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The article I chose to write about for the second writing assignment focuses on Scinax treefrogs in south-eastern Brazil and how sea level incursions has shaped their genetic differentiation. I chose to write about this paper because I find it interesting how species near each other can be different from one another due to several factors.
The authors of the article focused their field study on three species belonging to the S. perpusillus group, in specific three populations from land-bridge islands in south eastern Brazil and five mainland populations in the Brazilian Atlantic Forest located in the Sao Paulo state. The study was conducted to investigate the genetic differentiation of the Scinax perpusillus treefrogs that is said to have resulted from Pleistocene refugia and sea level incursions. The purpose of the investigation was to understand how fragmentation in Pleistocene forest and incursions at sea level led to genetic differentiation. The purpose of the investigation was also to determine if the S. perpusillus group from the three islands; Ilha dos Porcos Pequena, Ilha da Queimada Grande and Ilha do Mar Virado sampled showed any signs of genetic drift or isolation.
The field study was carried on through January 2002 to April 2006, during that time six to thirty-seven individuals who were considered breeding adults were sampled from the three land-bridge islands. Tissue samples such as liver and toe clips were collected from individuals and placed in a 95% ethanol solution for later DNA extraction and genetic analyses. One of the first methods of the study was to use a DNeasy Blood and Tissue Kit to extract the genomic DNA from the preserved tissue collected. Once extracted the polymerase chain reaction technique was used to amplify and sequence a mitochondrial fragment that spanned the 16S and ND1 genes. At the end of the mitochondrial dataset there was a total of thirty samples as it is said that, “two to six individuals per locality were included. ” It was then found from the microsatellite dataset that there was a total of 149 samples.
In looking at microsatellite diversity as well as population and relatedness among, the authors tested for departures from Hardy-Weinberg equilibrium and evidence of linkage disequilibrium. In comparing relative diversity and divergence between mainland and island localities the software Arlequin 3. 1 was used. Arlequin 3. 1 was used to calculate the “pairwise genetic distance, mean number of alleles and the expected heterozygosity versus observed heterozygosity” of the sampling localities. Data gained from Arlequin 3. 1 such as, pairwise genetic distance was used to find the potential loss of genetic diversity among the three island populations with the mainland populations that are genetically closer to them.
A Mantel test was said to then be used to assess “the effects of drift on genetic differentiation across mainland and island population” which was setup with 1000 permutations and 500 bootstraps. Permutations and bootstraps were used to determine if the estimates of pairwise genetic distance between the localities correlated with the geographic distance. It was later said that if genetic drift and gene flow were at equilibrium than there would be a pattern of “isolation by distance where genetic differentiation is correlated with geographic distance between population”. It was also said that, “if genetic drift is the [only] force shaping genetic differentiation between populations to be elevated regardless of geographic distance”. In researching the microsatellite diversity, population structure and relatedness of the three species of S. perpusillus, fifteen alleles were said to be discovered from the eight loci. Though no evidence was found on the large allele dropout or as said “the scoring bias due to stutter, or null alleles across all populations”.
Overall, allelic richness was lower for the “island populations relative to their mainland counterparts and the expected heterozygosity was significantly lower only on Ilha do Mar Virado”. As Ilha Mar Virado has the lowest expected relatedness intervals from the three islands. It was concluded that the estimation of genetic divergence and geographic did not correlate among the three islands and their two closest mainland populations. There was also no correlation significant enough between the “mean heterozygosity and genetic divergence between island populations and the closet mainland populations”. At the end of the study the authors concluded that out of the three islands the only one that supports a Scinax island population is Ilha dos Porcos Pequena. This is said to be due to it forming a “monophyletic lineage in the mitochondrial phylogeography” as well as showing “no signs of introgression with mainland populations” regarding the microsatellite analyses. Though the species in Porcos Pequena are genetically divergent from the neighboring mainland the ones from Ilha do Mar Virado and Ilha da Queimada Grande are not genetically differentiated from that of their neighboring mainland.
At the end the authors stated that, “they detected a significant pattern of isolation by distance between mainland populations but not between island populations and mainland populations” which is said to suggest that genetic variation in the island populations has to do with genetic drift. The main conclusion agreed upon by the authors was that, “variation in genetic signatures across the three islands indicates that the populations experienced different demographic processes after marine incursions fragmented the distribution of the S. perpusillus group”.
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