@article {Chen094995, author = {Minmin Chen and Michael C. Fontaine and Yacine Ben Chehida and Jinsong Zheng and Zhigang Mei and Yujiang Hao and Kexiong Wang and Min Wu and Qingzhong Zhao and Ding Wang}, title = {Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean}, elocation-id = {094995}, year = {2016}, doi = {10.1101/094995}, publisher = {Cold Spring Harbor Laboratory}, abstract = {Understanding demographic trends and patterns of gene flow in an endangered species, occupying a fragmented habitat, is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 153 individuals, we identified 3 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 (<=106 individuals) and census sizes. 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 industrial revolution. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only 2\% of the pre-collapsed size, concomitant with the industrial revolution. These results provide background information for devising mitigation strategies to prevent YFP extinction.}, URL = {https://www.biorxiv.org/content/early/2016/12/17/094995}, eprint = {https://www.biorxiv.org/content/early/2016/12/17/094995.full.pdf}, journal = {bioRxiv} }