Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

Background The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences from the mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used for DNA barcoding to identify the species. This study used the COI sequences to identify Neocaridina species in Taiwan and to examine their geographical and temporal origins. Results In total, 479 specimens were collected from 35 localities, which covered almost all rivers in Taiwan. In addition, some sequences were downloaded from GenBank. The maximum likelihood (ML) tree displayed that all sequences were sorted into 13 taxa (clades), and all sequences in Taiwan were sorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species have declined recently in Taiwan. Conclusions All results support that (1) there are four Neocaridina species in Taiwan, which are N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island in four colonization events; (3) N. sp. colonized Taiwan first; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from the Japanese islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan last; and (6) the cyclic glacial and landform changes in East Asia shaped the colonization events and population structures of the Neocaridina species.

Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

Background The freshwater species in Taiwan Island have been documented originated from mainland China and Japan Islands multiple times and by multiple colonization routes. Moreover, the sequences from mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used as DNA barcoding to identity species. This study used the COI sequences to identify Neocaridina species in Taiwan and examine their geographical and temporal origins. Results In total, 479 specimens were collected form 35 localities, which almost covers all rivers in Taiwan. The ML tree displayed that all sequences were assorted into 13 taxa (clades), and all sequences in Taiwan were assorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species in Taiwan declined recently. Conclusions All results support that (1) there are four Neocaridina species in Taiwan and they correspond to N. davidi , N. saccam , N. ketagalan and an undescribed Neocaridina species ( N. sp .); (2) these four species colonized Taiwan Island by four colonization events; (3) N. sp . colonized Taiwan before the Taiwan Island developed its shape and then restricted in East Taiwan; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from Japan Islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan lastly; and (6) the cyclic glacial and landform changes shaped the colonization events and population structures of Neocaridina species.

Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

Background The freshwater species in Taiwan Island have been documented originated from mainland China and Japan Islands multiple times and by multiple colonization routes. Moreover, the sequences from mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used as DNA barcoding to identity species. This study used the COI sequences to identify Neocaridina species in Taiwan and examine their geographical and temporal origins. Results In total, 479 specimens were collected form 35 localities, which almost covers all rivers in Taiwan. The ML tree displayed that all sequences were assorted into 13 taxa (clades), and all sequences in Taiwan were assorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species in Taiwan declined recently. Conclusions All results support that (1) there are four Neocaridina species in Taiwan and they correspond to N. davidi , N. saccam , N. ketagalan and an undescribed Neocaridina species ( N. sp .); (2) these four species colonized Taiwan Island by four colonization events; (3) N. sp . colonized Taiwan before the Taiwan Island developed its shape and then restricted in East Taiwan; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from Japan Islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan lastly; and (6) the cyclic glacial and landform changes shaped the colonization events and population structures of Neocaridina species.

Geographical and temporal origins of Neocaridina species (Decapoda: Caridea: Atyidae) in Taiwan

Background The freshwater species in Taiwan Island have been documented originated from mainland China and Japan Islands multiple times and by multiple colonization routes. Moreover, the sequences from mitochondrial DNA cytochrome c oxidase subunit I (COI) have been used as DNA barcoding to identity species. This study used the COI sequences to identify Neocaridina species in Taiwan and examine their geographical and temporal origins. Results In total, 479 specimens were collected form 35 localities, which almost covers all rivers in Taiwan. The ML tree displayed that all sequences were assorted into 13 taxa (clades), and all sequences in Taiwan were assorted into four clades. The Bayesian skyline plots revealed that these four Neocaridina species in Taiwan declined recently. Conclusions All results support that (1) there are four Neocaridina species in Taiwan and they correspond to N. davidi, N. saccam, N. ketagalan and an undescribed Neocaridina species (N. sp.); (2) these four species colonized Taiwan Island by four colonization events; (3) N. sp. colonized Taiwan before the Taiwan Island developed its shape and then restricted in East Taiwan; (4) after the island reached its shape, N. ketagalan and N. saccam colonized Taiwan from Japan Islands and mainland China, respectively; (5) N. davidi colonized northern Taiwan lastly; and (6) the cyclic glacial and landform changes shaped the colonization events and population structures of Neocaridina species.

Bayesian coalescent inference of hepatitis A virus populations: evolutionary rates and patterns

Hepatitis A virus (HAV) is a hepatotropic member of the family Picornaviridae. Previous studies suggested that HAV may evolve more slowly than other members of the family. To estimate HAV substitution rates precisely, we used a Bayesian Markov chain Monte Carlo (MCMC) approach on temporally sampled HAV VP1 full-length sequences from strains isolated in France. A mean rate of evolutionary change of 9.76×10−4 nucleotide substitution per site per year was found. The results also revealed that the synonymous rate found for HAV is lower than that of other members of the family. Bayesian skyline plots revealed a sharp decline in the effective number of infections in 1996, coinciding with the introduction of HAV vaccine.

Bayesian inference of population expansions in domestic bovines

The past population dynamics of four domestic and one wild species of bovine were estimated using Bayesian skyline plots, a coalescent Markov chain Monte Carlo method that does not require an assumed parametric model of demographic history. Four domestic species share a recent rapid population expansion not visible in the wild African buffalo ( Syncerus caffer ). The estimated timings of the expansions are consistent with the archaeological records of domestication.