scholarly journals Genetic diversity and phylogenetic analyses of 11 cohorts of captive rhesus macaques from Chinese zoos

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6957
Author(s):  
Qian Su ◽  
Yongfang Yao ◽  
Qin Zhao ◽  
Diyan Li ◽  
Meng Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rhesus Macaques ◽  
Phylogenetic Analyses ◽  
Genetic Management ◽  
Southeastern China ◽  
Mitochondrial Dna Control Region ◽  
Clade B ◽  
In Captivity ◽  
High Level ◽  
Major Haplogroups

Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003, K = 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques.

Simple Sequence Repeat (SSR) Polymorphisms and Population Genetics in Sichuan Wild Rhesus Macaques

2011 ◽  
Vol 343-344 ◽  
pp. 690-697
Author(s):  
Di Yan Li ◽  
Yong Fang Yao ◽  
Xiao Feng Huang ◽  
An Chun Cheng ◽  
Huai Liang Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Rhesus Macaques ◽  
Genetic Management ◽  
Future Studies ◽  
Ssr Loci ◽  
Different Populations ◽  
Polymerase Chain ◽  
High Level ◽  
Simple Sequence

Cross-species amplification of twenty-five SSR loci from the DNA of five rhesus macaques of diverse regional origins was conducted using human primers for the polymerase chain reaction (PCR). Seven of these primer pairs, which consistently and unambiguously amplified polymorphic fragments from these five samples, were also used to amplify SSR loci for 111 Sichuan wild rhesus macaques of five different populations. The analysed microsatellite markers produced 109 alleles, varied from 4 to 16 alleles each locus. The number of alleles per population ranged from 6.79 to 11.38. Polymorphic information content showed that all seven loci were highly informative (mean = 0.9017±0.0166, >0.5). The average observed heterozygosity was less than the expected (mean = 0.6795 and mean = 0.8559, respectively). Genetic differentiation among the populations was considerably low with the overall and pairwise FST values (mean = 0.0375), and showed fairly low level of inbreeding (indicated by a mean FIS value of 0. 0.1991). Maintaining genetic diversity is a major issue in conservation biology. In comparison to other captive Macaca mulatta studies, these wild rhesus macaque populations showed a relatively high level of genetic diversity, and there was low gene flow among these populations. Careful genetic management is important for maintaining genetic variability levels. None of the seven informative loci are linked which screened in this study can be applied in future studies on population and conservation genetics of natural primate populations.

Mitochondrial D-loop Genetic Diversity Studies of Rhinoceros unicornis in Assam, India

2020 ◽  
Author(s):  
Puranjit Das ◽  
Rita Choudhury
Keyword(s):  
Genetic Diversity ◽  
National Park ◽  
Natural Habitats ◽  
Mitochondrial Dna Control Region ◽  
Non Invasive ◽  
Rhinoceros Unicornis ◽  
Total Genetic Diversity ◽  
D Loop ◽  
High Level ◽  
Diversity Studies

In Assam wild populations of great Indian rhinoceros are found in three protected areas namely Kaziranga National Park, Orange National Park and Pobitora Wildlife Sanctuary. But it remains an area of investigation whether these three populations are homogeneous or not. To resolve this matter present genetic study was performed on mitochondrial DNA control region by using non invasive dung samples collected from the three natural habitats. The study showed a high level of genetic diversity of rhinoceros population in three habitats of Assam with 24 haplotypes from 196 samples and 21 variable sites in 413bp long nucleotide sequences was recorded. The Fst value also showed differences between the groups; and significant values obtained between Kaziranga and Pobitora with Orang groups. AMOVA analyses revealed the total genetic diversity is 91.62% and diversity between populations is only 8.38%. Thus the higher genetic variability found in Indian rhinoceros populations is important for future survivability, management and translocation to new habitat.

scholarly journals Epigenetic patterns associated with an ascidian invasion: a comparison of closely related clades in their native and introduced ranges

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nicola A. Hawes ◽  
Achira Amadoru ◽  
Louis A. Tremblay ◽  
Xavier Pochon ◽  
Brendon Dunphy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Phylogenetic Analyses ◽  
Native Range ◽  
Didemnum Vexillum ◽  
Colonial Ascidian ◽  
Introduced Populations ◽  
Clade B ◽  
Low Levels ◽  
Native And Introduced Ranges

Abstract Environmentally induced epigenetic modifications have been proposed as one mechanism underlying rapid adaptive evolution of invasive species. Didemnum vexillum is an invasive colonial ascidian that has established in many coastal waters worldwide. Phylogenetic analyses have revealed that D. vexillum populations consist of two distinct clades; clade B appears to be restricted to the native range (Japan), whereas clade A is found in many regions throughout the world, including New Zealand. The spread of D. vexillum clade A suggests that it might be intrinsically more invasive than clade B, despite low levels of genetic diversity compared to populations from the native region. This study investigated whether D. vexillum clade A exhibits epigenetic signatures (specifically differences in DNA methylation) associated with invasiveness. Global DNA methylation patterns were significantly different between introduced clade A colonies, and both clades A and B in the native range. Introduced colonies also showed a significant reduction in DNA methylation levels, which could be a mechanism for increasing phenotypic plasticity. High levels of DNA methylation diversity were maintained in the introduced population, despite reduced levels of genetic diversity, which may allow invasive populations to respond quickly to changes in new environments. Epigenetic changes induced during the invasion process could provide a means for rapid adaptation despite low levels of genetic variation in introduced populations.

scholarly journals Assessment of genetic diversity of Turkish and Algerian native sheep breeds

2020 ◽  
Vol 115 (1) ◽  
pp. 5
Author(s):  
Abdelkader AMEUR AMEUR ◽  
Onur YILMAZ ◽  
Nezih ATA ◽  
Ibrahim CEMAL ◽  
Semir Bechir Suheil GAOUAR
Keyword(s):  
Genetic Diversity ◽  
Production Systems ◽  
Productivity Loss ◽  
Genetic Management ◽  
Breeding Programs ◽  
Sheep Breeds ◽  
Genetic Clusters ◽  
Native Sheep ◽  
Sheep Production ◽  
High Level

In Algeria and Turkey, the sheep production systems are based on the under extensive rural conditions and their genetic management has led to increased homozygosity and hence productivity loss. The identification of inter-breed and intra-breed genetic diversity plays a key role in the shaping of conservation and breeding programs. The present study was conducted to investigate the genetic diversity of native sheep breeds reared in Turkey and Algeria. A total of 240 animals from four Algerian (Hamra, Ouled Djellal, Sidaou, and Tazegzawt) and four Turkish (White Karaman, South Karaman, Karacabey Merino, and Kıvırcık) native sheep breeds were genotyped with fourteen microsatellite markers recommended by FAO. A total of 340 alleles were detected from fourteen markers studied. All the eight breeds exhibited moderate to high levels of genetic diversity, with a slight superiority of the Algerian sheep breeds. Overall FIS value was low, but highly significant (p < 0.001). It may have been due to the high inbreeding within the population. The mean global coefficient of gene differentiation (GST) showed that approximately 94.0 % of the genetic variation was within-population. The highest number of private alleles with a frequency above 5 % was observed in Ouled Djellal sheep. Structure analysis of populations studied revealed the most appropriate K with four genetic clusters. As the result, the dendrogram showed that the Algerian sheep breeds were completely separated from the Turkish sheep breeds furthermore the Bayesian clustering revealed a high level of admixture, especially in Algerian sheep populations.

scholarly journals MITOCHONDRIAL DNA STUDY OF MONGOLIAN EQUUS CABALLUS

2018 ◽  
pp. 77-86
Author(s):  
Bolor-Oyut B ◽  
Ochirkhuyag B ◽  
Khulan J
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Sequence Variation ◽  
Haplotype Diversity ◽  
Sequence Analyses ◽  
Mitochondrial Dna Control Region ◽  
Evolutionary Studies ◽  
High Level

In order to assess the genetic diversity and maternal lineages of Mongolian native horse populations, we examined using mitochondrial DNA control region sequence analyses. The control region of mitochondrial DNA is widely used for population and evolutionary studies because of its high level of sequence variation, in addition to a lack of recombination and maternal heritance. To determine genetic diversity and maternal heritance, we collected 19 blood samples of Darhad horses from Khuvsgul, Tes horses from Zavkhan and Taij horses from Dundgobi, Mongolia.In this study, 16 haplotypes and 51 polymorphic sites were detected. Haplotype diversity was 0.9766 and nucleotide diversity was 0.0212 in Mongolian native horses. Finally, 5 horse haplogroups (A, C, D, F, I) were identified in 16 haplotypes in this study.

scholarly journals Mitochondrial DNA control region diversity in Common Terns Sterna hirundo from Slovenia and Croatia

Acrocephalus ◽  
2019 ◽  
Vol 40 (180-181) ◽  
pp. 69-78
Author(s):  
Ida Svetličić ◽  
Jelena Kralj ◽  
Miloš Martinović ◽  
Davorin Tome ◽  
Tilen Basle ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Diversity Indices ◽  
Common Tern ◽  
Sterna Hirundo ◽  
Mitochondrial Dna Control Region ◽  
High Level

Abstract63 Common Tern Sterna hirundo samples from Croatia and Slovenia were analysed with respect to their genetic diversity and differentiation. Samples originated from two freshwater populations (areas of the rivers Sava and Drava) and one coastal population (Sečovlje Salina). The molecular marker of choice was 709 bp long fragment of the mitochondrial control region, the fastest-evolving part of the mitochondrial genome. 21 haplotypes with 12 polymorphic sites were identified. Overall haplotype diversity was substantial and estimated at 0.8599, while the overall nucleotide diversity was low and estimated at 0.0025. Diversity indices were highest for the Drava population, followed by the Sava and the lowest for the Sečovlje population. Overall genetic structure was significantly low (Fst=0.0377) and attributed to the differences in haplotype frequencies between the populations. The high level of genetic diversity found in continental populations illustrates the importance of their habitats as reservoirs of genetic diversity and calls for their further protection and management.

scholarly journals Assessment of genetic diversity of Turkish and Algerian native sheep breeds

2020 ◽  
Vol 115 (1) ◽  
pp. 5
Author(s):  
Abdelkader AMEUR AMEUR ◽  
Onur YILMAZ ◽  
Nezih ATA ◽  
Ibrahim CEMAL ◽  
Semir Bechir Suheil GAOUAR
Keyword(s):  
Genetic Diversity ◽  
Production Systems ◽  
Productivity Loss ◽  
Genetic Management ◽  
Breeding Programs ◽  
Sheep Breeds ◽  
Genetic Clusters ◽  
Native Sheep ◽  
Sheep Production ◽  
High Level

In Algeria and Turkey, the sheep production systems are based on the under extensive rural conditions and their genetic management has led to increased homozygosity and hence productivity loss. The identification of inter-breed and intra-breed genetic diversity plays a key role in the shaping of conservation and breeding programs. The present study was conducted to investigate the genetic diversity of native sheep breeds reared in Turkey and Algeria. A total of 240 animals from four Algerian (Hamra, Ouled Djellal, Sidaou, and Tazegzawt) and four Turkish (White Karaman, South Karaman, Karacabey Merino, and Kıvırcık) native sheep breeds were genotyped with fourteen microsatellite markers recommended by FAO. A total of 340 alleles were detected from fourteen markers studied. All the eight breeds exhibited moderate to high levels of genetic diversity, with a slight superiority of the Algerian sheep breeds. Overall FIS value was low, but highly significant (p < 0.001). It may have been due to the high inbreeding within the population. The mean global coefficient of gene differentiation (GST) showed that approximately 94.0 % of the genetic variation was within-population. The highest number of private alleles with a frequency above 5 % was observed in Ouled Djellal sheep. Structure analysis of populations studied revealed the most appropriate K with four genetic clusters. As the result, the dendrogram showed that the Algerian sheep breeds were completely separated from the Turkish sheep breeds furthermore the Bayesian clustering revealed a high level of admixture, especially in Algerian sheep populations.

scholarly journals Genetic Diversity and Population Structure of Two Endangered Neotropical Parrots Inform In Situ and Ex Situ Conservation Strategies

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 386
Author(s):  
Carlos I. Campos ◽  
Melinda A. Martinez ◽  
Daniel Acosta ◽  
Jose A. Diaz-Luque ◽  
Igor Berkunsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Management Strategies ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Genetic Management ◽  
Captive Populations ◽  
In Captivity ◽  
In The Wild ◽  
Genetic Signatures

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

scholarly journals Infection rate and genetic diversity of Giardia duodenalis assemblage C in Iranian stray dogs, targeting the glutamate dehydrogenase gene

2021 ◽  
Vol 14 (2) ◽  
pp. 419-425
Author(s):  
Asghar Fazaeli ◽  
Mohammad Hasan Kohansal ◽  
Adel Spotin ◽  
Ali Haniloo ◽  
Abbasali Nourian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Glutamate Dehydrogenase ◽  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Giardia Duodenalis ◽  
Stray Dogs ◽  
Dehydrogenase Gene ◽  
Northwest Iran ◽  
High Level ◽  
Enteric Protozoan

Background and Aim: Giardia duodenalis is one of the most common enteric protozoan parasites in vertebrates, such as humans, domestic and wild animals, causing giardiasis. To the best of our knowledge, little is known about the genetic diversity of G. duodenalis assemblages. This study aimed to identify genetic diversity of G. duodenalis assemblages in Iranian stray dogs. Materials and Methods: A total of 450 fecal samples were collected from 2015 to 2016 from stray dogs of Northwest Iran. All specimens were observed microscopically following concentration and flotation techniques. Subsequently, DNA samples were extracted, amplified, and sequenced targeting the glutamate dehydrogenase gene. Results: The overall prevalence of G. duodenalis in infected dogs was estimated at 1.6%, based on microscopic and molecular diagnoses. Sequencing and phylogenetic analyses indicated a high level of genetic diversity of assemblage C (haplotype diversity; 0.802). Conclusion: The pairwise sequence distances between the identified isolates of assemblage C showed an intradiversity of 0.3%-1.3% and identity of 98.7%-100%. Current findings indicate that a significant genetic diversity of G. duodenalis assemblage C haplotypes is unequivocally circulates among stray dogs in Northwest Iran.

scholarly journals Polymorphisms of Mitochondrial COII and16S rRNA Gene in Meloidogyne enterolobii on Mulberry

2021 ◽  
Author(s):  
Hudie Shao ◽  
Pan Zhang ◽  
Chunping You ◽  
Chuanren LI ◽  
Yan Feng
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Nucleotide Diversity ◽  
Phylogenetic Analyses ◽  
Haplotype Diversity ◽  
Rrna Gene ◽  
Meloidogyne Enterolobii ◽  
High Level ◽  
Network Mapping ◽  
Cytochrome Oxidase Subunit Ii

Abstract This study explores the genetic diversity and polymorphisms of Meloidogdyne enterolobii (M enterolobii) on mulberry in China. The sequence of cytochrome oxidase subunit II (COII) and 16S rRNA gene in M enterolobii populations in Guangdong, Guangxi, and Hunan Provinces were PCR-amplified, sequenced, and analyzed for genetic diversity. The haplotypes (Hap) numbers, the total number of mutations, the average number of nucleotide differences (K), haplotype diversity (Hd), and nucleotide diversity (π) of mtCOII gene were 14, 25, 3.563, 0.942 and 0.00429, respectively. The significant differences in Fst value (0.125) and a high level of gene flow (2.83) were detected among the 19 M enterolobii populations. High genetic variation within each population and a small genetic distance among populations was observed. Both phylogenetic analyses and network mapping of the 14 haplotypes revealed a dispersed distribution pattern of the 19 M enterolobii populations. There was an absence of branches strictly corresponding to the 19 range sampling sites. The analysis of molecular variance (AMOVA) revealed that the genetic differentiation of M enterolobii populations was mainly contributed by the variation within each of the defined geographical groups. No significant correlation was found between the genetic distance and geographical distance of 19 M enterolobii populations. This study provides theoretical basis for the future control of M enterolobii and also provides a guarantee for the production of other hosts of M enterolobii.

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