Divergence times of the Rhoadsia clade (Characiformes: Characidae)

The family Characidae is the most diverse group of fishes in the Neotropics with challenging systematics. The three genera Carlana, Parastremma, and Rhoadsia, formerly considered the subfamily Rhoadsiinae, are now included in the subfamily Stethaprioninae. Previous phylogenetic analyses did not include all genera of Rhoadsiinae, specifically Parastremma. Here, we estimated the phylogenetic relationships and divergence times of the genera of Rhoadsiinae (the Rhoadsia clade) relative to the most representative genera of the Characidae. We used six molecular markers from the mitochondrial and nuclear genome to estimate the phylogeny and divergence times. We confirmed the monophyly of the Rhoadsia clade. Furthermore, we estimated that the Central American genus Carlana and the western Colombian genus Parastremma diverged approximately 13 Mya (95% HPD 8.36­18.11), consistent with the early-closure estimates of the Isthmus of Panama (~15 Mya). The genus Rhoadsia, endemic to Western Ecuador and Northern Peru, was estimated to originate at around 20 Mya (95% HPD 14.35­25.43), consistent with the Andean uplift (~20 Mya).(AU)

La familia Characidae es el grupo más diverso de peces en el Neotrópico con una sistemática compleja. Los tres géneros Carlana, Parastremma y Rhoadsia, antes considerados en la subfamilia Rhoadsiinae, ahora se consideran dentro de la subfamilia Stethaprioninae. Los análisis filogenéticos publicados no incluyen todos los géneros de Rhoadsiinae, específicamente Parastremma. Aquí, estimamos las relaciones filogenéticas y los tiempos de divergencia de los géneros de Rhoadsiinae (el clado Rhoadsia) en relación con los géneros más representativos de Characidae. Utilizamos seis marcadores moleculares del genoma mitocondrial y nuclear para estimar la filogenia y el tiempo de divergencia. Confirmamos la monofilia del clado Rhoadsia. Además, estimamos que el género centroamericano Carlana y el género colombiano occidental Parastremma divergieron aproximadamente hace 13 millones de años (95% HPD 8.36­18.11), lo que es consistente con recientes estimaciones del cierre del Istmo de Panamá (~15 millones de años). Se estimó que el género Rhoadsia, endémico del oeste de Ecuador y el norte de Perú, se originó hace alrededor de 20 millones de años (95% HPD 14.35­25.43), consistente con el levantamiento de los Andes (~20 millones de años).(AU)

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome of Lateolabrax maculatus (Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity of L. maculatus were 0.998 and 0.00169, respectively. Pairwise FST values between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajimas D values, Fus Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history of L. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation of L. maculatus.(AU)

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome of Lateolabrax maculatus (Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity of L. maculatus were 0.998 and 0.00169, respectively. Pairwise FST values between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history of L. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation of L. maculatus.

The Complete Mitochondrial Genome of the Donganyellow Chicken and Its Phylogenetic Analyses

Donganyellow chicken (Gallus gallusdomesticus, DYC) is one of the famous native breeds of Hunan province in China. It is the first time that the complete mitochondrialgenome sequence of DYC was reported. The total length of the mtDNA is16, 786bp. It contains 22transfer RNA genes, 2 ribosomal RNA genes,13 protein-coding genes and 1 D-loop region. The overall composition of the mtDNA is 30.27% for A, 23.74% for T, 32.50% for C and 13.49% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed20Galliformes species are divided into three major clades: Phasianidae, Numidiidae and Odontophoridae. In addition, our work confirmed that DYCand Taoyuan chickenhave a closegenetic relationship with fellow tribal members Xuefeng black-boned chicken and Huang Lang chicken. This work will provide an important data set for the study in genetic mechanism of chicken in Hunan province.(AU)

The Complete Mitochondrial Genome of the Donganyellow Chicken and Its Phylogenetic Analyses

Donganyellow chicken (Gallus gallusdomesticus, DYC) is one of the famous native breeds of Hunan province in China. It is the first time that the complete mitochondrialgenome sequence of DYC was reported. The total length of the mtDNA is16, 786bp. It contains 22transfer RNA genes, 2 ribosomal RNA genes,13 protein-coding genes and 1 D-loop region. The overall composition of the mtDNA is 30.27% for A, 23.74% for T, 32.50% for C and 13.49% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed20Galliformes species are divided into three major clades: Phasianidae, Numidiidae and Odontophoridae. In addition, our work confirmed that DYCand Taoyuan chickenhave a closegenetic relationship with fellow tribal members Xuefeng black-boned chicken and Huang Lang chicken. This work will provide an important data set for the study in genetic mechanism of chicken in Hunan province.

The complete mitochondrial genome of Corydoras nattereri (Callichthyidae: Corydoradinae)

The complete mitogenome of Corydoras nattereri , a species of mailed catfishes from southeastern Brazil, was reconstructed using next-generation sequencing techniques. The mitogenome was assembled using mitochondrial transcripts from the liver transcriptomes of three individuals, and produced a circular DNA sequence of 16,557 nucleotides encoding 22 tRNA genes, two rRNA genes, 13 protein-coding genes and two noncoding control regions (D-loop, OrigL). Phylogeographic analysis of closely related sequences of Cytochrome Oxydase C subunit I (COI) demonstrates high diversity among morphologically similar populations of C. nattereri . Corydoras nattereri is nested within a complex of populations currently assigned to C. paleatus and C. ehrhardti . Analysis of mitogenome structure demonstrated that an insertion of 21 nucleotides between the ATPase subunit-6 and COIII genes may represent a phylogenetically informative character associated with the evolution of the Corydoradinae.(AU)

O mitogenoma completo de Corydoras nattereri , uma espécie de bagres encouraçados do sudeste do Brasil, foi reconstruído através de técnicas de sequencimento de DNA de próxima geração. O mitogenoma foi produzido a partir de produtos de transcrição mitocondrial dos transcriptomas hepáticos de três indivíduos, resultando numa sequência de DNA circular de 16.557 nucleotídeos abrangendo 22 genes de tRNA, dois genes de rRNA, 13 genes codificadores de proteínas e duas regiões de controle não codificadoras (D-loop, OrigL). A análise filogenética de sequências proximamente relacionadas da subunidade I do gene Citocrome Oxidase C (COI) demonstrou a existência de elevada diversidade entre populações morfologicamente similares de C. nattereri . Corydoras nattereri está inserida num complexo de populações atualmente identificadas como C. paleatus e C. ehrhardti . A análise da estrutura do mitogenoma demonstra que a inserção de uma sequência de 21 nucleotídeos entre os genes da subunidade 6 da ATPase e do COIII representa um caráter filogeneticamente informativo associado à evolução de Corydoradinae.(AU)

Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences / Filogenia molecular de Toxoplasmatinae: comparação entre inferências baseadas em sequências genéticas mitocondriais e de apicoplasto

Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.(AU)

A filogenia da subfamília Toxoplasmatinae tem sido amplamente investigada com diversos marcadores moleculares. Neste estudo, a filogenia molecular da subfamília Toxoplasmatinae foi analisada através de genes de apicoplasto e mitocondriais. Foram analisadas sequências parciais de genes de apicoplasto codificadores da protease caseinolítica (clpC), e da subunidade beta da RNA polimerase (rpoB) e de gene mitocondrial codificador de citocromo B (cytB). Foram investigadas cepas adaptadas em laboratório de Sarcocystis neurona eSarcocystis falcatula, parasitos estreitamente relacionados, além de Neospora caninum, Neospora hughesi, Toxoplasma gondii (cepas RH, CTG e PTG),Besnoitia akodoni, Hammondia hammondi e duas linhagens geneticamente divergentes de Hammondia heydorni. A análise molecular, baseada em genes de organelas, não diferenciou claramenteN. caninum de N. hughesi, porém foi possível confirmar as duas linhagens de H. heydorni. Foram encontradas pequenas diferenças entre as cepas adaptadas em laboratório deS. falcatula e S. neurona em todos os marcadores moleculares avaliados. Concluindo, filogenias congruentes foram reconstruídas com os três diferentes genes que podem ser úteis em triagem de parasitos sarcocistídeos não identificados, para identificar sua relação com organismos da família Sarcocystidae. Os estudos evolutivos com genes organelares confirmam que o gênero Hammondia é parafilético. Osprimers utilizados para amplificação declpC e rpoB foram capazes de amplificar sequências genéticas de organismos do gênero Sarcocystis e da subfamília Toxoplasmatinae.(AU)