Phylogeography and genetic structure of the oriental river prawn <i>Macrobrachium nipponense</i> (Crustacea: Decapoda: Palaemonidae) in East Asia

<div><p>The oriental river prawn (<i>Macrobrachium nipponense</i>) is mainly distributed in East Asia. The phylogeography, population genetic structure and historical demography of this species in the East Asia were examined by using partial sequences of the cytochrome oxidase subunit I (COI) and 16S rRNA in mitochondrial DNA. Ten populations that included 239 individuals were collected from Taiwan (Shihmen Reservoir, SMR, Mingte Reservoir, MTR and Chengching Lake Reservoir, CLR), mainland China (Taihu Lake, TLC, Min River, MRC, Jiulong River, JRC and Shenzhen Reservoir, SRC), Japan (Biwa Lake, BLJ and Kasumigaura Lake, KLJ) and Korea (Han River, HRK). The nucleotide diversity (<i>π</i>) of all individuals was 0.01134, with values ranging from 0.0089 (BLJ, Japan) to 0.01425 (MTR, Taiwan). A total of 83 haplotypes were obtained, and the haplotypes were divided into 2 main lineages: lineage A included the specimens from BLJ, KLJ, CLR, MTR, TLC, MRC and JRC, and lineage B comprised the ones from HRK, SRC, SMR, MTR, TLC, MRC and JRC. Lineage A could be further divided two sub-lineages (A₁ and A₂). Individuals of lineage A₂ were only from TLC. Demographic expansion was observed in each lineage, starting within the second-to-latest interglacial period for lineage A and within the last glacial period for lineage B. All <i>F</i>_ST values among the ten populations were significantly different, except for the values between MRC and JRC, and SMR and SRC. The phylogeography and genetic structure of <i>M</i>. <i>nipponense</i> in East Asia might be influenced by Pleistocene glacial cycles, lake isolation and human introduction. The possible dispersal routes of <i>M</i>. <i>nipponense</i> in the East Asia were also discussed.</p></div

Sampling localities and haplotypes frequencies of <i>Macrobrachium nipponense</i> in Taiwan.

<p>Numbers of lineages A and B in each sampling site are also shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0173490#pone.0173490.t001" target="_blank">Table 1</a>.</p

Matrix of pairwise <i>F</i>_<i>ST</i> (below diagonal) and <i>P</i> values (above diagonal) among 10 populations of <i>Macrobrachium nipponense</i> in East Asia.

<p>Matrix of pairwise <i>F</i>_<i>ST</i> (below diagonal) and <i>P</i> values (above diagonal) among 10 populations of <i>Macrobrachium nipponense</i> in East Asia.</p

Neighbour-Joining (NJ) tree based on mtDNA 16S rRNA and COI sequences with bootstrap values (NJ/ML, respectively) shown adjacent to the corresponding two lineages for <i>Macrobrachium nipponense</i>.

<p>The numbers at the nodes indicate bootstrap values (expressed as percentage) with 1,000 replicates.</p

The observed pair-wise differences and the expected mismatch distributions under the sudden expansion model of oriental river prawn.

<p>(a) All populations, (b) Lineage A, (c) Lineage B.</p

Matrix of pairwise <i>FST</i> (below diagonal) and <i>P</i> values (above diagonal) among 9 populations of <i>Macrobrachium nipponense</i> in Taiwan.

<p>Matrix of pairwise <i>FST</i> (below diagonal) and <i>P</i> values (above diagonal) among 9 populations of <i>Macrobrachium nipponense</i> in Taiwan.</p

UPGMA tree showing relationships among the 9 sampling sites.

<p>UPGMA tree showing relationships among the 9 sampling sites.</p

Sampling localities and haplotypes frequencies of <i>Macrobrachium nipponense</i> in Taiwan.

<p>Numbers of lineage A and B in each sampling site were also shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145927#pone.0145927.t001" target="_blank">Table 1</a>.</p

AMOVA results for 9 populations of <i>Macrobrachium nipponense</i> in Taiwan.

<p>AMOVA results for 9 populations of <i>Macrobrachium nipponense</i> in Taiwan.</p

Neighbor-joining (NJ) tree based on mtDNA 16S + COI sequences with bootstrap values (NJ/ML, respectively) shown adjacent to corresponding two lineages for <i>Macrobrachium nipponense</i>.

<p>Number at the nodes indicate bootstrap values (expressed as percentage) with 1,000 replicates.</p