Computational protocol: Increased human occupation and agricultural development accelerates the population contraction of an estuarine delphinid

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Protocol publication

[…] The entire genome was extracted from muscle (stored in ice) or skin (stored in formalin) using the phenol/chloroform method. Fifteen microsatellite loci (SCA9, SCA17, SCA22, SCA27, SCA37, SCA39, SCA54, SGATA25, SGATA30, SGATA42, SGATA45, Ttr11, Dde66, SCO11, and SCO28) were amplified using fluorescently labeled primers following the source papers. The PCR products were sequenced using the commercial services of Invitrogen (Guangzhou, CN). The sizes of the alleles was determined using GeneMarker v2.2.0. The presence of allelic dropout, null alleles and stuttering of microsatellite genotypes were tested with Micro-Checker 2.2.3, and the linkage disequilibrium of pairwise loci was calculated using PopGene v1.3 fyeh. Since the inference of demographic parameter could be biased with the presence of genetic structure, we used STRUCTURE 2.3.4 to reconstruct the hierarchical assignment of individuals following Bayesian clustering method. The analyses were conducted under admixture model with the number of clusters (K) ranging from 1 to 10. Ten replicates were run for each K, with 10,000 burn-in period and then followed by 1,000,000 iterations. […]

Pipeline specifications

Software tools GeneMarker, POPGENE
Application Population genetic analysis
Organisms Homo sapiens, Chanodichthys dabryi, Sousa chinensis