Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean

Abstract

1Understanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.Dispersal and gene flow in a meta-population maintain local demographic and genetic variation, thus increasing the probability of species persistence 1,2 . Persistence of wide-ranging animals occupying fragmented landscapes depends on the matrix quality of the habitat and the ability of individuals to move among habitat patches 3 , and corridors facilitating this movement across such landscape [4][5][6]

Analysis of the population genetics of the Yangtze finless porpoise population in the Poyang Lake Basin: Insight of conservation recommendations

“…This indicates that habitat fragmentation caused by hydrological changes and human activities has affected population exchange in the main lake area, although the YFPs in the main lake area are able to move freely during the rainy season. Studies showed that females can reproduce in the natal YFP population (Chen et al, 2016). When YFPs group in a sand pit connected to the main channel by shallow waters, the population can persist for short periods.…”