scholarly journals Cryptic species and genetic structure in Didemnum granulatum Tokioka, 1954 (Tunicata: Ascidiacea) from the southern Brazilian coast

2014 ◽  
Vol 74 (4) ◽  
pp. 923-932 ◽  
Author(s):  
JL Bouzon ◽  
SM Vargas ◽  
JF Oliveira Neto ◽  
PH Stoco ◽  
FP Brandini
Keyword(s):  
Spatial Distribution ◽  
Genetic Structure ◽  
Cryptic Species ◽  
Nucleotide Diversity ◽  
Mitochondrial Gene ◽  
Haplotype Diversity ◽  
Single Species ◽  
Brazilian Coast ◽  
Neighbor Joining ◽  
Haplotype Networks

Didemnum granulatum is a colonial fouling ascidian that lives in subtidal substrates, worldwide. It exhibits two morphotypes, orange and beige. In this study, we verified if the color morphotypes and/or the spatial distribution of specimens in different islands might be associated to patterns of genetic structure of a single species, or if they represent distinct cryptic species. Specimens were collected in four islands, along the coast of the Santa Catarina state. A segment of 490 bp from the mitochondrial gene cytochrome c oxidase subunit 1 (COI) was amplified from 45 samples. Twenty-one haplotypes were identified. The total haplotype diversity (0.912) and the total nucleotide diversity (0.044) were high. The global Fst of the populations analyzed was 0.97, with most of the variation occurring between orange and beige groups (82.19%). The variation found between populations within groups was 15.37%, and 2.45% within populations. Haplotype networks and the neighbor-joining tree showed clear genetic divergence between individuals of distinct colors, and between the islands. These evidences strongly support the presence of a complex of two cryptic species for D. granulatum occupying the studied area. Both species were also highly genetically structured between islands, suggesting that the conservation process of these populations is complex.

Bottlenose dolphin communities from the southern Brazilian coast: do they exchange genes or are they just neighbours?

2015 ◽  
Vol 66 (12) ◽  
pp. 1201 ◽  
Author(s):  
Ana Paula Borges Costa ◽  
Pedro Fruet ◽  
Fábio Gonçalves Daura-Jorge ◽  
Paulo César Simões-Lopes ◽  
Paulo Henrique Ott ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bottlenose Dolphin ◽  
Gene Diversity ◽  
Mitochondrial Gene ◽  
Distinct Group ◽  
Unknown Origin ◽  
Brazilian Coast ◽  
Tissue Samples ◽  
Scale Population ◽  
Free Ranging

The genetic structure of bottlenose dolphin communities found along the southern Brazilian coast is reported in this study. Genetic structure analysis using biopsy samples from free ranging dolphins and tissue samples from stranded dolphins revealed a fine-scale population structure among three distinct groups. The first genetically distinct group was composed of resident dolphins of Laguna with a high degree of site fidelity. The second group was composed of one photo-identified dolphin, previously recognised by its interaction with fishermen, and dolphins that stranded near the mouth of Tramandaí Lagoon. Moderate nuclear and low mitochondrial gene diversity was found in dolphins of those coastal communities, whereas most of the dolphins stranded along the coast showed markedly higher levels of gene diversity at both markers. These stranded dolphins of unknown origin formed the third distinct group, which may be part of a larger offshore community. These results demonstrate the presence of at least three bottlenose dolphin clusters along this portion of the Brazilian coast, with the coastal specimens appearing to be only neighbours of a larger offshore community that eventually strands along the coast, highlighting the importance of the establishment of management and conservation measures for the species at a local scale.

scholarly journals Spread beyond the border: Small Scale genetic structure of the introduced Banggai cardinalfish (Pterapogon kauderni) population in the Bali Strait

2021 ◽  
Vol 26 (3) ◽  
pp. 165-172
Author(s):  
I Nyoman Giri Putra ◽  
Ni Luh Putu Ria Puspitha ◽  
Endang Wulandari Suryaningtyas ◽  
Endang Wulandari Suryaningtyas
Keyword(s):  
Genetic Structure ◽  
Native Species ◽  
Population Genetic ◽  
Nucleotide Diversity ◽  
Dna Marker ◽  
Haplotype Diversity ◽  
Small Scale ◽  
Aquarium Trade ◽  
High Haplotype Diversity ◽  
Multiple Introduction

The living marine aquarium trade has been known to mediate various aquatic invaders to spread and established a new population outside of their natural home range. In most cases, the introduce species cause a cascaded effect which harm the native species and their ecosystem. The successful of the invasion event often related to the genetic properties of the introduced species. Therefore, using a molecular approach based on a mitochondrial DNA marker, the present work aimed to evaluate the population genetic structure of the introduced P. kauderni population in Bali Strait. Samples were collected from four sites in Gilimanuk Bay, Bali Strait. Our results showed  a high haplotype diversity and low nucleotide diversity that might be a signal of a bottleneck. Overall, we found five haplotypes comprising two unique haplotypes and three shared haplotypes. Genetic structure was detected in some localities, which indicates Pterapogon kauderni might originated from various genetically distinct populations. However, we could not conclusively determine the observed patterns of the genetic structure within each site. These patterns are likely related to the multiple introduction event of P. kauderni in Bali Strait. Additional samples from both side (introduced and native habitat) combined with more rapidly evolving markers may describe the structure more clearly.

Polymorphism and Genetic Diversity among Cassava Cultivars based on ITS1-5.8S-ITS2 Sequences of rDNA

2017 ◽  
Vol 6 (6) ◽  
pp. 220-227
Author(s):  
Djirabaye Nadjiam ◽  
Aliou Guisse ◽  
Mbacké Sembéne ◽  
Fatimata Mbaye
Keyword(s):  
Genetic Diversity ◽  
Bayesian Approach ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Genetic Erosion ◽  
Nucleotide Sequences ◽  
Its2 Region ◽  
Neighbor Joining ◽  
High Haplotype Diversity ◽  
The Bayesian Approach

Cassava is an important crop in the southern area of the Chad and it is char- acterized by many cultivars. But these cultivars have never been evaluated at the molecular level. Therefore, the objective of this study was to analyze their genetic diversity and their phylogenetic relationships. After DNA extraction, amplification and sequencing, the nucleotide sequences of the ITS1- 5.8S-ITS2 region of the ribosomal DNA of 12 selected cultivars have been analyzed. The Neighbor-Joining method, Maximum Parsimony, Maximum Likelihood and the Bayesian approach allowed studying the ancestral links. The identified nucleotide sequences have 542 bp. The targeted genes showed 468 conserved sites and 59 polymorphic sites. The nucleotide frequency was 18.64% for Adenine, 14.01% for Thymine, 34.46% for Cytosine and 32.89% for Guanine. The (G + C) content was 67.35% compared to 32.65% for the (A+T). The substitution rate was in favor of the transversions (67.46%) against the transitions (32.54%). The analysis revealed high haplotype diversity (Hd=0.954) and low nucleotide diversity (π=0.026) with an average number of pairwise nucleo de di erences (k=14.045). On the all popula on, 9 haplotypes, including 6 individual and 3 double, were identified. Gene c di eren a on is medium (FST=0.314) with a low number of migrants (Nm=0.55) and a medium genetic distance (0.028). Phylogenetic analysis based on the Bayesian approach revealed three groups of cul vars with the existence of two strongly supported clades. The cultivars studied are characterized by demographic stability or moderate population growth.They will be incorporated in the breeding program in order to limit their genetic erosion and to select the interesting characters. 

scholarly journals Molecular Characteristics of Batanghari, Tambago, Orange, and Mandiangin Giant Gourami Strains

2017 ◽  
Vol 9 (3) ◽  
pp. 592
Author(s):  
Agus Nuryanto ◽  
Anatasia Endang Pulungsari
Keyword(s):  
Cytochrome B ◽  
Nucleotide Diversity ◽  
Taxonomic Status ◽  
Single Species ◽  
Genetic Distances ◽  
Cytochrome B Gene ◽  
Molecular Characteristics ◽  
Neighbor Joining ◽  
Morphological Variations ◽  
Genetic Structures

<p class="IsiAbstrakIndo"><span lang="EN-GB">Morphological variations among geographic and can be identified as different species. However, a lot of studies proved that morphological variations are also common in conspecific individuals. Therefore, precise identification using additional characters is vital, such as using a molecular marker. Here, we characterized Batanghari, Tambago, Orange, and Mandiangin gourami strains using the cytochrome b gene to evaluate their taxonomic status. Partial sequences of cytochrome b gene were sequenced for 40 individuals. Taxonomic status was checked for giant gourami sequences available in GenBank. Kimura 2-Parameter genetic distances were calculated in MEGA6 software. Haplotype and nucleotide diversity within population and </span><span lang="EN-GB">Φ</span><sub><span lang="EN-GB">st</span></sub><span lang="EN-GB">-value among populations were estimated in Arlequin software. Phylogenetic relationship was reconstructed using the neighbor-joining method in MEGA6 software based on Kimura 2-parameter model with 1000 pseudobootstraps. Taxonomic identification results in 99% sequences homology to </span><em><span lang="EN-GB">Osphronemus goramy</span></em><span lang="EN-GB"> sequences (accession number KU984978.1 and AY763768.1), means that all strains belong to single species. Low genetic distances, medium haplotype and low-level nucleotide diversity were observed among strains. Pairwise </span><span lang="EN-GB">Φ</span><sub><span lang="EN-GB">st</span></sub><span lang="EN-GB">-comparison indicates no genetic differences among Sumatera strain, whereas strong genetic structures observed between Sumatera and Mandiangin strains. The phylogenetic tree showed that Mandiangin formed separate subclades from other strains with bootstraps value of 100%. This finding has important implication for breeding sciences and efforts.</span></p>

scholarly journals Molecular Identification of some Indian Muscid flies (Diptera: Muscidae) based on mitochondrial gene COII

2017 ◽  
Author(s):  
Devinder Singh ◽  
Ramandeep Achint
Keyword(s):  
Molecular Identification ◽  
Nucleotide Diversity ◽  
Diagnostic Marker ◽  
Mitochondrial Gene ◽  
Haplotype Diversity ◽  
Morphological Characters ◽  
Genetic Distances ◽  
Veterinary Importance ◽  
Coii Gene ◽  
Intraspecific Distance

ABSTRACTTaxonomic identification of flies having medical and veterinary importance is often complicated due to the lookalike morphological characters. Molecular identification of five Indian muscid flies (Musca domestica, Musca sorbens, Musca crassirostris, Stomoxys calcitrans and Haematobia irritans) has been attempted on the basis of mitochondrial COII gene. Sequences of 500-520 bp were analysed and found to be A+T rich. Rate of transitions was higher than transversions. The average haplotype diversity was 0.833 and nucleotide diversity was 0.02547 within the different species, which were calculated with the DnaSP Version 5.0. The genetic distances calculated by K2P model, showed the interspecific distances range more than 8.2%, while the intraspecific distance range had not exceed 0.8%. The 1000 bootstrapped Neighbour-joining tree and Maximum likelihood tree were constructed to establish the phylogenetic relationship between the different muscid species. The results show the robustness of COII gene as a diagnostic marker. The data obtained from this study would be worthy for medical and veterinary entomologists for precise identification of imperative muscid species.

scholarly journals First Evidence of Cryptic Species Diversity and Population Structuring of Selaroides leptolepis in the Tropical Western Pacific

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo C. Halasan ◽  
Paul John L. Geraldino ◽  
Hsiu-Chin Lin
Keyword(s):  
Genetic Structure ◽  
Cryptic Species ◽  
Phylogenetic Trees ◽  
Rapid Expansion ◽  
Western Pacific ◽  
Genetic Structuring ◽  
Tropical Western Pacific ◽  
Haplotype Networks ◽  
Population Structuring ◽  
Genetic Structure And Diversity

The yellowstripe scad, Selaroides leptolepis (Carangidae), is an important fish commodity in the Tropical Western Pacific (TWP). It has a latitudinal Pacific range from south of Japan down to northern Australia, with the highest concentration in Southeast Asia. However, its TWP fishing grounds have long been a hotspot of unsustainable exploitations, thus threatening the remaining wild populations. Despite the species’ commercial significance, there is limited understanding of its genetic structure and diversity. Herein, the genetic structure of S. leptolepis was examined using mitochondrial COI and CytB sequences. Both markers denoted significant genetic structuring based on high overall FST values. Hierarchical analysis of molecular variance (AMOVA), maximum likelihood (ML) phylogenetic trees, and median-joining (MJ) haplotype networks strongly supported the occurrence of two allopatrically distributed lineages. These comprised of a widespread Asian lineage and an isolated Australian lineage. Within-lineage distances were low (K2P &lt; 1%) whereas across-lineage distances were remarkably high (K2P &gt; 6%), already comparable to that of interspecific carangid divergences. Haplotype sequence memberships, high genetic variations, and the geographic correlation suggested that the Australian lineage was a putative cryptic species. Historical demographic inferences also revealed that the species experienced rapid expansion commencing on the late Pleistocene, most likely during the end of the Last Glacial Maximum (∼20,000 years ago). The present study encouraged the application of lineage-specific management efforts, as the lineages are experiencing different evolutionary pressures. Overall, accurate knowledge of the species’ genetic distribution is fundamental in protecting its diversity and assuring stock sustainability.

scholarly journals Abundant Mitochondrial Genome Diversity, Population Differentiation and Convergent Evolution in Pines

Genetics ◽  
1998 ◽  
Vol 150 (4) ◽  
pp. 1605-1614
Author(s):  
Junyuan Wu ◽  
Konstantin V Krutovskii ◽  
Steven H Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Population Differentiation ◽  
Mitochondrial Gene ◽  
Dna Polymorphisms ◽  
Neighbor Joining ◽  
Closely Related Species ◽  
Breeding Programs ◽  
Length Polymorphisms ◽  
Polymerase Chain ◽  
Mitochondrial Genome Diversity

Abstract We examined mitochondrial DNA polymorphisms via the analysis of restriction fragment length polymorphisms in three closely related species of pines from western North America: knobcone (Pinus attenuata Lemm.), Monterey (P. radiata D. Don), and bishop (P. muricata D. Don). A total of 343 trees derived from 13 populations were analyzed using 13 homologous mitochondrial gene probes amplified from three species by polymerase chain reaction. Twenty-eight distinct mitochondrial DNA haplotypes were detected and no common haplotypes were found among the species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (HS) averaged 0.22, and population differentiation (GST and θ) exceeded 0.78. Analysis of molecular variance also revealed that &gt;90% of the variation resided among populations. For the purposes of genetic conservation and breeding programs, species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Neighbor-joining phenograms, however, strongly disagreed with those based on allozymes, chloroplast DNA, and morphological traits. Thus, despite its diagnostic haplotypes, the genome appears to evolve via the rearrangement of multiple, convergent subgenomic domains.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

scholarly journals More than meets the eye: syntopic and morphologically similar mangrove killifish species show different mating systems and patterns of genetic structure along the Brazilian coast

Heredity ◽  
2020 ◽  
Vol 125 (5) ◽  
pp. 340-352
Author(s):  
Waldir M. Berbel-Filho ◽  
Andrey Tatarenkov ◽  
Helder M. V. Espírito-Santo ◽  
Mateus G. Lira ◽  
Carlos Garcia de Leaniz ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mating Systems ◽  
Brazilian Coast ◽  
Mangrove Killifish

Genetic variability and demographic history of Heliothis virescens (Lepidoptera: Noctuidae) populations from Brazil inferred by mtDNA sequences

2011 ◽  
Vol 102 (3) ◽  
pp. 333-343 ◽  
Author(s):  
K.C. Albernaz ◽  
K.L. Silva-Brandão ◽  
P. Fresia ◽  
F.L. Cônsoli ◽  
C. Omoto
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Heliothis Virescens ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Haplotype Network ◽  
Demographic Expansion ◽  
Significant Genetic Structure ◽  
History Of

AbstractIntra- and inter-population genetic variability and the demographic history of Heliothis virescens (F.) populations were evaluated by using mtDNA markers (coxI, coxII and nad6) with samples from the major cotton- and soybean-producing regions in Brazil in the growing seasons 2007/08, 2008/09 and 2009/10. AMOVA indicated low and non-significant genetic structure, regardless of geographical scale, growing season or crop, with most of genetic variation occurring within populations. Clustering analyzes also indicated low genetic differentiation. The haplotype network obtained with combined datasets resulted in 35 haplotypes, with 28 exclusive occurrences, four of them sampled only from soybean fields. The minimum spanning network showed star-shaped structures typical of populations that underwent a recent demographic expansion. The recent expansion was supported by other demographic analyzes, such as the Bayesian skyline plot, the unimodal distribution of paired differences among mitochondrial sequences, and negative and significant values of neutrality tests for the Tajima's D and Fu's FS parameters. In addition, high values of haplotype diversity (Ĥ) and low values of nucleotide diversity (π), combined with a high number of low frequency haplotypes and values of θπ<θW, suggested a recent demographic expansion of H. virescens populations in Brazil. This demographic event could be responsible for the low genetic structure currently found; however, haplotypes present uniquely at the same geographic regions and from one specific host plant suggest an initial differentiation among H. virescens populations within Brazil.

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