Strong genetic differentiation among populations of the freshwater shrimp Caridina cantonensis in Hong Kong: implications for conservation of freshwater fauna in urban areas

2017 ◽  
Vol 68 (1) ◽  
pp. 187 ◽  
Author(s):  
Ling Ming Tsang ◽  
Kwok Ho Tsoi ◽  
Simon Kin-Fung Chan ◽  
Tony King-Tung Chan ◽  
Ka Hou Chu
Keyword(s):  
Genetic Diversity ◽  
Hong Kong ◽  
Genetic Differentiation ◽  
Urban Areas ◽  
Habitat Destruction ◽  
Freshwater Shrimp ◽  
Genetic Structuring ◽  
Unique Haplotype ◽  
High Genetic Diversity ◽  
Mitochondrial Coi

Freshwater organisms generally exhibit strong genetic structuring. Although understanding the level and spatial distribution of genetic diversity is crucial for conservation management planning, such information has received little attention until recently in highly developed cities where local extinction attributed to habitat destruction and urbanisation is intense. We compared the genetic divergence in mitochondrial COI of the freshwater shrimp Caridina cantonensis collected from 32 sites in Hong Kong, to determine the connectivity among populations and the levels of genetic diversity of the shrimp. We found that shrimp from different streams are genetically highly differentiated and each stream always has its own unique haplotype groups, even though some of the streams are separated only by a few kilometres, indicating very limited gene flow across streams. Moreover, genetic diversity within each stream is very low, usually with a single haplotype dominating the entire population, and genetic differentiation was observed among tributaries from the same drainage. The high genetic diversity of these species over short distances has significant conservation implications because a substantial amount of biodiversity may have already been lost as a result of past development. Careful conservation planning is essential for future development in Hong Kong and other cities.

scholarly journals Phylogeography of the Brittle Star Ophiura sarsii Lütken, 1855 (Echinodermata: Ophiuroidea) from the Barents Sea and East Atlantic

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 40
Author(s):  
Evgeny Genelt-Yanovskiy ◽  
Yixuan Li ◽  
Ekaterina Stratanenko ◽  
Natalia Zhuravleva ◽  
Natalia Strelkova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Barents Sea ◽  
Haplotype Diversity ◽  
Brittle Star ◽  
The Arctic ◽  
Coi Gene ◽  
High Genetic Diversity ◽  
Svalbard Archipelago ◽  
Mitochondrial Coi ◽  
The Barents Sea

Ophiura sarsii is a common brittle star species across the Arctic and Sub-Arctic regions of the Atlantic and the Pacific oceans. Ophiurasarsii is among the dominant echinoderms in the Barents Sea. We studied the genetic diversity of O.sarsii by sequencing the 548 bp fragment of the mitochondrial COI gene. Ophiurasarsii demonstrated high genetic diversity in the Barents Sea. Both major Atlantic mtDNA lineages were present in the Barents Sea and were evenly distributed between the northern waters around Svalbard archipelago and the southern part near Murmansk coast of Kola Peninsula. Both regions, and other parts of the O.sarsii range, were characterized by high haplotype diversity with a significant number of private haplotypes being mostly satellites to the two dominant haplotypes, each belonging to a different mtDNA clade. Demographic analyses indicated that the demographic and spatial expansion of O.sarsii in the Barents Sea most plausibly has started in the Bølling–Allerød interstadial during the deglaciation of the western margin of the Barents Sea.

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 Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

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 Diet breadth and its relationship with genetic diversity and differentiation: the case of southern beech aphids (Hemiptera: Aphididae)

2004 ◽  
Vol 94 (3) ◽  
pp. 219-227 ◽  
Author(s):  
C. Gaete-Eastman ◽  
C.C. Figueroa ◽  
R. Olivares-Donoso ◽  
H.M. Niemeyer ◽  
C.C. Ramírez
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Diet Breadth ◽  
Aphid Species ◽  
Insect Species ◽  
Herbivorous Insect ◽  
Genetic Structuring ◽  
Closely Related Species ◽  
Single Host ◽  
Southern Beech

AbstractHerbivorous insect species with narrow diet breadth are expected to be more prone to genetic differentiation than insect species with a wider diet breadth. However, a generalist can behave as a local specialist if a single host-plant species is locally available, while a specialist can eventually behave as a generalist if its preferred host is not available. These problems can be addressed by comparing closely related species differing in diet breadth with overlapping distributions of insect and host populations. In this work, diet breadth, genetic diversity and population differentiation of congeneric aphid species from southern beech forests in Chile were compared. While at the species level no major differences in genetic diversity were found, a general trend towards higher genetic diversity as diet breadth increased was apparent. The aphid species with wider diet breadth, Neuquenaphis edwardsi (Laing), showed the highest genetic diversity, while the specialist Neuquenaphis staryi Quednau & Remaudière showed the lowest. These differences were less distinct when the comparisons were made in the same locality and over the same host. Comparison of allopatric populations indicates that genetic differentiation was higher for the specialists, Neuquenaphis similis Hille Ris Lambers and N. staryi, than for the generalist N. edwardsi. Over the same host at different locations, genetic differentiation among populations of N. edwardsi was higher than among populations of N. similis. The results support the assumption that specialists should show more pronounced genetic structuring than generalists, although the geographical distribution of host plants may be playing an important role.

scholarly journals Assessment of Genetic Diversity and Population Genetic Structure of Santalum album L. in India by Genic and Genomic SSR markers

2021 ◽  
Author(s):  
Tanzeem Fatima ◽  
Ashutosh Srivastava ◽  
Vageeshbabu S Hanur ◽  
M. Srinivasa Rao
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Germplasm Conservation ◽  
Principal Component ◽  
Santalum Album ◽  
High Genetic Diversity ◽  
Information Index ◽  
Genomic Ssr ◽  
Santalum Album L

Sandalwood (Santalum album L.) is highly valued aromatic tropical tree. It is known for its high quality heartwood and oil. In this study 39 genic and genomic SSR markers were used to analyze the genetic diversity and population structure of 177 S. album accessions from 14 populations of three states in India. High genetic diversity was observed in terms of number of alleles 127 expected heterozygosity (He) ranged from 0.63-0.87 and the average PIC was 0.85. The selected population had relatively high genetic diversity with Shannons information index (I) >1.0. 0.02 mean coefficient of genetic differentiation (FST) and 10.55 gene flow were observed. AMOVA revealed that 92% of the variation observed within individuals. Based on cluster and Structure result individuals were not clustered as per their geographical origin. Furthermore the clusters were clearly distinguished by principal component analysis analysis and the result revealed that PC1 reflected the moderate contribution in genetic variation (6%) followed by PC2 (5.5%). From this study, high genetic diversity and genetic differentiation was found in S. album populations. The genetic diversity information of S. album populations can be used for selection of superior genotypes and germplasm conservation to promote the tree improvement of S. album populations.

scholarly journals Genetic diversity, natural selection and haplotype grouping of Plasmodium vivax Duffy-binding protein genes from eastern and western Myanmar borders

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Yubing Hu ◽  
Lin Wang ◽  
Huguette Gaelle Ngassa Mbenda ◽  
Myat Thu Soe ◽  
Chunyun Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Genetic Differentiation ◽  
Plasmodium Vivax ◽  
Binding Protein ◽  
Duffy Binding Protein ◽  
High Genetic Diversity ◽  
Low Level ◽  
Malaria Epidemiology ◽  
Greater Mekong Subregion

Abstract Background Merozoite proteins of the malaria parasites involved in the invasion of red blood cells are selected by host immunity and their diversity is greatly influenced by changes in malaria epidemiology. In the Greater Mekong Subregion (GMS), malaria transmission is concentrated along the international borders and there have been major changes in malaria epidemiology with Plasmodium vivax becoming the dominant species in many regions. Here, we aimed to evaluate the genetic diversity of P. vivax Duffy-binding protein gene domain II (pvdbp-II) in isolates from the eastern and western borders of Myanmar, and compared it with that from global P. vivax populations. Methods pvdbp-II sequences were obtained from 85 and 82 clinical P. vivax isolates from the eastern and western Myanmar borders, respectively. In addition, 504 pvdbp-II sequences from nine P. vivax populations of the world were retrieved from GenBank and used for comparative analysis of genetic diversity, recombination and population structure of the parasite population. Results The nucleotide diversity of the pvdbp-II sequences from the Myanmar border parasite isolates was not uniform, with the highest diversity located between nucleotides 1078 and 1332. Western Myanmar isolates had a unique R391C mutation. Evidence of positive natural selection was detected in pvdbp-II gene in P. vivax isolates from the eastern Myanmar area. P. vivax parasite populations in the GMS, including those from the eastern, western, and central Myanmar as well as Thailand showed low-level genetic differentiation (FST, 0.000–0.099). Population genetic structure analysis of the pvdbp-II sequences showed a division of the GMS populations into four genetic clusters. A total of 60 PvDBP-II haplotypes were identified in 210 sequences from the GMS populations. Among the epitopes in PvDBP-II, high genetic diversity was found in epitopes 45 (379-SIFGT(D/G)(E/K)(K/N)AQQ(R/H)(R/C)KQ-393, π = 0.029) and Ia (416-G(N/K)F(I/M)WICK(L/I)-424], Ib [482-KSYD(Q/E)WITR-490, π = 0.028) in P. vivax populations from the eastern and western borders of Myanmar. Conclusions The pvdbp-II gene is genetically diverse in the eastern and western Myanmar border P. vivax populations. Positive natural selection and recombination occurred in pvdbp-II gene. Low-level genetic differentiation was identified, suggesting extensive gene flow of the P. vivax populations in the GMS. These results can help understand the evolution of the P. vivax populations in the course of regional malaria elimination and guide the design of PvDBP-II-based vaccine.

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

2019 ◽  
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 of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) ranged from 0.070 to 0.905, and the average locus polymorphic information content (PIC) was 0.5354. The provenance ‘Was’ had the lowest 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, clones distributed in 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 smaller gene flow and higher degree of genetic differentiation compared with the other provenances, and was classified into one group. There was no 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; however, the genetic variation among provenances has no clear correlation with their geographical locations. Clones reflecting population genetic information can be selected to build a core resource bank, which could provide effective protection and promote the scientific utilization of the P. deltoids resource, laying a solid foundation for poplar breeding.

scholarly journals Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

2011 ◽  
Vol 57 (6) ◽  
pp. 717-724 ◽  
Author(s):  
Jiandong Yang ◽  
Zhihe Zhang ◽  
Fujun Shen ◽  
Xuyu Yang ◽  
Liang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Giant Panda ◽  
Population Decline ◽  
Management Strategies ◽  
Ailuropoda Melanoleuca ◽  
High Genetic Diversity ◽  
Giant Pandas ◽  
Allele Number ◽  
High Level

Abstract Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A), Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort.

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