Phylogenetic status and diet of red fox (Vulpes vulpes griffithii) inhabiting Ayubia National Park, Pakistan

Abstract The red fox (Vulpes vulpes) is a medium-sized carnivore that occurs in different regions of Pakistan, however, still lacks scientific data on its ecology and distribution. The current study investigated the phylogenetic status and diet of the red fox (V.v. griffithii) occurring in Ayubia National Park, Pakistan. Through camera trapping and molecular analysis, we confirmed the occurrence of red fox in the study area. Based on mitochondrial cytochrome B (304 bp) and limited sampling, nearly all red foxes of Ayubia National Park and surrounding Himalayan ranges fall within Holarctic maternal lineage, whereas red foxes found in plains of Pakistan are part of the basal Palearctic maternal lineage. Using 32 scats, we found that red fox diet comprises of 80% animal-based prey species (both wild and domestic) and 19% plant matter. The wild animal prey species included Cape hare (Lepus capensis) and flying squirrel (Pteromyini sp.), which constituted 17% and 15% of diet, respectively. Red foxes infrequently consumed House mouse (Mus musculus), Himalayan Palm civet (Paguma larvata) and sheep (Ovis aries), each comprising around 6% to 9% of red fox diet. The fox species also scavenged on domestic donkey opportunistically. Based on our sampling, our study suggests that the red fox (V.v. griffithii) that occurs in Ayubia National Park and across the lesser Himalayan ranges belongs to Holarctic maternal lineage. The study also highlights consumption of plant seeds by red foxes, indicating it may play an important ecological role in seed dispersal in Ayubia National Park.

Resumo A raposa-vermelha (Vulpes vulpes) é um carnívoro de médio porte que ocorre em diferentes regiões do Paquistão, porém ainda carece de dados científicos sobre sua ecologia e distribuição. O presente estudo investigou o status filogenético e a dieta da raposa-vermelha (V.v. griffithii) que ocorre no Parque Nacional de Ayubia, Paquistão. Por meio de armadilhas fotográficas e análises moleculares, confirmamos a ocorrência de raposa-vermelha na área de estudo. Com base no citocromo B mitocondrial (304 bp) e amostragem limitada, quase todas as raposas-vermelhas do Parque Nacional de Ayubia e áreas circundantes do Himalaia se enquadram na linhagem materna holártica, enquanto as raposas-vermelhas encontradas nas planícies do Paquistão fazem parte da linhagem materna basal paleártica. Usando 32 fezes, descobrimos que a dieta da raposa-vermelha compreende 80% de espécies de presas de origem animal (selvagens e domésticas) e 19% de matéria vegetal. As espécies de presas de animais selvagens incluíram a lebre-do-cabo (Lepus capensis) e o esquilo-voador (Pteromyini sp.), que constituíram 17% e 15% da dieta, respectivamente. As raposas-vermelhas consumiam raramente ratos domésticos (Mus musculus), algas do Himalaia (Paguma larvata) e ovelhas (Ovis aries), cada um compreendendo cerca de 6% a 9% da dieta da raposa-vermelha. A espécie de raposa também se alimentava de burros domésticos de forma oportunista. Com base em nossa amostragem, nosso estudo sugere que a raposa-vermelha (V.v. griffithii) que ocorre no Parque Nacional de Ayubia e nas cordilheiras menores do Himalaia pertence à linhagem materna holártica. O estudo também destaca o consumo de sementes de plantas por raposas-vermelhas, indicando que pode desempenhar um papel ecológico importante na dispersão de sementes no Parque Nacional de Ayubia.

Mitochondrial genome sequence characteristics and phylogenetic analysis of Schizothorax argentatus / 生物工程学报

Schizothorax argentatus that only distributes in the Ili River basin in Xinjiang is one of the rare and endangered species of schizothorax in China, thus has high scientific and economic values. In this study, the complete mitochondrial genome sequence of S. argenteus with a length of 16 580 bp was obtained by high-throughput sequencing. The gene compositions and arrangement were similar to those of typical vertebrates. It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding region (D-loop). The nucleotide compositions were A (30.25%), G (17.28%), C (27.20%), and T (25.27%), respectively, showing obvious AT bias and anti-G bias. Among the tRNA genes, only tRNA-Ser(GCU) could not form a typical cloverleaf structure due to the lack of dihydrouracil arm. The AT-skew and GC-skew values of the ND6 gene were fluctuating the most, suggesting that the gene may experience different selection and mutation pressures from other genes. The mitochondrial control region of S. argenteus contained three different domains, i.e., termination sequence region (ETAS), central conserved region (CSB-F, CSB-E, CSB-D, and CSB-B), and conserved sequence region (CSB1, CSB2, and CSB3). The conserved sequence fragment TT (AT) nGTG, which was ubiquitous in Cypriniformes, was identified at about 50 bp downstream CSB3. Phylogenetic relationships based on the complete mitochondrial genome sequence of 28 Schizothorax species showed that S. argenteus had differentiated earlier and had a distant relationship with other species, which may be closely related to the geographical location and the hydrological environment where it lives.

Genetic characterization of the rare Bruconha virus (Bunyavirales: Orthobunyavirus) isolated in Vale do Ribeira (Atlantic Forest biome), Southeastern Brazil

ABSTRACT Brazil is a great source of arbovirus diversity, mainly in the Amazon region. However, other biomes, especially the Atlantic Forest, may also be a hotspot for emerging viruses, including Bunyaviruses (Negarnaviricota: Bunyavirales). For instance, Vale do Ribeira, located in the Southeastern region, has been widely studied for virus surveillance, where Flavivirus, Alphavirus and Bunyaviruses were isolated during the last decades, including Bruconha virus (BRCV), a member of Orthobunyavirus genus Group C, in 1976. Recently, a new isolate of BRCV named Span321532 was obtained from an adult sentinel mouse placed in Iguape city in 2011, and a full-length genome was generated with nucleotide differences ranging between 1.5%, 5.3% and 5% (L, M and S segments, respectively) from the prototype isolated 35 years earlier. In addition, each segment placed BRCV into different clusters, showing the high variety within Bunyavirales. Although no evidence for reassortants was detected, this finding reiterates the need for new surveillance and genomic studies in the area considering the high mutation rates of arbovirus, and also to identify the hosts capable of supporting the continuous circulation of Orthobunyavirus.

HIV-1 Transmission among Injecting Drug Users is Principally Derived from Local Circulating Strains in Guangxi, China / 生物医学与环境科学（英文）

OBJECTIVE@#The mode of human immunodeficiency virus (HIV) transmission via injection drug use (IDU) still exists, and the recent shift in IDU-related transmission of HIV infection is largely unknown. The purpose of this study was to analyze the spatiotemporal sources and dynamics of HIV-1 transmission through IDU in Guangxi.@*METHODS@#We performed a molecular epidemiological investigation of infections across Guangxi from 2009 to 2019. Phylogenetic and Bayesian time-geographic analyses of HIV-1 sequences were performed to confirm the characteristics of transmission between IDUs in combination with epidemiological data.@*RESULTS@#Among the 535 subjects, CRF08_BC (57.4%), CRF01_AE (28.4%), and CRF07_BC (10.7%) were the top 3 HIV strains; 72.6% of infections were linked to other provinces in the transmission network; 93.6% of sequence-transmitted strains were locally endemic, with the rest coming from other provinces, predominantly Guangdong and Yunnan; 92.1% of the HIV transmission among people who inject drugs tended to be transmitted between HIV-positive IDUs.@*CONCLUSION@#HIV recombinants were high diversity, and circulating local strains were the transmission sources among IDUs in Guangxi. However, there were still cases of IDUs linked to other provinces. Coverage of traditional prevention strategies should be expanded, and inter-provincial collaboration between Guangxi, Yunnan, and Guangdong provinces should be strengthened.

Genetic diversity of Leishmania donovani isolates from cutaneous lesions of military personnel in the Mullaitivu and Kilinochchi districts of the Northern Province, Sri Lanka

Objective: To compare the DNA sequences of Leishmania (L.)donovani isolated from individuals in two districts of the Northern Province with other parts of Sri Lanka and neighboring countries. Methods: Samples were collected from military personnel at the Army Hospital, Narahenpita, Sri Lanka from November 2018 to March 2020. A portion of the samples was fixed, stained with Giemsa and observed under the light microscope. The genomic The DNA was extracted from the remaining portion of the samples using DNEasy blood tissue kit (Qiagen, Germany) and amplified using Leishmania genus-specific primers for molecular diagnosis initially. DNA was amplified using L. donovani species-specific primers by PCR and the amplified product was sequenced for comparison of nucleotide sequences. Results: Out of 76 suspected patients, at least one biological sample of 45 (59.2%) was positive for L. amastigotes upon microscopy. Overall, 33 (43.4%) were positive in Leishmania genus-specific PCR, but only 23 (30.3%) were positive in L. donovani specific PCR. The dendrogram indicates that the current sequences clustered together with those from Nepal and Gampaha districts (Western Province), Sri Lanka, while the Indian and Eastern African sequences clustered separately. Conclusions: The genetic diversity was low among the isolates, indicating a single and possibly a local point of origin. However, the similarity of Sri Lankan and Nepal strains indicate a possibility of a shared point of origin, which needs more extensive evidence to confirm.

Phylogenetic and Mutation Points Analysis of Sophora japonica cv. jinhuai Based on DNA Barcoding Sequences / 中国实验方剂学杂志

ObjectiveTo conduct phylogenetic analysis of internal transcribed spacer 2 （ITS2） and chloroplast gene segments including psbA-trnH， rbcL， and matK of Sophora japonica cv. jinhuai resource samples from different geographical sources， and to explore the genetic diversity of S. japonica cv. jinhuai. MethodPolymerase chain reaction （PCR） method was used to amplify the nucleic acid sequences of ITS2， psbA-trnH， rbcL， and matK of S. japonica cv. jinhuai. Neighbor joining （NJ） method was used to construct phylogenetic trees， and Kimura 2-Parameter （K2P） model was used to calculate the genetic distance of different samples. MEGA and BIOEDIT softwares were applied for mutiple alignment and analysis of ITS2， psbA-trnH， rbcL， and matK sequences of S. japonica cv. jinhuai. ResultThe lengths of ITS2 sequence were 278-279 bp. The lengths of psbA-trnH were 289 bp. The lengths of rbcL sequence were 673 bp. The lengths of matK sequences were 786-792 bp. There were 3 mutation points in ITS2 and psbA-trnH， no mutation point in rbcL， and 13 mutation points in matK. The samples of S. japonica cv. jinhuai were clustered into two groups based on the phylogenetic tree constructed by ITS2 sequences. The sample of seedling tree in Baibao was clustered into one group， while the other 25 samples were clustered into another group. For the psbA-trnH sequence， the success rate of PCR amplification of 28 samples of S. japonica cv. jinhuai was 100%. The 28 samples of S. japonica cv. jinhuai were clustered into three groups based on the clustering results of psbA-trnH sequence. The sample of seedling tree in Shaoshui was clustered into one group. The five samples of grafting tree and seedling tree in Miaotou， grafting trees in Jiantang， Wenqiao， and Daxu， and seeding tree in Xianshui were clustered into one group. The other 21 samples were clustered into another group. The 26 samples of S. japonica cv. jinhuai were clustered into two groups based on the phylogenetic tree constructed by matK sequences. The sample of seedling tree in Xianshui was clustered into one group， while the other 25 samples were clustered into another group. The clustering results of the rbcL sequence of S. japonica cv. jinhuai could not distinguish 28 resource samples. The phylogenetic tree constructed by the combined sequence of ITS2+psbA-trnH+rbcL+matK divided S. japonica cv. jinhuai resource samples into 4 groups. The 13 samples of seedling trees in Qiyang， Daoxian， Miaotou， Shaoshui， Shitang， Xianshui， Jiantang， and Xiangli， and grafting trees in Qiyang， Miaotou， Yongsui， Wenqiao， and Yangtang were clustered into one group. The sample of seedling tree in Wenqiao was clustered into one group. The sample of seedling tree in Daxu was clustered into one group. The remaining samples were clustered into another group. ConclusionPhylogenetic and mutation analysis provide the theoretic foundation to investigate the evolution of the resources of S. japonica cv. jinhuai， and evaluate their genuineness. The results of mutation points can be used to identify the related S. japonica cv. jinhuai resources. The findings of this study show that the combination of different gene sequences has an optimal effect on plant identification.

Nextstrain: una herramienta que analiza la epidemiología molecular del SARS-CoV-2 / Nextstrain: a tool to analyze the molecular epidemiology of SARS-CoV-2

La preocupación mundial por el nuevo coronavirus (2019-nCoV), como una amenaza global para la salud pública, fue el motor para que los análisis filogenéticos sufrieran un crecimiento exponencial. El objetivo de esta revisión fue describir el modo de funcionamiento y las bondades de la herramienta Nextstrain, así como el secuenciamiento del virus SARS-CoV-2 en el mundo. Se uso la interfaz de la página de Nextstrain para mostrar sus funcionalidades y los modos de visualización de datos, y se descargaron estos de la web GISAID para mostrar la cantidad de secuenciamientos del SARS-CoV-2 hasta la fecha. Nextstrain es un proyecto de código abierto creado por biólogos bioinformáticos, para aprovechar el potencial científico y de salud pública de los datos de genomas de patógenos. Nextstrain consiste en un conjunto de herramientas que toman secuencias sin procesar (en formato FASTA). Nextstrain realiza una alineación de secuencia de los datos de entrada en alineación de secuencia múltiple basada en la transformación rápida de Fourier. Se basa en el uso de dos softwares: Augur y Auspice. Nextstrain es una herramienta eficaz para mostrar datos epidemiológicos de manera simple para un público no especializado. Puede ser usado en la salud pública, ya que muestra datos en tiempo real de las epidemias y su distribución geográfica. Se puede usar para dar seguimiento a los brotes como es el caso del COVID-19(AU)

Worldwide concern about the novel coronavirus (2019-nCoV) as a global threat to public health is the reason for the exponential growth of phylogenetic analyses. The purpose of this review was to describe the mode of operation and advantages of the tool Nextstrain, as well as the sequencing of the SARS-CoV-2 virus worldwide. The interface of the Nextstrain page was used to show its functions and data visualization modes. These were downloaded from the website GISAID to show the number of SARS-CoV-2 sequencing processes performed so far. Nextstrain is an open code project created by bioinformatics biologists to make good use of the scientific and public health potential of data about genomes of pathogens. Nextstrain consists in a set of tools operating with unprocessed sequences (in FASTA format). Nextstrain performs a sequence alignment of the input data into a multiple sequence alignment based on fast Fourier transform. Its use is based on two software applications: Augur and Auspice. Nextstrain is an efficient tool by which lay people may obtain epidemiological data in a simple manner. It may be used in the public health sector, since it shows real time data about epidemics and their geographic distribution. It may also be used to follow-up outbreaks, as is the case with COVID-19(AU)

Genetic diversity of Hepatozoon spp. in rodents from Chile / Diversidade genética de Hepatozoon spp. em roedores do Chile

Abstract This study aimed to investigate the genetic diversity of Hepatozoon spp. in rodents from Valdivia, Chile. A total of 74 rodents (synanthropic n=38; wild n=36) were trapped in Valdivia. We performed conventional PCR assays for Apicomplexa organisms targeting two overlapping 18S rDNA gene fragments (600 bp and 900 bp) followed by sequencing of selected amplicons. Hepatozoon spp. occurrence was 82.43% (61/74). Twelve sequences obtained from the 600 bp and ten from the 900 bp 18S rDNA fragments were identified as Hepatozoon sp. Six sequences obtained from 18S rDNA-based overlapping PCR protocols were used for concatenated (1,400 bp) phylogenetic, haplotype and distance analyses. Hepatozoon spp. 18S rDNA concatenated sequences from the present study were detected in Oligoryzomys longicaudatus, Rattus norvegicus, Mus musculus, and Abrothrix longipilis grouped with Hepatozoon species earlier described in rodents and reptiles from Chile and Brazil. Nucleotide polymorphism of the six 18S rDNA sequences (1,400 bp) from this study, and other Chilean sequences from rodents and rodent's ticks, showed high diversity with a total of nine Chilean haplotypes. Three haplotypes from Valdivia were identified for the first time in this study, suggesting the circulation of novel haplotypes in rodents from southern Chile.

Resumo Este estudo teve como objetivo investigar a diversidade genética de Hepatozoon spp. em roedores de Valdivia, Chile. Um total de 74 roedores (sinantrópicos n=38; selvagens n=36) foram capturados. PCR convencional foi realizada para organismos Apicomplexa, visando dois fragmentos sobrepostos do gene 18S rDNA (600 bp e 900 bp), seguida pelo sequenciamento de amplicons selecionados. A ocorrência de Hepatozoon spp. foi de 82,43% (61/74). Doze sequências obtidas dos fragmentos de 18S rDNA de 600 pb e dez dos fragmentos de 18S rDNA de 900 pb foram identificadas como Hepatozoon sp. Seis sequências obtidas, a partir de protocolos de PCR sobrepostos, foram usadas para análises filogenéticas (1.400 bp), de haplótipos e de distância. Sequências concatenadas 18S rDNA do presente estudo foram detectadas em Oligoryzomys longicaudatus, Rattus norvegicus, Mus musculus e Abrothrix longipilis e agrupadas com Hepatozoon descrito em roedores e répteis do Chile e do Brasil. A análise de polimorfismos das seis sequências deste estudo, junto com outras sequências chilenas de roedores e carrapatos de roedores, mostrou alta diversidade com um total de nove haplótipos no Chile. Três haplótipos detectados em Valdivia foram identificados pela primeira vez neste estudo, sugerindo que novos haplótipos circulam em roedores do sul do Chile.

A new giant velvet worm from Costa Rica suggests absence of the genus Peripatus (Onychophora: Peripatidae) in Central America

Introduction: Neotropical onychophoran taxonomy and diversity has been poorly investigated. Recent studies have discovered problems in species classification: they have questioned the accepted genera and the actual number of species. This is true in Costa Rica, where several unidentified species have been reported. Objective: The objective of this investigation was to evaluate the occurrence of the accepted genera in this country, and to describe a new genus and species from Central America. Methods: In 2017, we collected one onychophoran in the Keköldi Indigenous Reserve in Talamanca, Limón, Costa Rica. The specimen gave birth to several offspring. Therefore, seven organisms were analyzed. Light microscopy was used to observe the gross morphology in all samples. The detailed morphology was studied in the biggest specimen with scanning electron microscopy; after that, we performed a phylogenetic analysis with the corresponding sequence of COI. Results: According to our results, a new genus and species of giant onychophoran was found. The genus was identified by its giant size, apical piece of seven scale ranks, large conical primary papillae, dorso-median furrow flanked by two-three accessory papillae, the absence of hyaline organs and a marked sexual dimorphism with respect to the number of legs. The new species presents a particular head pattern, as well as novel structures like cephalic papillae, accessory papillae with rudimentary apical pieces, and a lack of antennal chemoreceptors. Phylogenetic analysis rendered our genus as monophyletic and includes Peripatus solorzanoi, which is grouped within the Central American clade.As our species is clustered inside the Costa Rica-Panamanian group, it is not related to the Caribbean Island nor Guyanan Shield samples, home of Epiperipatus and Peripatus respectively. Therefore, we suggest that those genera do not occur in Central America, and a new genus exists: Mongeperipatus, gen. nov. Conclusion: We concluded that Costa Rica is home to a diversity of undescribed onychophorans that requires specific studies to help clarify the taxonomy and evolutionary relationships of the group to justify their protection.

Introducción: Los onicóforos del neotrópico han sido poco estudiados, especialmente en cuanto a taxonomía y diversidad. Sin embargo, estudios recientes sugieren que los géneros actuales son obsoletos y el número de especies existentes es desconocido. Por ejemplo, en Costa Rica, se han reportado diversos onicóforos que no han sido identificados exitosamente. Objetivo: El objetivo de este trabajo fue evaluar la presencia de los géneros aceptados en el país, y describir un nuevo género y especie para Centroamérica. Métodos: En el 2017, recolectamos un espécimen de onicóforo en la reserva indígena de Keköldi en Talamanca, Limón, Costa Rica, el cual dio a luz a varias crías. Incluyendo a este animal, estudiamos un total de siete especímenes. Mediante el uso de microscopía de luz, observamos las características morfológicas macroscópicas en todas las muestras. Asimismo, utilizamos la microscopía electrónica para analizar detalladamente la morfología en una de estas. Finalmente, realizamos un análisis filogenético con la secuencia correspondiente de COI. Resultados: Un nuevo onicóforo gigante fue descrito. Se propuso un nuevo género, el cual se distingue por su tamaño gigante, el número de filas de escamas en la pieza apical de las papilas primarias, sus grandes papilas primarias cónicas, la línea media flanqueada por dos-tres papilas accesorias, la ausencia de órganos hialinos y el dimorfismo sexual marcado respecto al número de patas. Esta especie presenta un patrón particular de papilas en su cabeza, además de estructuras nuevas como papilas modificadas en la cabeza (papilas cefálicas), papilas accesorias con piezas apicales rudimentarias y la ausencia de quimiorreceptores en las antenas. Los análisis filogenéticos lo sitúan como un género monofilético que incluye a Peripatus solorzanoi, tal clado se encuentra dentro del grupo de especies centroamericanas. Por lo tanto, la nueva especie se agrupa dentro de las muestras pertenecientes a Costa Rica-Panamá. Este grupo no se relaciona con los especímenes de las islas caribeñas ni del Escudo Guyanés, hogares de las especies tipo de Epiperipatus y Peripatus respectivamente. De modo que sugerimos que estos géneros no están presentes en Centroamérica. Así entonces, describimos el nuevo género Mongeperipatus para Costa Rica. Conclusión: Este país alberga una diversidad de onicóforos sin describir, que se requieren estudios puntuales que ayuden a aclarar la taxonomía y relaciones evolutivas del grupo para justificar la protección del filo.

Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia

Here we explore the use of community phylogenetics as a tool to document patterns of biodiversity in the Fitzcarrald region, a remote area in Southwestern Amazonia. For these analyses, we subdivide the region into basin-wide assemblages encompassing the headwaters of four Amazonian tributaries (Urubamba, Yuruá, Purús and Las Piedras basins), and habitat types: river channels, terra firme (non-floodplain) streams, and floodplain lakes. We present a robust, well-documented collection of fishes from the region including 272 species collected from 132 field sites over 63 field days and four years, comprising the most extensive collection of fishes from this region to date. We conduct a preliminary community phylogenetic analysis based on this collection and recover results largely statistically indistinguishable from the random expectation, with only a few instances of phylogenetic structure. Based on these results, and of those published in other recent biogeographic studies, we conclude that the Fitzcarrald fish species pool accumulated over a period of several million years, plausibly as a result of dispersal from the larger species pool of Greater Amazonia.(AU)

Aquí exploramos el uso de la filogenética de comunidades como herramienta para documentar patrones de biodiversidad en la región de Fitzcarrald, un área remota en el suroeste de la Amazonía. Para estos análisis subdividimos la región en grupos de toda la cuenca que abarcan las cabeceras de cuatro tributarios del Amazonas (cuencas Urubamba, Yuruá, Purús y Las Piedras) y en los tipos de hábitat: canales fluviales, arroyos de tierra firme (sin planicie aluvial) y lagos de planicie aluvial. Presentamos una colección de peces robusta y bien documentada que incluye 272 especies, colectadas a lo largo de cuatro años y 63 días de campo, en 132 puntos de monitoreo. Convirtiéndose en la colección más extensa de peces de esta región hasta la fecha. Realizamos un análisis filogenético preliminar de la comunidad basado en esta recopilación y recuperamos resultados en gran medida estadísticamente indistinguibles de la expectativa aleatoria, con sólo unos pocos casos de estructura filogenética. Basándonos en estos resultados y los publicados en otros estudios biogeográficos recientes, concluimos que el grupo de especies de peces de Fitzcarrald acumulado durante un período de varios millones de años, se debe posiblemente al resultado de la dispersión del mayor grupo de especies de la Gran Amazonia.(AU)

Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

Phylogenetic and mutation point analysis of DNA barcoding sequences in Polygonatum cyrtonema / 中草药

Objective: In this work, phylogenetic analysis was used to compare the ITS2 and psbA-trnH sequences of Polygonatum cyrtonema samples from different geographical sources, so as to explore the genetic diversity and genetic relationship of these resources. Methods: PCR method was used to amplify the regions of ITS and psbA-trnH, and the sequences of ITS2 and psbA-trnH were obtained after the amplified fragment sequences were blasted in NCBI database. The neighbor joining (NJ) and maximum parsimony (MP) methods were used to construct phylogenetic trees and Kimura two-parameter (K2-P) model was used to calculate the genetic distance of different samples. Mega and DNAman softwares were applied for mutiple alignment of ITS2 and psbA-trnH sequences of 25 samples of P. cyrtonema. Results: The lengths of ITS2 and psbA-trnH sequences of Anhui Qingyang and Fujian Taining samples of P. cyrtonema were 224 bp and 620 bp, respectively. The lengths of ITS2 and psbA-trnH of the remaining 24 samples were 225 bp and 621 bp, respectively. ITS2 and psbA-trnH had seven and four mutation points, respectively. These 25 samples were clustered into two groups based on ITS2 sequences. Five samples in Hunan and Guizhou were clustered into one group, while the other 20 samples were clustered into another group. The genetic distance showed that the samples from Huaxi and Jianhe in Guizhou Province and Jianyang in Fujian Province had the largest genetic distance. Phylogenetic tree constructed by psbA-trnH sequences were unable to distinguish 25 samples from different geographical sources. Conclusion: Phylogenetic and mutation analysis will provide the theoretic foundation to utilize the resources of P. cyrtonema, investigate their evolution, and evaluate their genuineness. The results of mutation point will also be used in the identification of related P. cyrtonema resources.

Molecular phylogenetics of Black Cobra (Naja naja) in Pakistan

Background: Snakes are found on every continent in the world except Antarctica, and on smaller land masses. Being ecologically important, they also cause a large number of bites, leading to millions of deaths. Mitochondrial and nuclear gene sequences are being used to identify, characterize, and infer genetic biodiversity among different snake species. Furthermore, phylogenetics helps in inferring the relationships and evolutionary histories among these species. Black cobra is one of the four most venomous snakes in Pakistan. Four mitochondrial (ND4, Cytochrome b, 12S rRNA, and 16S rRNA) and four nuclear (C-mos, RAG-1, BDNF, and NT3) genes were used to trace diversity and infer the phylogenetic relationship of black cobra in Pakistan. Results: Almost similar phylogenies were obtained through maximum likelihood and Bayesian inference, showing two species of cobra in Pakistan, namely, black cobra (Naja naja) and brown cobra (Naja oxiana). All Naja species were divided into three clades: black cobra (N. naja) and brown cobra (N. oxiana) cladding with different species of Naja; N. naja (Pakistan) cladding with N. naja from Nepal; and N. oxiana showed close relationship with Naja kaouthia from Thailand and Naja siamensis from Thailand. Conclusion: It was confirmed genetically that there are two cobra species in Pakistan, i.e., black and brown cobras. This study will help in not only genetic conservation but also developing anti-venom against snake species.

Insights into the evolution of extracellular leucine-rich repeats in metazoans with special reference to Toll-like receptor 4

The importance of the widely spread leucine-rich repeat (LRR) motif was studied considering TLRs, the LRR-containingprotein involved in animal immune response. The protein connects intracellular signalling with a chain of molecularinteractions through the presence of LRRs in the ectodomain and TIR in the endodomain. Domain analyses with humanTLR1-9 reported ectodomain with tandem repeats, transmembrane domain and TIR domain. The repeat number variedacross members of TLR and remained characteristic to a particular member. Analysis of gene structure revealed absence ofcodon interruption with TLR3 and TLR4 as exceptions. Extensive study with TLR4 from metazoans confirmed thepresence of 23 LRRs in tandem. Distinct clade formation using coding and amino acid sequence of individual repeatsillustrated independent evolution. Although ectodomain and endodomain exhibited differential selection pressure, withinthe ectodomain, however, the individual repeats displayed positive, negative and neutral selection pressure depending ontheir structural and functional significance.

Haplotype diversity in medically important red scorpion (Scorpiones: Buthidae: Hottentotta tamulus) from India

The medically important Indian red scorpion, Hottentotta tamulus, is one of the most poisonous scorpions of Indian subcontinent. We studied the haplotype diversity in eight populations of H. tamulus based on mitochondrial cytochrome oxidase subunit I (COI) partial gene sequence. Analyses revealed 22 haplotypes with a haplotype diversity of 0.941 and nucleotide diversity of 0.023. For the first two codon positions both transition and transversion types of substitutions were equally likely and the test for neutrality was not rejected. However, codon substitution pattern indicated that the gene has experienced purifying selection. Model-based clustering method indicated that the eight populations form three groups that correspond to high, moderate and low rainfall areas, indicating that there is biogeographical separation of haplotypes. Populations from three groups formed distinct clades in maximum likelihood analysis and median joining genetic network and were statistically supported by low within group and high among group variation in analyses of molecular variance. We provide the first account of haplotype diversity in Indian red scorpions and their biogeographical separation.

Historical biogeography of fishes from coastal basins of Maranhão State, northeastern Brazil

The Amazonian ichthyofauna is one of the most diverse in the world, yet fishes from the adjacent coastal basins of Maranhão State in Northeastern Brazil remain poorly known. We use phylogeographic, community phylogenetic and phylogenetic beta diversity methods to study the biogeographic history of fishes from the coastal basins of Maranhão State. We report a total of 160 fish species from the basins of the Maranhão region, representing a 93% increase over results of previous studies. All the fish species assemblages from Maranhão are polyphyletic, with only a few putative sister species pairs inhabiting the region. The modern watershed divides among Maranhão basins do not form substantial barriers to dispersal for freshwater fish species, and are more effectively modelled as biogeographic islands than as biogeographic provinces. In combination these results suggest that the Maranhão ichthyofauna was assembled under the influence of several macroevolutionary (extinction, dispersal) and landscape evolution processes, during the Miocene and Pliocene, as well as by the modern ecological characteristics of the region. The results indicate that the distinctive geological and climatic conditions and history of Northeastern Brazil strongly constrained the formation of aquatic faunas in coastal basins of Maranhão State.(AU)

A ictiofauna da Amazônia é uma das mais diversificadas do mundo, mas os peixes das bacias costeiras adjacentes do estado do Maranhão, no Nordeste do Brasil, ainda são pouco conhecidos. Utilizamos métodos filogeográficos, filogenia de comunidade e de diversidade beta filogenética para estudar a história biogeográfica de peixes das bacias costeiras do estado do Maranhão. Nós relatamos um total de 160 espécies de peixes das bacias da região do Maranhão, representando um aumento de 93% sobre os resultados de estudos anteriores. Todas as assembleias de espécies de peixes do Maranhão são polifiléticas, com apenas alguns supostos pares de espécies irmãs habitando a região. As divisões modernas das bacias hidrográficas do Maranhão não formam barreiras substanciais para a dispersão de espécies de peixes de água doce, e são mais efetivamente modeladas como ilhas biogeográficas do que como províncias biogeográficas. Em conjunto, esses resultados sugerem que a ictiofauna maranhense foi montada sob a influência de vários processos de evolução macroevolutiva (extinção, dispersão) e paisagística, durante o Mioceno e Plioceno, bem como pelas características ecológicas modernas da região. Os resultados indicam que as distintas condições geológicas e climáticas e a história do Nordeste do Brasil restringiram fortemente a formação de faunas aquáticas em bacias costeiras do estado do Maranhão.(AU)

Application of phylogenomics in Chinese medicine resources / 中国中药杂志

China is rich in the diversified Chinese medicine resources and is notable for the wide and long-term applications of Chinese medicine. However,the lack of genomic information on medicinal taxa leads to problems in relation to resource conservation and the downstream application of traditional Chinese medicine resources,which restricts the modernization process of traditional Chinese medicine. Molecular phylogenetics is an important tool to understand the origin and evolution of the earth's biodiversity and promote the conservation and use of medicinal taxa. With the development of sequencing technology,the combination of genomic data extends the traditional molecular phylogenetics to the research level of phylogenomics,making it more powerfully applied to all aspects of biological research. Undoubtedly,carrying out phylogenomic research on Chinese medicine species will greatly promote their resources conservation,molecular evaluation and identification,and the exploration and utilization of natural pharmacodynamic components,promoting the modernization of traditional Chinese medicine. This article starts with a brief introduction of the developing history and basic research methods of phylogenomics,and then reviews the current research progress in phylogenomics related to traditional Chinese medicine resources. Finally,it discusses the problems existing in the current research and the next direction of phylogenomics research in medicinal taxa. The article will hopefully provide a reference for relevant researches in future.

Amylosporus sulcatus sp. nov. (Russulales, Basidiomycota) from Southern China

Amylosporus sulcatus sp. nov. is described from Nonggang Nature Reserve, southern China, on the basis of morphological and molecular data. The morphological description and illustrations for the new species are provided. The species is characterized by pileate and stipitate basidiocarps. The pileus surface is obviously concentrically and radiately sulcate and tomentum, and the pore surface is snow white. Phylogenetic analyses based on sequences of the internal transcribed spacer and nuclear large subunit ribosomal DNA confirmed it to be a new species.

Distribution of HBV subgenotypes in Ribeirão Preto, Southeastern Brazil: a region with history of intense Italian immigration

Abstract Hepatitis B virus (HBV) is distributed worldwide, with geographical variations regarding prevalence of the different genotypes. The aim of this study was to determine the HBV genotypes and subgenotypes circulating in Southeast Brazil and compare the genetic sequences found with HBV sequences previously described in the world. Sequences from 166 chronic HBV carriers were analyzed using the fragment constituted by 1306 base pairs comprising surface and polymerase regions of the HBV genome. The sequences obtained were submitted to phylogenetic analysis. HBV subgenotypes A1, A2, D1-D4, F2a, and F4 were found. HBV genotype D was the most frequent, found in 99 patients (58.4%). Within this group, subgenotype D3 was the most prevalent, in 73 patients (42.9%). HBV genotype A was identified in 58 (36%) patients, subgenotype A1, in 48 (29.8%) subjects. Genotype F was identified in 9 (5.4%). According to the phylogenetic analysis, the sequences found were grouped with sequences from Europe, Asia and Middle East (subgenotypes D1, D2, D3) and sequences from Latin America and Africa (subgenotype A1). HBV D3 grouped in different clusters inside D3 clade, several of them with sequences isolated in Italy. We also identified eight families whose relatives were infected with the same HBV subgenotype, most with high similarity between sequences. In conclusion, the distribution of the HBV sequences obtained interweaved with sequences from other continents, corresponding to regions from where many immigrants came to this region, in accordance to the hypothesis that the HBV detected over there were brought during the colonization times.

Platynosomum fastosum (Trematoda: Dicrocoeliidae) from Cats in Vietnam: Morphological Redescription and Molecular Phylogenetics

The present study was performed to reveal the morphological characteristics and molecular phylogenetic position of Platynosomum fastosum Kossack, 1910. A total 167 specimens of P. fastosum were collected in 8 (4.9%) out of 163 sets of gall-bladders and bile ducts of cats. The number of worms was 1–105 per infected cat. This species was characterized by having a long and slender body, slightly larger ventral sucker than the oral sucker, indistinct prepharynx, small pharynx, short esophagus, bifurcation midway between 2 suckers, and ceca extending to the posterior end of the body. The length of the partial sequences of ITS1 and 5.8S rDNA of P. fastosum were 990 bp, GC-rich. AT/GC ratio was 0.9, there were 9 polymorphic sites, and intraspecific variations ranged from 0.1% to 0.9%. Phylogenetic analyses by neighbor-joining phylogram inferred from ITS1 rDNA sequences revealed that the genetic distance between P. fastosum specimens ranged from 0.3 to 1.5% while the smallest interspecific distance among dicrocoeliid species was 20.9 %. The redescription and genetic characters of P. fastosum are taxonomically important to recognize future different species of the genus Platynosomum showing high intraspecific and morphological variability.