The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae)

2012 ◽  
Vol 33 (1) ◽  
pp. 45-53 ◽  
Author(s):  
Cinthya Alejandra Ureña-Aranda ◽  
Alejandro Espinosa de los Monteros
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
20Th Century ◽  
Chihuahuan Desert ◽  
Haplotype Diversity ◽  
Genetic Homogeneity ◽  
Significant Percentage ◽  
Tectonic Processes ◽  
D Loop ◽  
Demographic Growth

Gopherus flavomarginatus (Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.

scholarly journals Climate change and conservation in a warm North American desert: effect in shrubby plants

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6572 ◽  
Author(s):  
Victoria Sosa ◽  
Israel Loera ◽  
Diego F. Angulo ◽  
Marilyn Vásquez-Cruz ◽  
Etelvina Gándara
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Gene Flow ◽  
North American ◽  
Chihuahuan Desert ◽  
Haplotype Diversity ◽  
Sierra Madre Oriental ◽  
Ecological Resistance ◽  
Sierra Madre ◽  
Shrubby Species

Background Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet’s last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. Methods Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. Results The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. Conclusion Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.

scholarly journals Diversitas Genetika dan Identifikasi Jenis Kelamin Burung Pelikan (Pelecanus conspicillatus Temminck, 1824) di Penangkaran Taman Margasatwa Ragunan Jakarta

2021 ◽  
Vol 17 (2) ◽  
pp. 105-114
Author(s):  
Anik Budhi Dharmayanthi ◽  
Achmad Muchsinin ◽  
Afriana Pulungan ◽  
Moch Syamsul Arifin Zein
Keyword(s):  
Genetic Diversity ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Bird Populations ◽  
Low Genetic Diversity ◽  
In Captivity ◽  
D Loop ◽  
Haplotype 1

Pelicans (Pelecanus conspicillatus) is one of the wild species that have a widely distribution. This bird has been successfully bred in Ragunan Zoo, Jakarta. The indicator of inbreeding in the captive population is shown by the decrease of nucleotide diversity and number of haplotypes. The result of genetic diversity analysis using D-loop fragment sequences showed low genetic diversity with nucleotide diversity (p) = 0.00064 ± 0.00010 and haplotype diversity (Hd) = 0.532 ± 0.061 in Pelecanus conspicillatus populations in the Ragunan Zoo. However, negative Fu's Fs value (-3,246) indicates population expansion. We found that there were seven haplotypes in bird populations in the captivity: haplotype 1, 2 and 3 consist of 43 individuals (65.15%), five individuals (7.57%), and 14 individuals (21.21%), respectively. For each haplotype 4, 5, 6 and 7 is only represented by one individual of Pelecanus conspicillatus (1.51%). The sex ratio of males to females is 1: 8.86 with four males identified as haplotype 1, and one male on haplotypes 3, 5 and 7, respectively. Genetic diversity data of the population is an important way for designing long-term plans and goals in efforts to maintain genetic diversity of the Pelecanus conspicillatus population in captivity.

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.

mtDNA D-loop sequence analysis of Kalang, Krayan, and Thale Noi buffaloes (Bubalus bubalis) in Indonesia and Thailand reveal genetic diversity

2021 ◽  
Vol 46 (2) ◽  
pp. 93-105
Author(s):  
S. Suhardi ◽  
P. Summpunn ◽  
S. Wuthisuthimethavee
Keyword(s):  
Genetic Diversity ◽  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Bubalus Bubalis ◽  
Relationship Patterns ◽  
Loop Region ◽  
Loop Sequence ◽  
D Loop

Kalang (KBuf), Krayan (KrBuf), and Thale Noi buffaloes (TBuf) are swamp buffalo genetic resources in Indonesia and Thailand. The maternally inherited mitochondrial DNA (mtDNA), particularly D-loop region is an important material for phylogenetic inference and analyzing genetic diversity. Therefore, the objectives of the present study were to evaluate genetic diversity and to reconstruct the phylogenetic tree within buffalo breeds in Kalimantan, Indonesia, and Phatthalung, Thailand using mtDNA D-loop sequences. A total of one hundred forty buffaloes (70 males and 70 females) were observed including 40 buffaloes from North (NK), 40 from East (EK), and 40 from South Kalimantan (SK) provinces Indonesia and 20 from Phatthalung (PT) province, Thailand. DNA samples were isolated from buffalo tail hairs. DNA sequences were manually assembled using BioEdit program with consideration of gaps and ambiguous sequences. The phylogenetic tree of buffalo was generated by PHYLIP software. The observed variables included haplotype diversity, genetic distance, and genetic tree. The 956 bp of amplified mtDNA D-loop fragment presented a total of 24 haplotypes with several mutations that included transitions (293), transversions (60), deletions (15), and insertions (20). The neighbor-joining tree using the Kimura 2 parameter model demonstrated two local buffalo clusters among buffalo from Kalimantan and Thailand with four buffalo relationship patterns observed from buffaloes in Kalimantan Island (KBuf and KrBuf), Indonesia. The Results of the present study demonstrated that the buffaloes sequence analysis revealed relatively high diversity and is a good basis to perform selection and modern buffalo breeding development.

Genetic diversity of a captive population of black muntjac revealed by a set of high polymorphism across-species microsatellites

2009 ◽  
Vol 59 (3) ◽  
pp. 273-281 ◽  
Author(s):  
Xiao-Wei Ni ◽  
Hai-Long Wu ◽  
Guo-Ping Zhu ◽  
Kai Meng
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Individual Identification ◽  
Source Population ◽  
Captive Population ◽  
Discrimination Power ◽  
Polymorphic Loci ◽  
D Loop ◽  
Population Genetic Variation ◽  
The Individual

AbstractEleven high polymorphic across-species loci were used to test the usefulness in the individual identification and parentage determination of black muntjac and to detect the genetic variation in a captive population of the animal. Discrimination power for individual locus ranged from 0.845 to 0.949 with the cumulative discrimination power across the eleven loci being up to 1. The combined exclusion probability across the eleven polymorphic loci in the absence and presence of genetic information on the second parent was 0.999 and 1, respectively. These results indicated that the eleven microsatellites would be highly diagnostic in individual identification and parentage testing for the species. The application of these polymorphic loci to evaluate population genetic variation indicated that the genetic diversity of the captive population (5.4 and 0.68 for A and He, respectively; n = 14) was significantly lower than that of the source population (7 and 0.785 for A and He, respectively; n=16). This supported our previous results discovered by mtDNA d-loop, i.e., the genetic diversity of the captive population had obviously declined over less than 20 years due to the paucity of founders. However, difference of observation heterozygosity between the captive and the source populations was not significant. These results indicated that loss of nuclear diversity in the captive population was first evidenced by A but not Ho. In order to retard the potential inbreeding effect, we suggested that some more wild animals should be introduced into the captive population and that a pedigree-based breeding program should be established.

scholarly journals Genetic diversity of H’mong short tail dog based on sequencing of the D-loop hypervariable -1 region (HV1)

2021 ◽  
Vol 19 (2) ◽  
pp. 245-257
Author(s):  
Pham Thanh Hai ◽  
Bui Xuan Phuong ◽  
Tran Huu Coi ◽  
Phung Thanh Tung ◽  
Ngo Quang Duc ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Haplotype Diversity ◽  
Good Health ◽  
Base Substitution ◽  
Nucleotide Polymorphisms ◽  
Northern Vietnam ◽  
Short Tail ◽  
Hunting Dogs ◽  
Indel Mutation ◽  
D Loop

The H'mong short tail dog is breed indigenous dogs, distributed in mountainousareas of northern Vietnam. H'mong short tail dog possesses many valuable properties such as intelligence, agility, good health, good shape, human friendliness, ease of training and it can fully meet the needs of war Dogs intelligence, strength, good parenting, people friendly and more importantly, still keeping wild characteristics of hunting dogs. The total 45 samples (blood) collected from 45 individuals in two provinces of Northern Vietnam (Ha Giang and Lao Cai), were used to assess genetic diversity based on sequencing hypervariable – 1 region (HV1) in D-loop genes. In the current study showed that genetic diversity of H'mong short tail dog was high with nucleotide diversity (Pi = 0.00801), haplotype diversity (Hd = 0.96162) and average number of nucleotide differences (Kt = 5.18384). Furthermore, 25 different haplotypes were recorded and divided into four main groups: A, B, C, and E. Of which, seven new haplotypes in haplogroups A (An1 to An7) and 18 haplotypes have been published in the world. In addition, H'mong short tail dog was found rare haplogroups (B1, C2, E1 and E4). Notably, there is none individuals contain haplotype of haplogroups (D and F). H'mong short tail dog were identified 38 single nucleotide polymorphisms, including 32 nucleotide base substitution/base insertion and 6 nucleotide indel mutation. Almost mutation was transversion (31/32) and only one nucleotide transition mutations. Phylogenetic tree shown that H'mong short tail dog have close relationship with dogs origin from East Asia (China, Japan and Korea).

scholarly journals Relationship Between Genetic Variation and Diversity of Tree Species in Tropical Forests in the El Ocote Biosphere Reserve, Chiapas, Mexico

2021 ◽  
Vol 14 ◽  
pp. 194008292097814
Author(s):  
Bárbara Cruz-Salazar ◽  
Lorena Ruiz-Montoya ◽  
Neptalí Ramírez-Marcial ◽  
Maricela García-Bautista
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Species Diversity ◽  
Tree Species ◽  
Haplotype Diversity ◽  
Biosphere Reserve ◽  
Genetic Distances ◽  
Community Diversity ◽  
Environmental Selection ◽  
Tree Communities

Knowledge of the genetic diversity of species in a biological community is useful for assessing the ecological and evolutionary processes that define the structure and dynamics of that community. We investigated the potential relationship between the trans-specific genetic diversity (or genetic diversity across tree species) and the diversity of tree species in a tropical subdeciduous forest. The nucleotide variation of the concatenated regions ITS 1 and ITS 3 (ITS1-3) was used to determine the trans-specific genetic diversity of 19 species of trees in five local communities at El Ocote Biosphere Reserve (REBISO), Chiapas, Mexico. Tree diversity was obtained by counting individual trees within 0.1 ha circular plots in each locality. The relationship between trans-specific genetic diversity and species diversity was established through simple linear regressions between genetic diversity parameters and community diversity. A correlation matrix was built with genetic distances (Kimura’s two-parameter model) and differences in species diversity between communities. A significant relationship was observed between nucleotide diversity (π) and species richness ( Sp), and a negative association between haplotype diversity and gamma diversity (γ). Our results show species-rich and genetically diverse tree communities and a weak association between trans-specific genetic variation and species diversity in tree communities at REBISO. This research suggests a possible ecological and genetic relationship within each community. Genetic diversity values may provide an important degree of variation upon which environmental selection pressures could operate, which may be helpful to face the current environmental modifications associated with climatic change.

scholarly journals Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

2021 ◽  
Author(s):  
Athumani Nguluma
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Haplotype Diversity ◽  
Capra Hircus ◽  
Maternal Origin ◽  
High Genetic Diversity ◽  
Ecological Zones ◽  
Goat Population ◽  
D Loop ◽  
Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

scholarly journals Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1970
Author(s):  
Emel Özkan Ünal ◽  
Fulya Özdil ◽  
Selçuk Kaplan ◽  
Eser Kemal Gürcan ◽  
Serdar Genç ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Loop Region ◽  
Geographical Regions ◽  
D Loop ◽  
Significant Comparison ◽  
Loop Regions ◽  
Frequent Haplotype

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.

scholarly journals Weak Population Structure of Perna Viridis in Indo-Pacific Region based on Nuclear and Mitochondrial DNA Marker

2021 ◽  
Author(s):  
Yingying Ye ◽  
Chengrui Yan ◽  
Ferruccio Maltagliati ◽  
Zeqin Fu ◽  
Baoying Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Haplotype Diversity ◽  
Its Region ◽  
Coi Gene ◽  
Perna Viridis ◽  
Thai Population ◽  
Mitochondrial Coi ◽  
Loop Region ◽  
D Loop

Abstract Perna viridis is a mussel commonly distributed along the Asian Indo-Pacific coasts. It is one of the main cultured species of that region. Previous studies focused mostly on the native populations within single countries; with the present study we analyzed the genetic diversity of P. viridis in a large study area, spanning from Oman to southern China. Three molecular markers were used, namely portions of the nuclear ITS region, and the mitochondrial COI gene and D-Loop region. The nuclear marker showed moderate levels of genetic diversity (haplotype diversity h = 0.543 to 0.897) and nucleotide diversity π = 0.0022 to 0.0064); whereas mitochondrial markers exhibited higher levels of genetic variability (h = 0.858 to 0.964 and π = 0.0012 to 0.0079). The estimates of inter-sample genetic divergence (FST) and the analysis of molecular variance highlighted that the Thai population is genetically divergent from the others. Our results showed the genetic variation of P. viridis at the rim of South China Sea and obtained the genetic basic information of P. viridis.

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