Published date: Sep 20 2015

Journal Title: KnE Life Sciences

Issue title: International Conference on Biological Sciences (ICBS-2013)

Pages: 119-123

DOI: 10.18502/kls.v2i1.129

Sena Adi Subrataadisubrata@ugm.ac.idFaculty of Forestry, Gadjah Mada University. Jl. Agro No.1. Bulaksumur, Yogyakarta 55281.

Despite the occurrence of a massive agricultural landscape change in Java, very few reliable studies evaluate its genetic consequence for impacted wildlife species. This study reported the genetic diversity of the Mandar besar (Porphyrio porphyrio) in the modified landscape of Java as a backdrop for such an evaluation. Aim of this study was to estimate genetic diversity and genetic structure of the species. I collected eighty-eight blood samples from five a-priory populations (Demak, Jombor, Kendal, Pagak, and Nawan) and genotyped them at ten selected microsatellite loci to estimate allelic richness (R) and expected heterozygosity (He), fixation index (FST) and genetic clusters (K). DNA was isolated using a commercial kit (Invitrogen) and amplified using touch-down polymerase-chain-reaction technique. Allele length was estimated using an automatic sequencer. Pre-analysis showed that all selected loci have null alleles frequency less than 0.2, successful amplification rate more than 80%, no significant linkage between loci and no deviation from HWE. Further analysis employing GDA and FSTAT showed that Demak population has richest genetic diversity in term of R, meanwhile Jombor was the poorest population. Analysis of population structure employing FSTAT and STRUCTURE showed that the population was likely structured into four subpopulations, as showed by FST (0.085; P<0.05) and K=4 (ln probability -1725.2+3.92). This study might reveal that genetic diversity and population structure of Mandar besar in Java were still in common level as compared to other aquatic bird species.

Keywords :Swamphen, bird, richness, genetic, wetlands

Amos, W., and J. Harwood. 1998. Factors affecting levels of genetic diversity in natural populations. Phil.Trans. R. Soc. Lond. (353):177-186
Earl, D., and B. vonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4, 359–361.
Eo, S.H., J.M. Doyle, and J.A. DeWoody. 2011. Genetic diversity in birds is associated with body mass and habitat type. Journal of Zoology283, 220–226.
Goudet, J. 1995. FSTAT (Version 1.2): A Computer Program to Calculate F-Statistics. Journal of Heredity 86, 485–486.
Goudet, J. 2005. FSTAT (ver.2.9.4), a program to estimate and test population genetics parameters.Available form http://www2.unil.ch/popgen/softwares/fstat.htm. Updated from Goudet (1995).
Grueber, C.E., J.M. Waters, and I.G. Jamieson, I.G., 2011. The imprecision of heterozygosity­fitness correlations hinders the detection of inbreeding and inbreeding depression in a threatened species. Molecular Ecology20, 67–79.
Jakobsson, M., and N.A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics23: 1801-1806.
Lewis, P. O., and D. Zaykin. 2001 GDA (GENETIC DATA ANALYSIS): Computer Program for the Analysis of Allelic Data (Univ. of Connecticut, Storrs, CT), Version 1.0 d16c.
Lambert, D.M., C.D. Millar, S. Anderson, and J.L. Craig. 1994. Single- and multilocus DNA fingerprinting of communally breeding Pukeko: do copulations or dominance ensure reproductive success ?. PNAS91 (20):9641-9645
Mousadik, A., and R.J. Petit. 1996. High level of genetic differentiation for allelic richness among populations of the argan tree Argania spinosa (L.) Skeels] endemic to Morocco. TAG Theoretical and Applied Genetics92, 832–839.
Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics155, 945–959.
Rosenberg, N.A. 2004. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes4, 137–138.
Sodhi, N., M. Posa, T. Lee, D. Bickford, L. Koh, and B. Brook. 2010. The state and conservation of Southeast Asian biodiversity. Biodiversity and Conservation19, 317–328.
Subrata, S.A., and I. Storch. 2012. A core set of microsatellite markers identified for use in population genetic studies of Purple Swamphen (Porphyrio porphyrio). Animal Biodiversity and Conservation (35).1: 23-26.
Taylor, P.B., 1998. Rails. A guide to the rails, crakes, gallinules and coots of the world. Pica Press [u.a.], Robertsbridge, Sussex.
Whitten, A.J., R.E. Soeriaatmadja, and S.A. Afiff. 1997. The ecology of Java and Bali. Oxford University Press, Oxford.
Zhao, S., C. Peng, H. Jiang, D. Tian, X. Lei, and X. Zhou. 2006. Land use change in Asia and the ecological consequences. Ecological Research21, 890–896.