Conservation biologists pay increasing attention to the interdependence between habitat structure and genetic patterns of species and to the importance of conserving genetic diversity. Habitat loss and fragmentation are among the mostly threats to biodiversity loss and species extinction. Black muntjac (Muntiacus crinifrons), one of the rarest deer in the world, is listed in Category Ⅰof the State Key Protected Wildlife List of China and Appendix Ⅰof the Convention on International Trade in Endangered Species (CITES), and is also considered as a vulnerable species by the World Conservation Union (ICUN). Because specific ecological characteristics and their interactions with environmental conditions, this specie is threatened by habitat fragmentation and many other severe problems. However, most studies have not provided clear insights into effects of habitat fragmentation on gene flow of the black muntjac. In order to understand the mechanisms and provide information for effective conservation strategies of the black muntjac, it is necessary to study how the influences of habitat fragmentation on gene flow of the black muntjac. The goal of this paper is to compare the degree of habitat fragmentation and gene flow and provide effective conservation of the black muntjac.
We digitized the vegetation map, topographic map, river map, road map and village map of Jiulong Mountain and Gutian Mountain Natural Reserves by geographical information system(GIS) to compartmentalize patch of habitat fragment and extracted mitochondrial DNA from black muntjac’s organize and feacal samples that collected in those patch. The result show that degree of habitat fragmentation in Jiulong Mountain Natural Reserve was lower. The medial gene flow(Nm) was 3.65 in Jiulong Mountain Natural Reserve and it was observably larger than in Gutian Mountain Natural Reserve. We show that habitat fragmentation affects gene flow among populations of the black muntjac. One of the main goals of conservation should be to resume habitat of the black muntjac in order to increase populations size, genetic diversity and gene flow.