundation within Pr. no. 16-16-10068.

scholarly journals Interspecific Comparisons of Genetic Population Structure in Members of the Jaera Albifrons Species Complex

1997 ◽  
Vol 77 (1) ◽  
pp. 77-93 ◽  
Author(s):  
Gary R. Carvalho ◽  
Stuart B. Piertney
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Species Complex ◽  
Niche Width ◽  
Allozyme Electrophoresis ◽  
Genetic Population ◽  
Interspecific Comparisons ◽  
The Relationship ◽  
Variability Data

Marked genetic differentiation in the intertidal isopod, Jaera albifrons (Crustacea: Isopoda) has been shown to occur on a scale of just a few metres on British shores. Allozyme electrophoresis at 21 enzyme-coding loci has been employed to examine genetic structure in other UK members of the complex (Jaera forsmani, J. ischiosetosa, J. praehirsuta), and explore the relationship between genetic diversity and perceived niche-width. Comparisons were made with the nonsibling species J. nordmanni. Three subpopulations of each species taken from each of two shores on Anglesey, UK (subpopulations N=30) were assayed for electrophoretic variability. Data from 11 polymorphic loci (P0·95) demonstrated marked genetic differentiation in all populations of J. albifrons and J. praehirsuta, and on one shore for each of J. ischiosetosa and J. nordmanni, with J. praehirsuta (GST=0·207) and J. albifrons (GST=0·121) showing the highest genetic differentiation. In contrast, J. forsmani exhibited population homogeneity on both shores studied. Genetic diversity ranged markedly across species (H0=0·165—0·040), with the two most widely distributed species, J. albifrons (H0=0·135) and J. ischiosetosa (Ho=0·165) exhibiting the highest genetic variability, providing support for the niche-width variation hypothesis. Data indicate that although habitat fragmentation and direct development is associated with microgeographic differentiation in Jaera spp., localized factors such as habitat continuity and exposure to water movements determines the magnitude of such effects.

The genetic population structure of lotic and lentic mayflies of theBaetis vernusgroup (Ephemeroptera: Baetidae)

2012 ◽  
Vol 144 (5) ◽  
pp. 679-690 ◽  
Author(s):  
Marcus K. Drotz ◽  
Eino Savolainen ◽  
Anssi Saura ◽  
Gunilla Ståhls
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Genetic Population Structure ◽  
Flowing Water ◽  
Gene Frequencies ◽  
Genetic Population ◽  
Population Genetic Differentiation ◽  
Gene Coi ◽  
Population Structuring ◽  
Unpredictable Environment

AbstractNymphs of lotic mayflies live in environments that are expected to give rise to different degrees of population structuring. Here we investigate two taxa adapted to different lifestyles.Baetis macaniKimmins (Ephemeroptera: Baetidae) lives in flowing water; brooks that may periodically dry out in the summer or freeze to the bottom in winter.Baetis jaerviiSavolainen is mostly found in sedge belts along the shores of lakes. Most insects living in flowing water show low levels of among-population genetic differentiation within and among catchments. Levels of differentiation in the lotic species are therefore assumed to be lower than in lenticB. jaervii. Here we test this hypothesis. Mitochondrial DNA and allele frequencies of nuclear genes were used to detect population structure in specimens originating from an extensive area from northern Finland. The genetic differentiation among populations of the loticB. macaniis more than twice the corresponding value for the lenticB. jaervii(FST0.33 versus 0.15, while the meanFSTbetween species was 0.33 and significant). The result is congruent within the cytochrome c oxidase subunit I gene (COI) partial gene frequencies. We argue that the significant genetic population structure, which only was found in the loticB. macani, is differentiated as a consequence to the unpredictable environment as contrasted to the stable environment in standing bodies of water.

scholarly journals Genetic Diversity and Population Genetic Structure of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River by Chloroplast Microsatellite Markers

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 592
Author(s):  
Bei Cui ◽  
Ping Deng ◽  
Sheng Zhang ◽  
Zhong Zhao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Yellow River ◽  
The Yellow River ◽  
Group Method ◽  
Chloroplast Microsatellite ◽  
Genetic Population ◽  
Geographic Population ◽  
Platycladus Orientalis

Ancient trees are famous for their life spans of hundreds or even thousands of years. These trees are rare, a testament to history and are important for scientific research. Platycladus orientalis, with the longest life span and a beautiful trunk, has become the most widely planted tree species and is believed to be sacred in China. Extensive declines in habitat area and quality pose the greatest threats to the loss of genetic diversity of ancient P. orientalis trees in the middle reaches of the Yellow River. Strengthening the protection of P. orientalis genetic resources is of great significance for the long-term development of reasonable conservation and breeding strategies. To better understand the genetic diversity and population structure of P. orientalis, we successfully analyzed four polymorphic chloroplast simple sequence repeat (cpSSR) loci and applied them to diversity and population structure analyses of 202 individuals from 13 populations in the middle reaches of the Yellow River. Based on the cpSSR data, 16 alleles were detected across 202 individuals, and a moderate level of genetic diversity was inferred from the genetic diversity parameters (H = 0.367 and AR = 1.964). The mean pairwise genetic differentiation coefficient (Fst) between populations was 0.153, indicating relatively high genetic population differentiations. Analysis of molecular variance (AMOVA) showed that only 8% of the variation occurred among populations. Structure analysis divided the 13 P. orientalis populations into two groups with no significant geographic population structure, which was consistent with the unweighted pair group method with arithmetic mean (UPGMA) and Mantel test results. These results may indicate that transplanting and cultivation by ancient human activities are the main factors responsible for the revealed pattern of genetic differentiation of ancient P. orientalis populations. Our research is of great significance for the future establishment of protection schemes and scientific breeding of P. orientalis.

scholarly journals Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 995
Author(s):  
Wanchana Aesomnuk ◽  
Siriphat Ruengphayak ◽  
Vinitchan Ruanjaichon ◽  
Tanee Sreewongchai ◽  
Chanate Malumpong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Mantel Test ◽  
Snp Markers ◽  
High Yield ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Geographical Regions

Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to indica and japonica groups. The indica group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise FST showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.

Sign in / Sign up

Export Citation Format

Share Document