Phylogeography

Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show ...

We here report the unexpected presence of the Italian wall lizard (Podarcis siculus campestris) on Gorgona Island, in the Parco Nazionale Arcipelago Toscano (Tuscan Archipelago, Tyrrhenian Sea, Tuscany, Central Italy). Field observations were carried out in 2020 confirming its presence on the island, where it had never been reported before. We recorded 37 GPS points of the species in three major areas of Gorgona (with 50 lizard records) and about 180 visual counts regarding all age classes (newborns, juveniles and adults). The species was found in the urban area (site of state prison) and in two grassy and bushed areas, around and along olive tree plantations. Seven individuals were captured and their tails were used to assess the sequence variation of the mitochondrial CYB gene. Biometrical parameters were also evaluated for six of these individuals. We detected three distinct CYB haplotypes that were compared to Podarcis siculus CYB sequences available in public databases. They re...

Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngheal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4-6.0). Subtyping was performed on 468 pooled swabs with M gene Ct<26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of intera...

Macadamia Felted Coccid (MFC), Acanthococcus ironsidei (Williams) (Hemiptera: Eriococcidae) was first discovered in 2005 on the Island of Hawaii. Host plants are restricted to Macadamia species, with Macadamia integrifolia Maiden & Betche (Proteaceae) being grown in Hawaii for nut production. Approximately 16,900 acres of macadamia nuts are harvested in Hawaii with estimated farm value of $ 48.8 million (2019 - 2020 records). MFC has become a problem in macadamia orchards where heavy infestations cause the death of young seedlings, reduction in nut production, and severe damage can eventually kill affected trees. Chemical control and extant natural enemies have not suppressed the population of MFC to a manageable level. Exploration in Australia started in November 2013 for the evaluation of potential parasitoids being host specific for introduction into Hawaii. A dominant solitary endoparasitoid of MFC from New South Wales was discovered and described as Metaphycus macadamiae Polasz...

RESUMEN: Se analizaron las muestras correspondientes a cuatro campañas estacionales de diferentes sectores del Golfo San Matías (Prov. de Río Negro, Argentina). Los filtrados se efectuaron verticalmente desde profundidades no mayores a 100 m hasta superficie con una red bicónica provista de una malla filtrante de 300 ¡L. Se clasificó el zooplancton a nivel de especie o de grandes grupos,

The impact of climate change and human activities on endangered plants has been a serious concern in forest ecology. Some Carpinus plants have become extinct. Thus, we need to pay more attention to the Carpinus plants that are not yet extinct but are endangered. Here, we employed the species distribution model (SDM) considering different climate change scenarios and human footprint to test the potential habitat changes of three Carpinus species (C. oblongifolia, C. tientaiensis, and C. purpurinervis) in the future. Our results showed that the mean diurnal range of temperature (MDRT), isothermality, mean temperature of wettest quarter, and human footprint were the most influential factors determining the distribution of C. oblongifolia. Precipitation seasonality (coefficient of variation), MDRT, and precipitation of driest quarter were the most important climatic factors affecting C. tientaiensis. The minimum temperature of the coldest month was the most important factor in the distr...

Trata-se de uma análise crítica sobre a importância do diagnóstico administrativo e situacional nos serviços deatenção básica, tendo em vista o planejamento das ações de saúde e a definição de prioridades. Analisou-se 10 artigospublicados no período de 1996-2006, os quais foram obtidos em consulta na base de dados SciELO. Esse estudo foidesenvolvido a partir da vivência do(s) autor (es) em uma unidade de Estratégia Saúde da Família, onde se verificou arelevância de planejar estratégias de ação de saúde levando-se em consideração as particularidades da área e da populaçãoassistida, a fim de que se obtenham resultados positivos, eficazes. Com a evolução das políticas de saúde observa-se queo fortalecimento da Atenção Básica é imprescindível para a real efetivação do Sistema Único de Saúde. Embora a Estratégiade Saúde da Família possibilite a ampliação do acesso aos serviços é necessário o desenvolvimento de instrumentos paraaumentar a efetividade das ações.

The wide geographical distribution of many fern species is related to their high dispersal ability. However, very limited studies surveyed biological traits that could contribute to colonization success after dispersal. In this study, we applied phylogenetic approaches to infer historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypods II). Because polyploids are suggested to have better colonization abilities and are abundant in Deparia, we also examined whether polyploidy could be correlated to long-distance dispersal events and whether polyploidy could play a role in these dispersals/establishment and range expansion. Maximum likelihood and Bayesian phylogenetic reconstructions were based on a four-region combined cpDNA dataset (rps16-matK IGS, trnL-L-F, matK and rbcL; a total of 4252 characters) generated from 50 ingroup (ca. 80% of the species diversity) and 13 outgroup taxa. Using the same sequence alignment and maximum likelihood trees, we carried out molecula...

Malaria remains a public health problem in Indonesia, therefore, a study was conducted to guarantee a reduction in malaria cases and to support an elimination program. This study aims to determine the patternof vector control in malaria-endemic areas of Central Java Province from August to December 2016, through searching of reports and articles on malaria vector control. Malaria eradication efforts that were carried out included curative treatment and preventive action, by controlling the vector. Meanwhile, malaria vector control in Central Java Province from 2011 to 2015, includes insecticide-treated mosquito nets, larvae fish spreading, repellent use, indoor residual spraying, and larviciding. However, several obstacles to malaria vector control include, increase in the number of breeding sites, population movements from malaria endemic areas, presence of imported cases, geographic condition, attitude and behavior of people, policy differences in governance, and insufficient cont...

Embora o grupo dos dinossauros sauropodomorfos seja amplamente conhecido em virtude dos gigantescos saurópodes, sua origem ainda é pouco compreendida em virtude da escassez de esqueletos completos ou datações precisas. Entretanto, novos achados e datações realizadas em rochas Triássicas do Brasil têm trazido à tona informações valiosas no que tange essa questão. A combinação desses novos dados com técnicas mais avançadas de investigação (e.g. tomografias computadorizadas) vem possibilitando o estabelecimento dos padrões macroevolutivos que direcionaram a evolução inicial do grupo. Através das descobertas realizadas nos leitos Triássicos do Rio Grande do Sul, podemos entender de forma mais refinada como foi que os sauropodomorfos passaram de animais pequenos e pouco abundantes aos maiores animais que já andaram sobre a Terra.

Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission li...

Fueling outbreaks The B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused fast-spreading outbreaks globally. Intrinsically, this variant has greater transmissibility than its predecessors, but this capacity has been amplified in some circumstances to tragic effect by a combination of human behavior and local immunity. What are the extrinsic factors that help or hinder the rapid dissemination of variants? Kraemer et al . explored the invasion dynamics of B.1.1.7. in fine detail, from its location of origin in Kent, UK, to its heterogenous spread around the country. A combination of mobile phone and virus data including more than 17,000 genomes shows how distinct phases of dispersal were related to intensity of mobility and the timing of lockdowns. As the local outbreaks grew, importation from the London source area became less important. Had B.1.1.7. emerged at a slightly different time of year, its impact might have been different. —CA

Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic approaches. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage disper...

Ukraine has one of the largest HIV epidemics in Europe, historically driven by people who inject drugs (PWID). The epidemic showed signs of stabilization in 2012, but the recent war in eastern Ukraine may be reigniting virus spread. We investigated the movement of HIV-infected people within Ukraine before and during the conflict. We analyzed HIV-1 subtype-A pol nucleotide sequences sampled during 2012-2015 from 427 patients of 24 regional AIDS centers and used phylogeographic analysis to reconstruct virus movement among different locations in Ukraine. We then tested for correlations between reported PWID behaviors and reconstructed patterns of virus spread. Our analyses suggest that Donetsk and Lugansk, two cities not controlled by the Ukrainian government in eastern Ukraine, were significant exporters of the virus to the rest of the country. Additional analyses showed that viral dissemination within the country changed after 2013. Spearman correlation analysis showed that incoming ...

The emergence of the SARS-CoV-2 Variant of Concern (VOC) Omicron has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela, by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in internation...

Background: Barcode coverage is difficult to assess for large regions due to incomplete species lists, inaccurate identifications, and cryptic diversity. However, as coverage approaches completion, it becomes possible to critically evaluate identifications and validate barcode lineages. We collate the results of the FISH-BOL barcode project and assess coverage for each family of bony shorefishes and reef fishes from the tropical western Atlantic Ocean. Methodology: We identify to species the public and private barcode lineages from the region on BOLD, confirming identifications by vouchers, phylogeographic deduction, and the process of elimination. The lineages and BINs are assigned to species from a comprehensive species list for the region. Results: We estimate 1029 of 1311 total bony shorefish species in the region are barcoded (78.5%). For reef-associated fishes, 902 of 1083 species are barcoded (83.3%). About 70 of the 181 species not yet barcoded are endemic species from Flori...