Population genetic structure of Sagittaria natans (Alismataceae), an endangered species in China, revealed by nuclear SSR loci analyses

Abstract The species Capoeta aculeata (Valenciennes, 1844) is one of the most important freshwater species endemic to Iran. However, the investigation of a population genetic structure of this species is limited by the low number of molecular markers currently described. In this study, we implemented next generation sequencing technology to identify polymorphic microsatellite markers and investigate the population genetic structure of C. aculeata sampled from three geographical sites in Iran. We sequenced 60 individuals from three populations occurring in the Zagros basin. We characterized and developed 36 novel polymorphic microsatellite markers and these loci were examined in 120 individuals from three populations occurring in the Zagros basin. The average number of alleles per locus varied from 1.7 to 16. (average = 7.89). The results showed that, the polymorphism information content (PCI) of these SSR loci varied from 0.254 to 0.888. The observed heterozygosity (Ho) per locus ranged from 0.170 to 0.881, while the expected heterozygosity (He) per locus was from 0.170 to 0.881. Among these SSR loci, 20 loci deviated significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (p< 0.05). These microsatellite markers could provide a valuable tool for future population and conservation genetics studies of C. aculeate populations and other closely related species.

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Genetic Diversity and Population Genetic Structure of Erythrophleum fordii Oliv., an Endangered Rosewood Species in South China

Forests ◽

10.3390/f9100636 ◽

2018 ◽

Vol 9 (10) ◽

pp. 636 ◽

Cited By ~ 3

Author(s):

Jing Tan ◽

Zhi-Gang Zhao ◽

Jun-Jie Guo ◽

Chun-Sheng Wang ◽

Jie Zeng

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Endangered Species ◽

Genetic Differentiation ◽

South China ◽

Population Genetic Structure ◽

Population Genetic ◽

The Mean ◽

Erythrophleum Fordii ◽

Private Alleles

Erythrophleum fordii Oliv. is a valuable rosewood species indigenous to the tropical and warm sub-tropical zones of Vietnam, Laos, and South China. The natural forests have been heavily fragmented mostly due to over-exploitation and over-utilization, and alteration to croplands and fast-growing plantations. Therefore, it has been included in the IUCN Red List of Endangered Species as an endangered species. In the present study, genetic diversity and population genetic structure of 11 populations were estimated by SSR makers in South China. Five high polymorphic loci were studied with a total of 34 alleles, among which, seven were private alleles. The mean number of alleles per locus (A), the mean number of efficient alleles per locus (Ae), the observed (Ho) and expected (He) heterozygosity, and Shannon’s index (I) of the 11 populations were 3.40, 2.31, 0.52, 0.56, and 0.90, respectively. Correlation analysis between genetic parameters and geographical factors showed that He and I were in significant negative correlation with longitude, indicating that genetic diversity of E. fordii reduced gradually from West to East in south China. FIS of eight populations with above five samples was on average 0.01, most loci conformed to Hardy-Weinberg equilibrium in these populations; their genetic differentiation coefficient (FST) was 0.18, indicating that genetic differentiation among populations was relatively low and there existed 18% genetic variation among populations. Gene flow (Nm) between these populations was 1.28. The Mantel test showed that genetic distance was not significantly correlated with geographical distance (p > 0.05). It was concluded that populations with high genetic diversity or private alleles, especially Longmen, Wuming and Pingxiang populations should be a priority for in situ conservations, meanwhile more populations and as many families as possible in each population should be collected for ex situ conservations of germplasm resources of this species in the future.

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Colonization history and human translocations explain the population genetic structure of the noble crayfish ( Astacus astacus ) in Fennoscandia: Implications for the management of a critically endangered species

Aquatic Conservation Marine and Freshwater Ecosystems ◽

10.1002/aqc.3632 ◽

2021 ◽

Author(s):

Johan Dannewitz ◽

Stefan Palm ◽

Lennart Edsman

Keyword(s):

Genetic Structure ◽

Endangered Species ◽

Population Genetic Structure ◽

Population Genetic ◽

Critically Endangered ◽

Astacus Astacus ◽

Colonization History ◽

Critically Endangered Species ◽

Noble Crayfish

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Population genetic structure in a threatened tree, Pyrus calleryana var. dimorphophylla revealed by chloroplast DNA and nuclear SSR locus polymorphisms

Conservation Genetics ◽

10.1007/s10592-013-0489-4 ◽

2013 ◽

Vol 14 (5) ◽

pp. 983-996 ◽

Cited By ~ 7

Author(s):

Shuri Kato ◽

Atsushi Imai ◽

Nishioka Rie ◽

Yuzuru Mukai

Keyword(s):

Genetic Structure ◽

Chloroplast Dna ◽

Population Genetic Structure ◽

Population Genetic ◽

Pyrus Calleryana ◽

Nuclear Ssr

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Population genetic structure of the endangered Butler’s Gartersnake (Thamnophis butleri): does the Short-headed Gartersnake (Thamnophis brachystoma) exist in Canada?

Canadian Journal of Zoology ◽

10.1139/cjz-2013-0068 ◽

2013 ◽

Vol 91 (11) ◽

pp. 810-819

Author(s):

Daniel W.A. Noble ◽

Jonathan D. Choquette ◽

John S. Placyk ◽

Ronald J. Brooks

Keyword(s):

Genetic Structure ◽

Endangered Species ◽

Population Genetic Structure ◽

Microsatellite Dna ◽

Population Genetic ◽

Population Genetic Study ◽

Closely Related Species ◽

Genetic Clusters ◽

Fragmented Distribution ◽

Conservation Of Endangered Species

Understanding population genetic structure is fundamental to conservation of endangered species. It is particularly important when working with species that are morphologically conserved because strong genetic divisions could represent cryptic species. Butler’s Gartersnake (Thamnophis butleri (Cope, 1889)) is an endangered species in Canada, having a fragmented distribution and being restricted to southwestern Ontario. Furthermore, it is difficult to distinguish morphologically from a closely related species, the Short-headed Gartersnake (Thamnophis brachystoma (Cope, 1892)). We use mitochondrial DNA (mtDNA) and seven microsatellite DNA loci to evaluate the genetic structure of Canadian T. butleri populations and to test for the presence of T. brachystoma in one of these populations. All individuals had the same mtDNA haplotype, and there was no evidence of multiple, syntopic genetic clusters, thereby rejecting the hypothesis that T. butleri and T. brachystoma co-exist in Canada. Two different model-based assignment tests using microsatellite DNA data suggest that there are four to five genetically distinct clusters of T. butleri (FST from 0.12 to 0.20). We provide the first population genetic study of T. butleri in Canada and refute the presence of T. brachystoma. Our results may provide guidance on recovery strategies for this species and identify areas to target fine-scale genetic analyses.

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