Phylogeography of the <i>Chydorus sphaericus</i> Group (Cladocera: Chydoridae) in the Northern Palearctic

<div><p>The biodiversity and the biogeography are still poorly understood for freshwater invertebrates. The crustacean <i>Chydorus sphaericus-brevilabris</i> complex (Cladocera: Chydoridae) is composed of species that are important components of Holarctic freshwater food webs. Recent morphological and genetic study of the complex has indicated a substantial species diversity in the northern hemisphere. However, we know little of the geographic boundaries of these novel lineages. Moreover, a large section of the Palearctic remains unexamined at the genetic level. Here we attempt to address the biodiversity knowledge gap for the <i>Chydorus sphaericus</i> group in the central Palearctic and assess its diversity and biogeographic boundaries. We sequenced nuclear (<i>ITS-2</i>) and mitochondrial (<i>COI</i>) gene regions of <i>Chydorus</i> specimens across the Palearctic and compared them with already available Holarctic sequences. We detected six main clades in the <i>C</i>. <i>sphaericus</i> group in the Palearctic, of which two of the groups are novel. Three of the more divergent clades are geographically widespread. The central portion of Eurasia (the Yenisey River basin) appears to be a narrow zone of secondary contact for phylogroups that expanded from European and Beringian refugia. As such, the previously unsampled central Palearctic represents an important region for understanding the evolutionary consequences of Pleistocene climatic oscillations on the <i>Chydorus sphaericus</i> group.</p></div

Complete subtree (collapsed in Fig 2) for the clades A1, A2 and A3 of the <i>Chydorus sphaericus</i> group showing support of the terminal clades.

<p>Geometric symbols for Eurasian taxa correspond to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168711#pone.0168711.g001" target="_blank">Fig 1</a>.</p

Between-group genetic distances of the “A”-groups of <i>Chydorus</i> for the <i>ITS-2</i> gene (Kimura 2-parameter) and <i>COI</i> gene (Tamura 3-parameter).

<p>Between-group genetic distances of the “A”-groups of <i>Chydorus</i> for the <i>ITS-2</i> gene (Kimura 2-parameter) and <i>COI</i> gene (Tamura 3-parameter).</p

Maximum likehood tree based on sequences of nuclear rDNA internal transcribed spacer (<i>ITS-2</i>) gene representing the diversity among clades of the group A1+A2+A3 from the <i>Chydorus sphaericus</i> group.

<p>The support values of individual nodes are based on different variants of phylogenetic analysis: ML / ME / BI.</p

Maximum likelihood tree based on sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene representing the diversity among phylogroups of the genus <i>Chydorus</i>.

<p>The support values of individual nodes are based on: Maximum likelihood (ML)/ Maximum Parsimony (MP) / Bayesian Inference (BI). Colors for main phylogroups correspond to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0168711#pone.0168711.g001" target="_blank">Fig 1</a>.</p

Median-joining cytochrome c oxidase subunit I (<i>COI</i>) haplotype network.

<p>Median vectors are indicated by small red circles. High-frequency haplotypes are labeled as well as the number of mutations for each branch (if not 1).</p

Median-joining <i>COI</i> haplotype network.

<p>Median vectors are indicated by small black circles.</p

Primers used to amplify mitochondrial and nuclear fragments used in this study.

<p>Primers used to amplify mitochondrial and nuclear fragments used in this study.</p

Sampling sites and distribution of major <i>COI</i> haplotype clades for Eurasian accessions of <i>Daphnia magna</i> (both original and sequences retrieved from GenBank).

<p>Colors and symbols correspond to those used in subsequent figures. The base map was obtained from the open domain plain map available at <a href="https://marble.kde.org/" target="_blank">https://marble.kde.org/</a>.</p

Comparison of mean frequencies of freshwater alleles at marker SNPs within and outside of identified DIs, at freshwater populations of different ages.

<p>Each two boxes correspond to the four young freshwater populations (anadromous from Lake Ershovskoye, Lake Martsy, Quarry Malysh, Quarry Goluboy). Statistical analysis was performed with two-tailed nonparametric Mann–Whitney <i>U</i> test. P values of <0.001 are designated with three (***) asterisks. Dashes, boxes and whiskers correspond to the median, standard deviation, and 5^th and 95^th percentiles, respectively. Red, marker SNPs (under the strong criterion) located within clumps; purple, marker SNPs (under the strong criterion) located outside clumps.</p