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.

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 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.

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 Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

2021 ◽  
Vol 12 ◽  
Author(s):  
Tian-Qi Shi ◽  
Hai-Mo Shen ◽  
Shen-Bo Chen ◽  
Kokouvi Kassegne ◽  
Yan-Bing Cui ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Positive Selection ◽  
Plasmodium Vivax ◽  
Yunnan Province ◽  
Duffy Binding Protein ◽  
Synonymous Mutations ◽  
Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

scholarly journals Whole-genome SNP analysis elucidates the genetic population structure and diversity of Acrocomia species

2020 ◽  
Author(s):  
Brenda G. Díaz ◽  
Maria I. Zucchi ◽  
Alessandro. Alves-Pereira ◽  
Caléo P. de Almeida ◽  
Aline C. L. Moraes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Structure ◽  
Genetic Relationships ◽  
Geographical Area ◽  
Taxonomic Classification ◽  
Genomic Diversity ◽  
Productive Capacity ◽  
Snp Analysis ◽  
Genetic Population

AbstractAcrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of seven species of Acrocomia including 117 samples of A. aculeata covering a wide geographical area of occurrence, using single nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS). The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.

scholarly journals Dynamic genetic diversity and population structure of Coreius guichenoti

ZooKeys ◽  
2021 ◽  
Vol 1055 ◽  
pp. 135-148
Author(s):  
Dongqi Liu ◽  
Feng Lan ◽  
Sicai Xie ◽  
Yi Diao ◽  
Yi Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Yangtze River ◽  
Fish Passage ◽  
The Yangtze River ◽  
Artificial Breeding ◽  
Significant Difference ◽  
High Elevations

To investigate the genetic effects on the population of Coreius guichenoti of dam constructions in the upper reaches of the Yangtze River, we analyzed the genetic diversity and population structure of 12 populations collected in 2009 and 2019 using mitochondrial DNA (mtDNA) control regions. There was no significant difference in genetic diversity between 2009 and 2019 (P > 0.05), but the population structure tended to become stronger. Genetic differentiation (FST) among five populations (LX, BB, YB, SF and JA) collected in 2009 was not significant (P > 0.05). However, some populations collected in 2019 were significantly differentiated (P < 0.05), indicating that the population structure has undergone change. A correlation analysis showed that the genetic diversity of the seven populations collected in 2019 was significantly negatively correlated with geographical height (r = −0.808, P = 0.028), indicating that the populations at high elevations were more vulnerable than those at low elevations. In order to prevent the further decrease of genetic diversity and population resources, some conservation and restoration suggestions, such as fish passage and artificial breeding, are put forward.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

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.

Genetic Diversity of Rice vampireweed (Rhamphicarpa fistulosa) Populations in Rainfed Lowland Rice in West Africa

Weed Science ◽  
2016 ◽  
Vol 64 (3) ◽  
pp. 430-440
Author(s):  
Norliette Zossou ◽  
Hubert Adoukonèou-Sagbadja ◽  
Daniel Fonceka ◽  
Lamine Baba-Moussa ◽  
Mbaye Sall ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Lowland Rice ◽  
Rice Grain ◽  
High Genetic Diversity ◽  
Genetic Groups ◽  
Rainfed Lowland ◽  
Rice Genotypes ◽  
The Relationship ◽  
Aflp Technique

Rice vampireweed belongs to the Orobanchaceae and is found in Africa and Australia. It is a hemiparasitic weed of lowland rice genotypes and causes losses of 40 to 100% of rice grain yield. Our study addressed the genetic diversity of rice vampireweed in Benin and Senegal. The specific objectives of this research were to study the genetic diversity of rice vampireweed accessions in Benin and Senegal and the relationship between the different genotypes of rice vampireweed through agroecological areas. To achieve these objectives, the genetic diversity of rice vampireweed accessions using the AFLP technique was studied. Based on our results, dendrogram classification has distinguished four different genetic groups. The populations of Benin and Senegal are genetically diverse. Substantial genetic differentiation (GST) exists among agroecological areas within Benin and Senegal (GST = 0.17). The high genetic diversity of rice vampireweed in Benin and Senegal presents a challenge for the development of resistant rice germplasm.

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.

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