Development of fourteen novel microsatellite markers of Crocodylus palustris, the Indian mugger, and their cross-species transferability in ten other crocodilians (original) (raw)
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The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation
Conservation Genetics Resources, 2020
Microsatellite DNA is among the several molecular tools used for determining genetic variability and inbreeding depression in threatened populations. It has been used extensively for population genetics studies in conservation of crocodilians. Even though single nucleotide polymorphisms have higher precision compared to microsatellite DNA markers, microsatellites offer a cost advantage which is particularly important to researchers in the global south. Here, we review the role of microsatellite DNA as a conservation tool in crocodilians. Employing appropriate keywords in three online databases, we studied 78 publications, where microsatellite DNA had been used to study crocodilian species. We found that 504 species-specific markers were designed for 13, out of a total of 24 crocodilian taxa. Genus Crocodylus had the highest number of speciesspecific markers and was the most studied taxa using microsatellites. Moreover, microsatellite markers developed for C. porosus were successful in cross amplification of microsatellite markers in 19 other crocodilian species. Microsatellite based studies had highest focus on analyses of multiple populations of a single species. Based on our review of microsatellite based studies on populations of crocodilian species, we recommend that microsatellite DNA markers are an effective conservation tool that can provide critical information on population structures of threatened crocodilian species.
Conservation Genetics, 2009
We developed 16 microsatellite loci from an F 2 hybrid between Aquilegia formosa and Aquilegia pubescens . In samples of 28 individuals, we found an average of 14 alleles per locus from each parental species. We tested these loci for cross-amplification in 10 additional species of Aquilegia and found that all 16 loci amplified in other North American species and 12 consistently amplified in European or Asian species. Nine loci amplified in the sister species to Aquilegia , Semiaquilegia adoxoides . The success of cross-species amplification suggests that these microsatellites should prove useful for studies in a broad range of Aquilegia species.
Development of Microsatellite Markers for Siamese Crocodile (Crocodylus siamensis)
New microsatellite markers were developed for Siamese crocodile (Crocodylus siamensis) by constructing a library for microsatellite DNA. Construction and characterization of the library are described in the present study. Twenty microsatellite markers were developed from a (AC) 15 enriched microsatellite DNA library. Among the twenty microsatellite loci, ten (50%) were polymorphic, where as the rest were monomorphic (with two to four alleles per locus). The microsatellite sequences obtained could be classified structurally into perfect repeats (80%) and imperfect repeats (20%). No incomplete repeat type was observed. These markers were tested in five individuals of the same species and these tests resulted in twenty new microsatellites markers for C. siamensis. Low number of alleles (1-4 alleles) with an average of 1.7 alleles per locus was observed. The average length of uninterrupted repeats from the selected clones was 12.3.
Genetics and Molecular Research, 2014
We tested microsatellites that were developed for the saltwater crocodile (Crocodylus porosus) for cross-species amplification and to provide an estimate of inter-and intraspecific variation among four species of Neotropical crocodiles (C. rhombifer, C. intermedius, C. acutus, and C. moreletii). Our results indicated that with the exception of 2 loci in C. intermedius, all 10 microsatellite loci were successfully amplified in the 4 species, producing a set of variably sized alleles that ranged in number between 2 and 14 alleles per locus. Similarly, private alleles (i.e., unique alleles) also were reported in all 4 species for at least 3 loci. The mean observed and expected heterozygosities (averaged across species for all 10 loci combined) ranged from 0.39 to 0.77 and from 0.44 to 0.78, respectively. In addition to this, we evaluated these microsatellites in 2 populations of C. acutus and C. moreletii to assess their utility in estimating intraspecific levels of polymorphisms. These ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 13 (3): 5492-5502 (2014) Assessment of microsatellites in Neotropical crocodiles microsatellites also showed considerable allelic variation in population level analysis. The set of 10 microsatellite loci in our study had the potential to be used as a tool in population and conservation genetic studies of Neotropical crocodiles.
Revista De Biologia Tropical, 2022
Introduction: There is low evidence of genetic diversity and hybridization processes within Crocodylus acutus and C. moreletii populations. Objetive: To evaluate genetic diversity and some phylogenetic relationships in wild and captive populations of C. acutus and C. moreletii using the Barcode of Life Data System (COX1, cytochrome C oxidase subunit 1 gene). Methods: 28 individuals phenotypically like C. acutus located in the state of Guerrero, Oaxaca and Quintana Roo were sampled, as well as animals belonging to C. moreletii located in the states of Tabasco, Campeche, and Quintana Roo. 641 base pairs of nucleotide sequence from COX1 were used to obtain the haplotype and nucleotide diversity per population, and a phylogenetic and network analysis was performed. Results: Evidence of hybridization was found by observing C. moreletti haplotypes in animals phenotypically determined as C. acutus, as well as C. acutus haplotypes in animals classified as C. moreletti. Low haplotypic diversity was observed for C. acutus (0.455 ± 0.123) and for C. moreletii (0.505 ± 0.158). A phylogenetic tree was obtained in which the sequences of C. acutus and C. moreletii were grouped into two well-defined clades. Organisms identified phenotypically as C. acutus but with C. moreletii genes were separated into a different clade within the clade of C. moreletii. Conclusions: There are reproductive individuals with haplotypes different from those of the species. This study provides a small but significant advance in the genetic knowledge of both crocodile species and the use of mitochondrial markers, which in this case, the COX1 gene allowed the detection of hybrid organisms in wild and captive populations. Conservation efforts for both species of crocodiles should prevent the crossing of both threatened species and should require the genetic identification of pure populations, to design effective conservation strategies considering the possibility of natural hybridization in areas of sympatry.
Genetics and Molecular …, 2006
Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral characteristics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Caiman latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.
2006
Microsatellite DNA markers have been used to assess genetic diversity and to study ecological behavioral characteristics in animals. Although these markers are powerful tools, their development is labor intensive and costly. Thus, before new markers are developed it is important to prospect the use of markers from related species. In the present study we investigated the possibility of using microsatellite markers developed for Alligator mississipiensis and Caiman latirostris in South American crocodilians. Our results demonstrate the use of microsatellite markers for Paleosuchus palpebrosus, Caiman crocodilus and Caiman yacare.
High levels of population genetic differentiation in the American crocodile (Crocodylus acutus)
The American crocodile ( Crocodylus acutus ) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching and unintentional translocation of individuals). Moreover, recent work suggests C. acutus as a complex of cryptic species with preliminary proposals for taxonomic reassignment. Until recently, most population genetics research has primarily focused on present hybrid zones with other new world crocodilians . In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic d...