Dataset Information

Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka.

ABSTRACT: The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A complete region spanning 1.14?kb and ?1?kb was amplified by HotStart PCR and sequenced by Sanger sequencing. The Cyt b sequence revealed 85 substitution sites, no indels and 17 parsimony informative sites, whereas D-loop showed 189 variable sites, 51 parsimony informative sites with 5' functional domains TAS, CSB-F, CSBs (1, 2, 3) preceding tandem repeat at 3' end. Current data highlights the intraspecific variations in these target regions and variations validated using suitable evolutionary models points out that the overall point mutations observed in the region are transitions leading to no structural and functional alterations. The mitochondrial data generated uncover the genetic diversity within species and conservationist can utilize the data to estimate the effective population size or for forensic identification of animal or its seizures during unlawful trade activities.

SUBMITTER: Lalitha R

PROVIDER: S-EPMC6057446 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka.

Lalitha R R Chandavar V R VR

Journal of advanced research 20171121

The freshwater Testudine species have gained importance in recent years, as most of their population is threatened due to exploitation for delicacy and pet trade. In this regard, Lissemys punctata, a freshwater terrapin, predominantly distributed in Asian countries has gained its significance for the study. A pilot study report on mitochondrial markers (Cyt b and D-loop) conducted on L. punctata species from southern Karnataka, India was presented in this investigation. A co ...[more]

PMID: 30046490

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Project description:The genus Cooperia includes important parasites of ruminants and currently contains 34 accepted species. However, even for those species infecting livestock, there is a considerable lack of molecular information and many species are only identifiable using subtle morphological traits. The present study aimed to provide molecular data to allow diagnosis of Cooperia species infecting cattle. Partial sequences of two mitochondrial (cytochrome oxidase 2, 12S rRNA gene) and two nuclear genes (isotype 1 β tubulin gene including two introns, internal transcribed spacers (ITS) were obtained from morphologically identified specimens of Cooperia pectinata, Cooperia punctata and Cooperia spatulata as well as from larvae of pure Cooperia oncophora and C. punctata laboratory isolates. Pairwise identity of ITS-2 sequences was very high and it was the only region able to identify a specimen as Cooperia sp. However, the ITS-2 was unreliable for diagnosis at the species level. All other marker sequences could not unequivocally be allocated to the genus Cooperia but allowed clear species identification with the exception of the pair C. punctata/C. spatulata for which no significant differences were found for any marker sequence. Maximum-likelihood phylogenetic analyses of individual genes as well as a multi-locus analysis covering all four sequences confirmed that specimen identified as C. spatulata were randomly distributed throughout the C. punctata cluster and formed no group of their own. In contrast, the other Cooperia species formed clearly separated and statistically supported clusters. These data indicate that C. spatulata is most likely only a morphotype of C. punctata and the name should be considered a synonym. Combinations of nuclear and mitochondrial markers should be used to identify morphotypes or cryptic species to benefit from excellent barcoding properties of the latter but allowing proper phylogenetic analyses and controlling for lineage sorting that might occur for mitochondrial genotypes within a species.

Project description:BackgroundIt is argued that Indian gender minorities displayed differential mental health problems and suicide attempts. Hence, the study was intended to understand the prevalence of anxiety, depression and suicidality among this group, specifically those living in a metropolitan city in South India.MethodsThe data was generated from a cross-sectional study that employed a structured questionnaire to collect information about experiences of anxiety, depression and suicidal behavior among gender-diverse individuals in Bangalore, the capital city of Karnataka state. The study used stratified simple random sampling of eligible individuals who were 18 years of age and older and who were enrolled in an HIV prevention program implemented for gender-diverse individuals run by the Karnataka Health Promotion Trust and the University of Manitoba at the time of the study (2012). Bivariate and multivariate analyses were used to assess the relative contribution of various factors that affect suicide ideation or actual attempts among the gender diverse participants.ResultsResults showed that 62% whose main source of income was Basti (socially sanctioned practice of begging), 52% of Hijras, 56% who lived with their Gurus, 58% who were not happy with their physical appearance, 55% who consumed alcohol daily, and 63% who experienced high depression had ever thought of or attempted suicide in the month prior to the survey. However, multivariate analysis showed that respondents who were not happy with their physical appearance and thought of changing it had significantly higher odds (AOR = 2.861; CI 1.468,5.576; p = 0.002) of either having thoughts that it was better being dead or wished they died. Similarly, those who experienced high depression, their odds of either having had thoughts of or having attempted suicide increased by three times (AOR = 3.997; CI 1.976, 8.071; p < 0.000).ConclusionsIt is observed that a high percentage of gender minorities had attempted suicide or thought of suicide during the month preceding the data collection. The findings bring new insights on the proximate determinant of physical appearance on the suicidality of gender minorities assigned male at birth and appropriate to account for this while addressing the mental health issues.

Dataset Information

Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka.

Publications

Intraspecific variations in <i>Cyt b</i> and D-loop sequences of Testudine species, <i>Lissemys punctata</i> from south Karnataka.

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