Preliminary assessment of genetic diversity and population connectivity of the Mugger Crocodile in Iran

2018 ◽  
Vol 39 (1) ◽  
pp. 126-131 ◽  
Author(s):  
João Carlos Campos ◽  
Asghar Mobaraki ◽  
Elham Abtin ◽  
Raquel Godinho ◽  
José Carlos Brito
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Conservation Status ◽  
Diversity Indices ◽  
Population Connectivity ◽  
Circuit Analysis ◽  
Habitat Connectivity ◽  
Preliminary Assessment ◽  
Tissue Samples ◽  
Western Asia

The Mugger Crocodile (Crocodylus palustris) is a threatened reptile inhabiting the Indian Sub-continent and Western Asia. Despite its “Vulnerable” conservation status, data about population genetic structure and connectivity are unavailable. This study makes a preliminary assessment of the genetic diversity, population structure and habitat connectivity ofC. palustrisin Iran. Ten tissue samples collected along the Sarbaz-Bahukalat basins were analysed and a set of 12 microsatellites was genotyped. Genetic diversity indices were estimated and population substructuring was assessed through Bayesian clustering analysis. Potential connectivity was verified through Remote Sensing water indexes, further implemented in a circuit analysis. Low genetic diversity was observed (mean observed heterozygosity = 0.35; mean expected heterozygosity = 0.43) and no population structure was found (K = 1). Water index and circuit analysis suggested possible connection among sites. This study highlights the potential vulnerability of crocodile populations and the importance of habitat connectivity for their persistence in the arid regions of Iran.

scholarly journals Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1441
Author(s):  
Filippo Cendron ◽  
Francesco Perini ◽  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Andrea Criscione ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Conservation Status ◽  
Geographical Area ◽  
Snp Array ◽  
Local Economy ◽  
Conservation Strategies ◽  
Snp Analysis ◽  
Runs Of Homozygosity ◽  
Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

scholarly journals Population connectivity and larval dispersal of the exploited mangrove crab Ucides cordatus along the Brazilian coast

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4702 ◽  
Author(s):  
Fábio B. Britto ◽  
Anders J. Schmidt ◽  
Adriana M.F. Carvalho ◽  
Carolina C.M.P. Vasconcelos ◽  
Antonia M. Farias ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Connectivity ◽  
Brazilian Coast ◽  
Fishery Resource ◽  
Ucides Cordatus ◽  
Migration Rates ◽  
Mangrove Crab ◽  
Key Species

Background The mangrove crab Ucides cordatus is considered a key species for the ecological balance of mangrove forests and a major source of employment and income for traditional crab collectors in Brazil. Several studies evidenced weak genetic variation among populations due to an efficient larval transport. However, gene flow patterns of the species is poorly understood, with no information about migration rates. The influence of the two main Brazilian currents in larval dispersion is also not clear. In order to provide baseline information for conservation, planning and management of this important fishery resource, the present study aimed to estimate and evaluate spatial distribution of genetic diversity, migration rates and gene flow directivity among populations of U. cordatus in Brazil. Methods Nine microsatellites were used to resolve population structure of 319 crabs collected from six sites located along the Brazilian coast. The degree of geographical differentiation included estimates of genetic diversity, population structure and gene flow models, with spatial analysis of shared alleles (SAShA), isolation by distance tests, AMOVA, discriminant analysis of principal components (DAPC) and Bayesian clustering. We estimated the amount of ongoing gene flow between clusters using the coalescent-based method implemented in Migrate-N. Results Loci were highly polymorphic (average of 12.4 alleles per locus) evidencing high genetic variability. There was significant differentiation among localities, despite of the low value of FST (= 0.019; P < 0.001). FST and Jost’s D indexes were also estimated in pairwise comparisons and showed significant differences between most of the surveyed site pairs (P < 0.05). Structure evidenced a single genetic group among samples, however SAShA pointed to a non-panmictic condition (P = 0.011). AMOVA detected four statistical significant clusters with low level of differentiation (FCT = 0.037; P = 0.023). The gene flow model that best described the population connectivity was the island model, with ∼24 crabs being exchanged among localities per generation. Discussion The high migration rates found among localities seem to be the main force acting to sustain the distribution of the genetic diversity of U. cordatus. Despite the high gene flow and the weak population structure among samples, the significant genetic differences found suggest that gene flow alone does not bypass the effects of genetic drift, natural selection and/or human exploitation. These findings are vital for the establishment of a database to be used in the development of conservation programs.

scholarly journals Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

2020 ◽  
Author(s):  
Pamela Vega-Polo ◽  
Maria M. Cobo ◽  
Andrea Argudo ◽  
Bernardo Gutierrez ◽  
Jennifer Rowntree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Anthropogenic Activities ◽  
Conservation Status ◽  
Ecological Factors ◽  
Andean Region ◽  
Key Factor ◽  
Distance Model

AbstractThe Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 homologous SSR markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE=0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated to the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystems as a whole.

scholarly journals Genetic diversity and population structure of endangered rosewood from the Peruvian Amazon using ISSR markers

2020 ◽  
Vol 50 (3) ◽  
pp. 204-212
Author(s):  
Stalin Juan Vasquez GUIZADO ◽  
Muhammad Azhar NADEEM ◽  
Fawad ALI ◽  
Muzaffer BARUT ◽  
Ephrem HABYARIMANA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Population Level ◽  
Diversity Indices ◽  
Issr Markers ◽  
Neighbor Joining ◽  
Peruvian Amazon ◽  
Over Exploitation ◽  
Issr Primers

ABSTRACT Rosewood, Aniba rosaeodora is an endangered species in Amazon forests and its natural stands have been heavily depleted due to over-exploitation for the cosmetic industry. This study aimed to investigate the genetic diversity and population structure of 90 rosewood accessions from eight localities in the Peruvian Amazon through 11 Inter Simple Sequence Repeats (ISSR) primers. The ISSR primers produced a sum of 378 bands, of which 375 (99.2%) were polymorphic, with an average polymorphism information content (PIC) value of 0.774. The mean effective number of alleles (Ne), Shannon informative index (I), gene diversity (He) and total gene diversity (Ht) were 1.485, 0.294, 0.453 and 0.252, respectively. Analysis of molecular variance (AMOVA) showed the presence of maximum variability within populations (88%). The Structure algorithm, neighbor joining and principal coordinate analysis (PCoA) grouped the 90 rosewood accessions into three main populations (A, B and C). Diversity indices at the inter-population level revealed a greater genetic diversity in population A, due to higher gene flow. The neighbor-joining analysis grouped populations A and B, while population C was found to be divergent at the inter population level. We concluded that population A reflects higher genetic diversity and should be prioritized for future management and conservation plans.

scholarly journals Genetic diversity in westernmost European populations of Halimione verrucifera (M. Bieb.) Aellen

2021 ◽  
Vol 26 (2) ◽  
pp. 2541-2547
Author(s):  
MIHNEA VLADIMIRESCU ◽  
◽  
IOANA CĂTĂLINA PAICA ◽  
CRISTIAN BANCIU ◽  
GABRIEL MIHAI MARIA ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Diversity Indices ◽  
Genetic Distances ◽  
Marginal Populations ◽  
Banding Patterns ◽  
Pcr Products ◽  
South Eastern Europe ◽  
Hardy Weinberg Equilibrium ◽  
Population Survival

Halimione verrucifera – an extreme halophyte plant species spread mainly in Asia with a few locations in South Eastern Europe – have the westernmost marginal populations in Romania. In order to asses population fitness and conservation status, genetic diversity among and within population was estimated using ISSR markers.A set of 6 primers were utilized after selection from a primer set which showed clear and reproducible banding patterns, generating a total number of 86 loci. A presence/absence matrix was generated by evaluating the gel electrophoresis banding patterns of PCR products. From this, genetic distances between individuals and populations were calculated, which were used in all subsequent generation of genetic diversity indices, assuming the Hardy-Weinberg equilibrium. Result revealed a low expected heterozygosity for both populations. Further testing by constructing an UPGMA dendrogram and a PCoA analysis confirmed that populations are clearly separated and with levels of genetic diversity that could ensure population survival in time and space.

scholarly journals Genetic Diversity and Structure of Oryza rufipogon Griff. Populations in the Philippines

2020 ◽  
Author(s):  
Sandy Jan E. Labarosa ◽  
Neah Rosandra Sevilla ◽  
Dindo Agustin A. Tabanao ◽  
Nenita B. Baldo ◽  
Helen L.V. Ebuña ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Conservation Status ◽  
The Philippines ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Diversity Assessment ◽  
Comparison Results ◽  
Genetic Diversity And Structure

ABSTRACTOryza rufipogon Griff. or ‘Rufi’ is the wild progenitor of the cultivated rice, Oryza sativa L. In the Philippines, Rufi was previously known to be found only in Lake Apo, Bukidnon. However, a new population was identified in Lake Napalit in the same province. Based on previous morphological diversity assessment, both populations are unique for at least three characters, i.e., leaf, culm, and awn lengths. Environmental parameters such as rainfall and air temperature also differed between the two lakes. With these, an assessment of Rufi’s genetic diversity at the molecular level is beneficial to further ascertain its usefulness in rice breeding and gain insights on its conservation status. Thus, this study estimated the degree of genetic diversity and determined the population structure of 41 samples of natural Rufi populations in the Philippines using SSR markers. A total of 98 genome wide polymorphic SSR markers were selected to examine the genetic diversity and structure of Rufi populations, along with seven rice cultivars for comparison. Results showed that Philippine Rufi populations have lower genetic diversity compared to cultivated rice accessions and other Rufi populations in Southeast Asia and China. This low genetic diversity suggested that Rufi populations might be in a genetic bottleneck, perhaps due to observed unsustainable farming practices near their habitat and lack of awareness of their importance. A significant population structure and differentiation were determined using the STRUCTURE and phylogenetic analyses. Population differentiation might be due to geographic isolation which prevented gene flow between the two populations and the unique climatic conditions between the two lakes.

scholarly journals Mitochondrial DNA variation and population structure of the Critically Endangered saiga antelope Saiga tatarica

Oryx ◽  
2006 ◽  
Vol 40 (1) ◽  
pp. 103-107 ◽  
Author(s):  
M.V. Kholodova ◽  
E.J. Milner-Gulland ◽  
A.J. Easton ◽  
L. Amgalan ◽  
Iu.A. Arylov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Population Decline ◽  
Conservation Action ◽  
Separate Species ◽  
Tissue Samples ◽  
Dna Variation ◽  
Saiga Antelope ◽  
Saiga Tatarica ◽  
Essential Prerequisite

We analysed the mtDNA control region (HV1) of 93 tissue samples from all five populations of the saiga antelope Saiga tatarica. The results show a slight but clear distinction between S. t. mongolica and S. t. tatarica, supporting the current designation of S. t. mongolica as a subspecies rather than a separate species. Levels of genetic diversity were low in S. t. mongolica, consistent with the small size of its population and long isolation. Although populations of S. t. tatarica have reasonable levels of genetic diversity, their conservation status is perilous. The Kalmykian and Kazakhstan samples each contained unique haplotypes, although the species as a whole appears polyphyletic, consistent with recent fragmentation and rapid population decline. An understanding of the population genetics of this species is an essential prerequisite for conservation action.

scholarly journals Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243420
Author(s):  
Pamela Vega-Polo ◽  
Maria Mercedes Cobo ◽  
Andrea Argudo ◽  
Bernardo Gutierrez ◽  
Jennifer Rowntree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Anthropogenic Activities ◽  
Conservation Status ◽  
Ecological Factors ◽  
Andean Region ◽  
Key Factor ◽  
Species Specific

The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.

Infraspecific genetic variation and population structure of Salvia nemorosa L. (Lamiaceae) in Iran

2019 ◽  
Vol 26 ◽  
pp. 127-136 ◽  
Author(s):  
Seyed M. Talebi ◽  
Reza Rezakhanlou ◽  
Alex V. Matsyura
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
Conservation Status ◽  
Molecular Study ◽  
Medicinal Species ◽  
High Genetic Diversity ◽  
Genetic Groups ◽  
Nj Tree ◽  
Two Populations

Salvia nemorosa is widely distributed in different parts of Iran, while, there is no information about its population genetic structure and genetic diversity. The current information of its potential protection or conservation status in Iran is almost absent and unclear. Our investigation was the first molecular study of this medicinal species. We performed analysis of genetic variability and population structure of 11 populations of S. nemorosa in Iran using ISSR technique. We revealed intra and inter-population genetic diversity in the studied populations. Genetic parameters widely varied among the studied populations and confirmed their high genetic diversity. Moreover, AMOVA test showed significant molecular variation among and within the populations. The arrangement of populations and their individuals in NJ tree, PCA and MDS plots was in agreement with AMOVA results and individuals of five groups were overlapped. The Nm value showed low amount of gene flow among the populations. Based on STRUCTURE analysis and UPGMA tree of genetic distance, six genetic groups were identified among the studied populations, while two populations had significant differences and could be definite as ecotypes.

scholarly journals Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

Agronomy ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 647 ◽  
Author(s):  
Ünal Karık ◽  
Muhammad Azhar Nadeem ◽  
Ephrem Habyarimana ◽  
Sezai Ercişli ◽  
Mehtap Yildiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Diversity ◽  
Diversity Indices ◽  
Primer Binding Site ◽  
Neighbor Joining ◽  
Marker System ◽  
Information Index ◽  
Geographical Regions ◽  
The World

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant.

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