Pierre Loti'nin yüzüncü doğum yıldönümü

Taha Toros Arşivi, Dosya Adı: Pierre Lotiİstanbul Kalkınma Ajansı (TR10/14/YEN/0033) İstanbul Development Agency (TR10/14/YEN/0033

DataSheet_1_Complete mitochondrial genomes of the “Acmaeidae” limpets provide new insights into the internal phylogeny of the Patellogastropoda (Mollusca: Gastropoda).docx

The subclass Patellogastropoda (called “true limpets”) is one of the most primitive groups of the Gastropoda and contains approximately 350 species worldwide. Within this subclass, internal phylogeny among family members, including relationships of the “Acmaeidae” with other patellogastropod families, remains incompletely clarified. Here, we newly determined two complete mitochondrial genome sequences of “Acmaeidae” (Acmaea mitra and Niveotectura pallida) and one sequence from Lottiidae species (Discurria insessa) and combined them with mitochondrial genome sequences of 20 other published limpet species for phylogenetic analysis of the sequence dataset (nucleotides and amino acids) of 13 protein-coding genes using maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed monophyly of Patellogastropoda species that were subsequently subdivided into two clades [clade I (Nacellidae, Pectinodontidae, Acmaeidae, and Patellidae) and clade II (Eoacmaeidae and Lottiidae)]. The sister relationship between the Acmaeidae and Pectinodontidae species revealed by phylogenetic analysis was also supported by sharing their similar gene arrangement patterns, which differ substantially from those of clade II members including the Lottiidae species. The polyphyletic relationship between Acmaeidae (grouped with Pectinodontidae as a sister taxon in clade I) and Lottiidae species (grouped with Eoacmaeidae in clade II) corroborates that they are phylogenetically distinct from each other. This mitochondrial genome phylogeny contradicts previous morphology-based hypotheses, yet highlights that Acmaeidae and Pectinodontidae are the most closely related. Further in-depth analysis of the complete mitochondrial genome sequences based on a broad range of samples including those from relatively unstudied and/or underrepresented taxa is required to fully understand the mitochondrial genome evolution and a more comprehensive phylogeny among the major groups of the Patellogastropoda.</p

Mismatch distribution of <i>Thais clavigera</i> based on COI.

<p>The dotted line with circles represents the observed distribution, whereas the solid line shows the expected value under the sudden demographic expansion model.</p

Demographic history of <i>Thais clavigera</i> estimated using Bayesian skyline plots from COI data.

<p>The black line represents the median population estimates, while the blue lines are the upper and lower bounds of the 95% confidence interval.</p

Map of East Asia showing the sampling sites of <i>Thais clavigera</i> and the summer ocean currents redrawn from [9].

<p>Populations are labelled with numbers that correspond with those shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129715#pone.0129715.t001" target="_blank">Table 1</a>. Shaded sea areas indicate regions 120 m in depth that would have been exposed during periods of low sea level. EKWC, East Korea Warm Current; TSWC, Tsushima Warm Current; KSC, Kuroshio Current; YSWC, Yellow Sea Warm Current; SBCC, Subei Coastal Current; CCC, China Coastal Current; TWC, Taiwan Warm Current. Dashed lines (——) represent a border of water bodies among South China Sea, East China Sea and Pacific Ocean.</p

Sampling information, geographic coordinates, diversity indices, and neutrality tests for 29 <i>Thais clavigera</i> populations based on COI.

<p>Sampling information, geographic coordinates, diversity indices, and neutrality tests for 29 <i>Thais clavigera</i> populations based on COI.</p

Pairwise Φ_ST among <i>Thais clavigera</i> populations based on COI (below diagonal) and associated <i>P</i>-values (above diagonal) after the sequential Bonferroni correction.

<p>Significant pairwise Φ_ST and <i>P</i> values are bolded (<i>P</i> < 0.05). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129715#pone.0129715.t001" target="_blank">Table 1</a> for detailed information on site abbreviation.</p><p>Pairwise Φ_ST among <i>Thais clavigera</i> populations based on COI (below diagonal) and associated <i>P</i>-values (above diagonal) after the sequential Bonferroni correction.</p

Network of <i>Thais clavigera</i> using COI data.

<p>The size of circles is proportional to haplotype frequency and median vectors are indicated with a red pie chart. The different shadings of the haplotypes refer to the respective locations in terms of the three population groupings: (a) potential refuges (PC, Pacific Ocean; ECS, East China Sea; SCS, South China Sea; ES, East Sea [SJ, Sea of Japan]); (b) ocean currents (KSC, Kruoshio Current with the branch currents; CCC, China Coastal Current and Subei Coastal Current); (c) Changjiang River (CJS, the South of Changjiang River; CJN, the North of Changjiang River).</p