The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation

Vashistha, Gaurav; Sharma, Deepika; Dhakate, Parag Madhukar; Khudsar, Faiyaz A.; Kothamasi, David

doi:10.1007/s12686-020-01164-6

Cited by 5 publications

(3 citation statements)

References 79 publications

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“…Although many conservation researchers are in the process of transferring from genetics to genomics, several studies indicate that the data obtained by microsatellites are informative to answer numerous questions (e.g. those related to diversity within populations, differentiation between populations, and inbreeding), in addition to being much less expensive and therefore more accessible for a greater number of researchers ( Puckett, 2017 ; Vashistha et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity and conservation in Bromeliaceae based on SSR markers

Bered,

Barcellos,

Costa

2023

GMB

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Bromeliaceae has been used as a model Neotropical group to study evolutionary and diversification processes. Moreover, since large parts of the Neotropics are under anthropogenic pressure, a high percentage of possibly threatened species occurs. Despite this, concrete proposals for conservation based on genetic data are lacking. We compilated all genetic data obtained by nuclear microsatellites for Bromeliaceae and compared the levels of genetic diversity of subfamilies and their taxa, considering traits of life history and distribution in conservation and no conservation areas. We retrieved a total of 87 taxa (ca. 2.5% of the family size) and most present a mixed mating system, anemochoric dispersion, are ornithophilous, and were sampled outside Conservation Units, the majority occurring in the Atlantic Forest. Also, we found differences in some genetic indexes among taxa concerning seed dispersal mechanisms (e.g. Zoochoric taxa with higher diversity and lower inbreeding), mating systems (e.g. autogamous taxa showed higher inbreeding), outside/inside conservation units (allelic richness higher in not protected areas), and among different subfamilies (e.g. higher genetic diversity in Bromelioideae). The results obtained in this review can be useful for proposing conservation strategies, can facilitate the comparison of related taxa, and can help advance studies on the Bromeliaceae family.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity and conservation in Bromeliaceae based on SSR markers

Bered,

Barcellos,

Costa

2023

GMB

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“…Crocodilians are large reptilian species and are globally distributed in both freshwater and marine water habitats. According to the International Union for Conservation of Nature (IUCN) Red List, there are 23 extant species of crocodiles, of which 7 are ‘critically endangered’, 4 are ‘vulnerable’ and 12 are of ‘least concern’ ( Choudhury and De Silva, 2013 ; Vashistha et al. , 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Monitoring the stress physiology of free-ranging mugger crocodiles (Crocodylus palustris) across diverse habitats within Central Gujarat, India

Desai,

Bhowmik,

Srinivasan

et al. 2024

Conservation Physiology

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Animals face several challenges in their natural environment, and to cope with such conditions, they may exhibit contrasting physiological responses that directly affect their overall well-being and survival. In this study, we assessed physiological responses via faecal glucocorticoid metabolite (fGCM) measurements in free-ranging mugger crocodiles inhabiting diverse habitats in Gujarat, India. We sampled muggers within Charotar, a rural area (Zone A) with local people having high tolerance towards the presence of muggers, and Vadodara, a region having both urban (Zone B) and rural (Zone C) areas with high levels of human–mugger conflict (HMC). Further, muggers in Vadodara live in water bodies that are mostly polluted due to sewage disposal from adjoining chemical industries. To measure fGCM (mean ± SEM, ng/g dry faeces) levels in muggers, scats were collected during both breeding (N = 107 scats) and non-breeding (N = 22 scats) seasons from all three zones. We used captive muggers (a focal enclosure) to biologically validate (via capture and restraint) the selected fGCM assay (11-oxoetiocholanolone assay). We showed a significant (P < 0.05) 11-fold increase in fGCM levels between pre-capture (540.9 ± 149.2, N = 11) and post-capture (6259.7 ± 1150.5, N = 11) samples. The validated assay was applied to free-ranging muggers during the breeding season, and Zone A showed significantly (P < 0.05) lower fGCM levels (542.03 ± 71.3) compared to muggers of Zone B (1699.9 ± 180.8) and Zone C (1806.4 ± 243.2), both zones having high levels of HMC with polluted water bodies. A similar contrast in fGCM levels was also observed during the non-breeding season. Overall, the study demonstrated that fGCM levels in muggers varied across habitats, and such variation could be due to a multitude of ecological factors that the species experience in their immediate local environment. Moreover, high fGCM levels in muggers of Vadodara during both breeding and non-breeding seasons may indicate a condition of chronic stress, which could be maladaptive for the species.

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“…Simple sequence repeats (SSRs), or microsatellites, are highly variable genetic markers useful for a wide variety of applications in genetic analysis, including genetic mapping, population structure and gene flow analysis, identification of conservation units, and kinship analysis (Gerber et al, 2000; Vashistha et al, 2020; Zamudio & Wieczorek, 2000). Since the first application of SSRs in the 1990s, they have been extensively and continuously used in evolutionary, ecological, and conservation research even in the genomics era (Ali et al, 2019; Allendorf, 2017; Shahabzadeh et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

Wang

Gao

Liu

et al. 2022

Ecology and Evolution

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Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.

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The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation

Cited by 5 publications

References 79 publications

Genetic diversity and conservation in Bromeliaceae based on SSR markers

Genetic diversity and conservation in Bromeliaceae based on SSR markers

Monitoring the stress physiology of free-ranging mugger crocodiles (Crocodylus palustris) across diverse habitats within Central Gujarat, India

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data

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