scholarly journals High genetic diversity and mixing of coastal horseshoe crabs (Tachypleus gigas) across major habitats in Sundaland, Indonesia

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11739
Author(s):  
Naila Khuril Aini ◽  
Yusli Wardiatno ◽  
Hefni Effendi ◽  
Ali Mashar ◽  
Hawis Madduppa
Keyword(s):  
Dna Sequences ◽  
Horseshoe Crab ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Haplotype Network ◽  
Structured Populations ◽  
Conservation Strategy ◽  
Genetic Connectivity ◽  
High Genetic Diversity ◽  
Geographic Ranges

Species with limited dispersal abilities are often composed of highly genetically structured populations across small geographic ranges. This study aimed to investigate the haplotype diversity and genetic connectivity of the coastal horseshoe crab (Tachypleus gigas) in Indonesia. To achieve this, we collected a total of 91 samples from six main T. gigas habitats: Bintan, Balikpapan, Demak, Madura, Subang, and Ujung Kulon. The samples were amplified using primers for mitochondrial (mt) AT-rich region DNA sequences. The results showed 34 haplotypes, including seven shared and 22 unique haplotypes, across all localities. The pairwise genetic differentiation (FST) values were low (0 to 0.13) and not significantly different (p > 0.05), except among samples from Ujung Kulon-Madura and Kulon-Subang (p < 0.05). Additionally, the 34 analysis of molecular variance (AMOVA) showed the most variation within populations (95.23%) compared to less among populations (4.77%). The haplotype network showed evidence of shared haplotypes between populations. Tajima’s D and Fu’s FS test values indicated a population expansion. Our results showed a low level of differentiation, suggesting a single stock and high connectivity. Therefore, a regionally-based conservation strategy is recommended for the coastal horseshoe crab in Indonesia.

scholarly journals Demographic history of the fragmented yellowthroated bulbul (Pycnonotus xantholaemus) population in the Deccan Peninsula, India

2020 ◽  
Vol 43 ◽  
pp. 199-207
Author(s):  
A Jha ◽  
K Vasudevan
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Genetic Connectivity ◽  
Founder Population ◽  
Effective Population ◽  
Genetic Structuring

The yellow-throated bulbul (YTB) is an endemic passerine restricted to scrub forests along hill slopes with exposed rocky outcrops in the Deccan Peninsula, India. It is found in small, discontinuous populations and is vulnerable to extinction due to ongoing habitat loss and subsequent population decline. To assess the genetic connectivity and past demography, we sequenced 1050 nucleotide base pairs of the mitochondrial control region of 60 individuals that represent distinct populations in the geographic range of the species. We recovered 39 haplotypes defined by 81 variable sites. Haplotype diversity was high with low nucleotide diversity, suggesting rapid population growth from a founder population with a small effective population size. The negative values of Tajima’s D and Fu’s Fs and small positive value of Ramos-Onsins and Rozas’ R2 suggest deviation from neutrality and population expansion. The haplotype network and demographic expansion parameters further suggest historical population expansion. Mismatch analysis statistics and Bayesian skyline plots estimate population expansion during the late Pleistocene. Although the species presently occurs in small, disconnected we found no structuring of the population. Dispersal events are the most likely explanation for the absence of genetic structuring in the YTB population. These results represent important data for the design of a conservation plan for this endemic and globally threatened species.

Genealogical relationship inference to identify areas of intensive poaching of the Orange-fronted Parakeet (Eupsittula canicularis)

BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Gabriela Padilla-Jacobo ◽  
Tiberio C. Monterrubio-Rico ◽  
Horacio Cano-Camacho ◽  
María Guadalupe Zavala-Páramo
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Coastal Region ◽  
Central American ◽  
Illegal Trade ◽  
Wild Populations ◽  
High Genetic Diversity ◽  
Genealogical Relationship ◽  
Genetic Pool

Abstract Background The Orange-fronted Parakeet (Eupsittula canicularis) is the Mexican psittacine that is most captured for the illegal pet trade. However, as for most wildlife exploited by illegal trade, the genetic diversity that is extracted from species and areas of intensive poaching is unknown. In this study, we analyzed the genetic diversity of 80 E. canicularis parakeets confiscated from the illegal trade and estimated the level of extraction of genetic diversity by poaching using the mitochondrial DNA sequences of cytochrome b (Cytb). In addition, we analyzed the genealogical and haplotypic relationships of the poached parakeets and sampled wild populations in Mexico, as a strategy for identifying the places of origin of poached parakeets. Results Poached parakeets showed high haplotype diversity (Hd = 0.842) and low nucleotide diversity (Pi = 0.00182). Among 22 haplotypes identified, 18 were found exclusively in 37 individuals, while four were detected in the remaining 43 individuals and shared with the wild populations. A rarefaction and extrapolation curve revealed that 240 poached individuals can include up to 47 haplotypes and suggested that the actual haplotype richness of poached parakeets is higher than our analyses indicate. The geographic locations of the four haplotypes shared between poached and wild parakeets ranged from Michoacan to Sinaloa, Mexico. However, the rare haplotypes detected in poached parakeets were derived from a recent genetic expansion of the species that has occurred between the northwest of Michoacan and the coastal region of Colima, Jalisco and southern Nayarit, Mexico. Conclusions Poached parakeets showed high genetic diversity, suggesting high extraction of the genetic pool of the species in central Mexico. Rarefaction and extrapolation analyses suggest that the actual haplotype richness in poached parakeets is higher than reflected by our analyses. The poached parakeets belong mainly to a very diverse genetic group of the species, and their most likely origin is between northern Michoacan and southern Nayarit, Mexico. We found no evidence that poachers included individuals from Central American international trafficking with individuals from Mexico in the sample.

scholarly journals High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 469 ◽  
Author(s):  
Yanwen Deng ◽  
Tingting Liu ◽  
Yuqing Xie ◽  
Yaqing Wei ◽  
Zicai Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Human Disturbance ◽  
Haplotype Diversity ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Conservation Strategies ◽  
High Genetic Diversity ◽  
Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

Population genetic structure of the endangered yellow spotted mountain newt (Neurergus derjugini: Amphibia, Caudata) inferred from mitochondrial DNA sequences

2019 ◽  
pp. 37-47 ◽  
Author(s):  
Tayebe Salehi
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Transition Period ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Haplotype Network ◽  
Molecular Dating ◽  
Middle Pleistocene ◽  
Restricted Gene Flow ◽  
Historical Factors

The yellow spotted mountain newt (Neurergus derjugini) is a critically endangered species restricted to fragmented habitats in highland streams of the middle Zagros Mountain in Iran and Iraq. We examined the species phylogeography by investigating sequences of a mitochondrial fragment of the ND2 gene for 77 individuals from 15 locations throughout the species known distribution. We found relatively high haplotype diversity (0.82 ± 0.025) but low nucleotide diversity (0.0038 ± 0.00022) across all populations. Phylogenetic trees supported monophyly, and the segregation of haplotypes was concordant with the haplotype network. We found a significant correlation between geographical and genetic distances among populations (r = 0.54, P ˂ 0.01), suggesting restricted gene flow. Molecular dating suggested that haplogroups diverged during the early or middle Pleistocene. Bayesian skyline plot provided evidence for an expansion of populations during the Pleistocene-Holocene transition period. Taken together, isolation by distance due to low dispersal capability, habitat fragmentation, and historical factors have shaped the current population structure of N. derjugini.

scholarly journals Molecular investigations on the Rajanpuri strain of Beetal goat breed of Pakistan by complete mtDNA displacement region and microsatellite markers

2021 ◽  
Vol 52 (5) ◽  
Author(s):  
Abdul Wajid ◽  
Tanveer Hussain ◽  
Faiz M. M. T. Marikar ◽  
Muneeb M. Musthafa ◽  
Kamran Abbas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Allelic Diversity ◽  
Local Strain ◽  
Goat Breed ◽  
High Genetic Diversity ◽  
Mode Shift ◽  
Bottleneck Analysis ◽  
Beetal Goat

The mitochondrial DNA sequences of DNA-D loops (mtDNA) from 105 individuals (11 Beetal goat Rajanpuri strains and 94 sequences extracted from GenBank) from 19 geographically and phenotypically defined domestic goat breeds in Pakistan were analysed in this experiment. In this study, we examined variability and molecular phylogeny of breeds. A total of 81 haplotypes were observed in 105 individuals, with a haplotype diversity of 0.984±0.006 and nucleotide diversity of 0.03953±0.00843. Phylogenetic analysis based on the mtDNA hyper variable segment (HVI) of the control region (481 bp), showed four mtDNA haplogroups (A, B1, C, and D) identified in Pakistani domestic goats, in which haplogroup A (84.11%) was dominant and widely distributed among all investigated breeds. The study revealed that all Rajanpuri strain haplotypes belonged to haplogroup A. The Rajanpuri is a rare local strain of Beetal goat breed located in western Punjab province of Pakistan. The results of genetic diversity based on 11 microsatellite loci revealed allelic diversity (3.6363) and high genetic diversity (0.8342) in the examined Rajanpuri goat breeds. The analysis for signature bottleneck events, using three models, revealed significant deviation of Rajanpuri goats from mutation drift equilibrium. The qualitative test of mode shift analysis also supported the results obtained under three models, indicating the presence of a recent genetic bottleneck in the Rajanpuri strain. This study provides the first information on the mtDNA architecture, genetic diversity and bottleneck analysis, which will be useful in the conservation and management of the highly valued Rajanpuri goat.

scholarly journals Population Genetic Structure of Neoschoengastia Gallinarum in China Based on Mitochondrial DNA Markers

2021 ◽  
Author(s):  
Jia-Meng Tao ◽  
Saeed-EI Ashram ◽  
Yuan Zhang ◽  
Ya-Biao Weng ◽  
Rui-Qing Lin
Keyword(s):  
Genetic Structure ◽  
Body Surface ◽  
Southern China ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
The Body ◽  
High Genetic Diversity ◽  
Structure Variation ◽  
Distribution Rule ◽  
Tandem Genes

Abstract Background: Neoschoengastia gallinarum is a widespread agricultural pest in China.The larvae of N. gallinarum are parasitic on the body surface of poultry. Performance, carcass quality, and normal marketing of mite infected broilers are severely affected by pruritus and pockmark lesions on the body surface. In China, N. gallinarum research has primarily focused on occurrence regularity, biology, and control methods. The genetic structure, variation, and genetic relationship between the N. gallinarum populations in China are still unclear.Methods: Genetic variations and structure among populations of N. gallinarum was examined and analyzed based on the nucleotide sequences of a 1522 nt variable region of the mitochondrial tandem genes (COI, COII, and ND5) among 4 populations from 7 collection sites in southern China.Results: A total of 192 individuals in 4 populations were analyzed. The tandem genes sequences were aligned, and 75 haplotypes were detected, 4 of these shared between populations. The range of haplotype diversity was from 0.860 (FJ) to 0.978 (GX). The pairwise FST values among populations were higher (0.096-0.551).The haplotype network mediation map and phylogenetic tree showed that the haplotypes were divided into two clade, Which did not completely follow the distribution rule of geographical populations. The AMOVA result showed that the percentage of variation within populations (72.94%) was higher than that among populations (27.06%). Neutral test and mismatch analysisrevealed that N. gallinarum had not experienced an obvious population expansion in recent historical periods, and the population size was relatively stable.Conclusions: The N. gallinarum population showed high genetic diversity based on mitochondrial tandem genes analysis and strong ecological adaptability. Despite the fact that geogrphic isolation causes certain genetic differentiation among populations, N. gallinarum high gene flow among populations as a result of human trade activities, and there was no obvious geographical genetic structure.

scholarly journals Phylogenetics and population genetics ofPlotosus canius(Siluriformes: Plotosidae) from Malaysian coastal waters

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1930 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
S.M. Nurul Amin ◽  
Natrah Fatin Mohd Ikhsan
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius(Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics ofP. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure ofP. caniusfor the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification ofTandanus tandanusmicrosatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho= 0.79). This alongside the highFisvalues estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotypeKR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure inP. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

scholarly journals High Genetic Diversity of an Invasive Alien Species: Comparison between Fur-Farmed and Feral American Mink (Neovison vison) in China

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 472
Author(s):  
Lina Zhang ◽  
Yan Hua ◽  
Shichao Wei
Keyword(s):  
Genetic Diversity ◽  
Alien Species ◽  
Dna Sequences ◽  
American Mink ◽  
Population Expansion ◽  
Northeastern China ◽  
Neovison Vison ◽  
High Genetic Diversity ◽  
Genetic Characteristics ◽  
Short Period

Genetic characteristics play an important role in alien species for achieving high adaptation and rapid evolution in a new environment. The American mink (Neovison vison) is one of the best-known and most widespread invasive species that has successfully invaded the Eurasian mainland over quite a short period, including most parts of northeastern China. However, genetic information on farmed and feral American mink populations introduced in China is completely lacking. In this study, we combined mitochondrial DNA sequences and polymorphic microsatellites to examine the genetic divergence and genetic diversity of farmed and feral American mink populations. Our results suggest that there is admixture of individuals of different genetic characteristics between farmed and feral populations of mink. Furthermore, the genetic diversity of both farmed and feral American mink populations was high, and no bottleneck or population expansion was detected in most of the populations. These findings not only highlight the genetic characteristics of American mink in northeastern China but also contribute to the general understanding of the invasiveness of farmed species.

scholarly journals Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters

2016 ◽  
Author(s):  
Nima Khalili Samani ◽  
Yuzine Esa ◽  
S.M Nurul Amin ◽  
Natrah Fatin Mohd Ikhsan
Keyword(s):  
Genetic Structure ◽  
Small Sample Size ◽  
Genomic Structure ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Peninsular Malaysia ◽  
Small Sample ◽  
Coi Gene ◽  
Genetic Connectivity ◽  
Significant Finding

Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental researches on biological characteristics of P.canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P.canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395 to 0.771 and 0.033 to 0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (H0) value of 0.2168, which was lower than the standard heterozygosity in marine populations (H0= 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940 at which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P.canius, and should be necessary highlighted for appropriate management and conservation of species. Though, further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.

scholarly journals Phylogeography of the oyster borer (Haustrum scobina)

2021 ◽  
Author(s):  
◽  
Sebastian Logan
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Haplotype Diversity ◽  
Genetic Connectivity ◽  
Long Distance Dispersal ◽  
Genetic Structuring ◽  
Long Distance ◽  
Ecological Processes

<p>An effective investigation of the underlying ecological processes that shape genetic diversity and connectivity typically requires comparisons among phylogeographic studies of multiple species. Phylogeographic studies of New Zealand’s coastal marine benthos have historically relied on post hoc speculation rather than directed research questions to investigate ecological processes. There has also been a lack of studies on direct developing marine molluscs. Direct developers are expected to have a low potential for dispersal and thus show a pattern of genetic isolation by distance across their distributions. Recent research indicates that this assumption may frequently be violated by instances of long distance dispersal/translocation. The oyster borer (Haustrum scobina) is an endemic direct-developing marine mollusc found in high abundances at rocky intertidal environments across the entirety of New Zealand. This distribution and life history makes H. scobina an ideal target to study genetic connectivity in a species expected to show low realised dispersal and high population genetic structuring. This thesis research used 379 new DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) to investigate the phylogeography of H. scobina across the southern North Island. In addition 16 new COI sequences were inadvertently sequenced from the morphologically similar congener Haustrum albomarginatum. Results from both species support the recently proposed division of H. scobina and H. albomarginatum as separate species. H. scobina populations show significant geographic structure and a lack of haplotype diversity across the south-eastern North Island concordant with results of another previous study of a direct developer. This finding suggests that ecological processes may be producing similar population genetic structures for direct developers generally. Contrast between high and low haplotype diversities in northern and southern H. scobina populations respectively, indicates that southern H. scobina populations may have originated via recolonisation from northern populations following a range contraction during the Last Glacial Maximum. Evidence of multiple long distance dispersal/translocation events was found indicating that long distance dispersal via rafting and/or inadvertent human-mediated translocations may have occurred frequently. Results are then discussed with a view to inform further research in to New Zealand direct developers.</p>

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