scholarly journals Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
E. Boissin ◽  
S. R. Thorrold ◽  
C. D. Braun ◽  
Y. Zhou ◽  
E. E. Clua ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Spatial Scales ◽  
Biological Information ◽  
Shark Species ◽  
Central Pacific ◽  
South Central ◽  
The Pacific ◽  
Reef Sharks

Abstract Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (FST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.

Prominent genetic structure across native and introduced ranges of Pluchea indica, a mangrove associate, as revealed by microsatellite markers

2020 ◽  
Vol 13 (3) ◽  
pp. 341-353
Author(s):  
Yuting Lin ◽  
Achyut Kumar Banerjee ◽  
Haidan Wu ◽  
Fengxiao Tan ◽  
Hui Feng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Scales ◽  
Large Spatial Scale ◽  
Introduced Range ◽  
Native And Introduced Ranges ◽  
Mangrove Associate

Abstract Aims Pluchea indica is a mangrove-associate species, known for its medicinal properties in its native range and being invasive in part of its introduced range. This study aimed to assess geographic distribution of genetic variation of this species across its distribution range, identify the factors influencing its genetic structure and use this information to suggest conservation and management strategies in its native and introduced ranges, respectively. Methods We assessed the genetic diversity and population structure of 348 individuals from 31 populations across its native (Asia) and introduced (USA) ranges for 15 nuclear microsatellite loci. The spatial pattern of genetic variation was investigated at both large and regional spatial scales with the hypothesis that geographic distance and natural geographic barriers would influence the population structure with varying levels of differentiation across spatial scales. Important Findings We found relatively high genetic diversity at the population level and pronounced genetic differentiation in P. indica, as compared with the genetic diversity parameters of mangroves and mangrove associates in this region. Most of the populations showed heterozygote deficiency, primarily due to inbreeding and impediment of gene flow. Analysis of population structures at large spatial scale revealed the presence of two major clusters across the species’ natural range separating populations in China from those in Indonesia, Malaysia, Singapore, Thailand, Cambodia and Philippines, and that the USA population might have been introduced from the population cluster in China. Genetic differentiation between populations was also observed at the regional scale. A large number of populations showed evidence of genetic bottleneck, thereby emphasizing the risk of local extinction. Based on these findings, our study recommends in situ conservation strategies, such as to prioritize populations for conservation actions and to maintain genetic diversity.

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 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.

scholarly journals Fine-Scale Population Structure but Limited Genetic Differentiation in a Cooperatively Breeding Paper Wasp

2020 ◽  
Vol 12 (5) ◽  
pp. 701-714 ◽  
Author(s):  
Sarah E Bluher ◽  
Sara E Miller ◽  
Michael J Sheehan
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Cooperative Breeding ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Paper Wasp ◽  
Paper Wasps ◽  
Natal Philopatry ◽  
Continental Scale ◽  
Cooperatively Breeding

Abstract Relatively little is known about the processes shaping population structure in cooperatively breeding insect species, despite the long-hypothesized importance of population structure in shaping patterns of cooperative breeding. Polistes paper wasps are primitively eusocial insects, with a cooperative breeding system in which females often found nests in cooperative associations. Prior mark-recapture studies of Polistes have documented extreme female philopatry, although genetic studies frequently fail to detect the strong population structure expected for highly philopatric species. Together these findings have led to lack of consensus on the degree of dispersal and population structure in these species. This study assessed population structure of female Polistes fuscatus wasps at three scales: within a single site, throughout Central New York, and across the Northeastern United States. Patterns of spatial genetic clustering and isolation by distance were observed in nuclear and mitochondrial genomes at the continental scale. Remarkably, population structure was evident even at fine spatial scales within a single collection site. However, P. fuscatus had low levels of genetic differentiation across long distances. These results suggest that P. fuscatus wasps may employ multiple dispersal strategies, including extreme natal philopatry as well as longer-distance dispersal. We observed greater genetic differentiation in mitochondrial genes than in the nuclear genome, indicative of increased dispersal distances in males. Our findings support the hypothesis that limited female dispersal contributes toward population structure in paper wasps.

Genetic diversity and population structure of small yellow croaker (Larimichthys polyactis) in the Yellow and East China seas based on microsatellites

2019 ◽  
Vol 32 ◽  
pp. 16
Author(s):  
Qiqun Cheng ◽  
Wenming Chen ◽  
Li Ma
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
East China ◽  
Rank Test ◽  
Northwestern Pacific ◽  
Allele Frequency Distribution ◽  
China Seas ◽  
Larimichthys Polyactis ◽  
Small Yellow Croaker

Small yellow croaker (Larimichthys polyactis), a member of family Sciaenidae, is mainly distributed in the northwestern Pacific Ocean. To assess the genetic diversity and population structure of this species across its range, we genotyped 150 L. polyactis individuals sampled in five locations along the coast of the Yellow and East China seas using 20 polymorphic microsatellites. A total of 499 alleles were detected at 20 loci across all individuals, and a relatively high level of genetic diversity was observed, with observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) ranging from 0.233 to 1.000, from 0.438 to 0.955, and from 0.367 to 0.953 per locus-location combination, respectively. Analysis of molecular variance (AMOVA) (FST = 0.00915, P < 0.001), pairwise FST, and corrected average pairwise differences indicated that there was extremely low, but statistically significant genetic differentiation among the studied populations. However, Bayesian assignment analysis revealed a high number of immigrants among populations and no obvious genetic differentiation. The Wilcoxon signed-rank test and mode-shift indicator of allele frequency distribution support the inferrence that L. polyactis had not experienced a recent genetic bottleneck. Overall, the results suggest that, despite low genetic differentiation in this species, the small yellow croaker forms a single panmictic population with high genetic variation and gene flow in the studied area. This study will provide useful information for conservation and sustainable exploitation of this important aquatic living resource.

Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers

2012 ◽  
Vol 92 (4) ◽  
pp. 417-423 ◽  
Author(s):  
Jinjun Li ◽  
Qingyuan Yuan ◽  
Junda Shen ◽  
Zhengrong Tao ◽  
Guoqing Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Evolutionary Relationships ◽  
Distance Estimate ◽  
Cluster Analyses ◽  
Nei's Genetic Distance

Li, J., Yuan, Q., Shen, J., Tao, Z., Li, G., Tian, Y., Wang, D., Chen, L. and Lu, L. 2012. Evaluation of the genetic diversity and population structure of five indigenous and one introduced Chinese goose breeds using microsatellite markers. Can. J. Anim. Sci. 92: 417–423. The aim of this study was to determine the genetic diversity and evolutionary relationships among five indigenous Chinese goose breeds and one introduced goose breed using 29 microsatellite markers. A total of 334 distinct alleles were observed across the six breeds, and 45 of the 334 alleles (13.5%) were unique to only one breed. The indigenous geese showed higher diversity in terms of the observed number of alleles per locus (4.48–5.90) and observed heterozygosity (0.46–0.53) compared with the introduced breed (3.97 and 0.29, respectively). The pairwise genetic differentiation (FST) between the six goose breeds ranged from 0.04 between Panshi Grey goose (PS) and Yongkang Grey goose to 0.47 between PS and Landes goose; similarly, Nei's genetic distance varied between 0.25 and 0.75. However, the FST between the indigenous Chinese goose breeds was very small. In addition, genetic distance estimate, phylogenic, and cluster analyses of the genetic relationships and population structure revealed that some indigenous goose breeds had hybridized more frequently, resulting in a loss of genetic distinctiveness.

Molecular and morphological evolution in the south-central Pacific skink Emoia tongana (Reptilia : Squamata): uniformity and human-mediated dispersal

1999 ◽  
Vol 47 (5) ◽  
pp. 425 ◽  
Author(s):  
Christopher C. Austin ◽  
George R. Zug
Keyword(s):  
Pacific Islands ◽  
Morphological Evolution ◽  
Research Effort ◽  
Tropical Pacific ◽  
The South ◽  
Central Pacific ◽  
South Central ◽  
The Poor ◽  
The Pacific ◽  
Minimal Research

Human-mediated and waif dispersal are both responsible for the distribution of lizards on tropical Pacific islands. The component of each of these dispersal modes to the Pacific herpetofauna, however, is unclear. Morphological conservatism of Pacific lizards, the poor paleontological record on tropical Pacific islands, and minimal research effort in the Pacific (compared with other island systems) has hampered our understanding of waif versus human-mediated patterns. We examine morphological and genetic variation of Emoia concolor and E. tongana (formerly E. murphyi), two scincid lizards, from the south-central Pacific, to assess modes of dispersal and population structure. Emoia tongana from Tonga and Samoa is genetically uniform, suggesting that these are synanthropic populations recently introduced, presumably from Fiji. Relatively large genetic divergence is evident for populations of E. concolor within the Fijian archipelago, suggesting prehuman intra-archipelago dispersal and isolation.

Sign in / Sign up

Export Citation Format

Share Document