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Publications related to Phylogenetics (10,000)
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Article
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Background: The oral microbiota plays vital roles in both oral and systemic health, but limited studies have explored the transition of the female oral microbiota from preconception to pregnancy along with pronounced hormonal fluctuations. Aim: To characterize the oral microbiota among women in preconception and pregnancy through a prospective s...
Article
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Background Boxwood blight disease caused by Calonectria henricotiae and C. pseudonaviculata is of ecological and economic significance in cultivated and native ecosystems worldwide. Prior research has focused on understanding the population genetic and genomic diversity of C. henricotiae and C. pseudonaviculata , but gene family evolution in the co...
Article
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Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use these data to investigate the transmissibility, introduction, and onward transmission o...
Article
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Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea , projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental meta...
Article
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While there is little doubt that the species is the lowest independent evolutionary unit, understanding the many different species concepts is a difficult task, even for university students. In the present study, we propose a didactic sequence that involves fieldwork, laboratory analyses, experimental cultures, and computational work in an integrat...
Article
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Background CesA and Cs l gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. Results In this study, w...
Article
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In the present study, the taxonomic position of Bacillus tepidiphilus was re-evaluated. Bacillus tepidiphilus (B. tepidiphilus) SYSU G01002T showed the highest 16S rRNA gene sequence similarity with the type strain Peribacillus alkalitolerans (P. alkalitolerans) (97.7%). In the phylogenetic (based on 16S rRNA sequence) and phylogenomic (based on 71...
Article
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The mathematical analysis of random phylogenetic networks via analytic and algorithmic methods has received increasing attention in the past years. In the present work we introduce branching process methods to their study. This approach appears to be new in this context. Our main results focus on random level-k networks with n labeled leaves. Altho...
Article
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A new virus, named Mutum virus, related to members of the family Tymoviridae , was isolated from mosquitoes ( Mansonia spp.) in clone C6/36 cells, and its complete genome was sequenced. Its genome is 6494 nt in size with an organization resembling that of tymovirids. The isolated virus is phylogenetically related to two viruses isolated from Culex...
Article
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The allotetraploid Solanaceae plant Nicotiana benthamiana contains two closely related receptor-like proteins (RLPs), NbEIX2 and NbRXEG1, which regulate the recognition of VdEIX3 and PsXEG1 respectively. VdEIX3, PsXEG1, and their homologs represent two types of microbe-associated molecular patterns (MAMPs) that are widespread in diverse pathogens....
Article
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Salvia korolkowii (Lamiaceae) has been considered a species of highest conservation priority due to its narrow distribution and isolated taxonomic position. The species has been known from Uzbekistan and, questionably, Kyrgyzstan and treated as endemic to the Western Tian-Shan. Its modern conservation status according to the IUCN Criteria has not b...
Article
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China is known for its abundant plant resources, but biodiversity conservation faces unprecedented challenges. To provide feasible suggestions for sustainable conservation, we used the species richness algorithm and complementary algorithm to study distribution patterns of 34,082 seed plants based on 1,007,196 county-level distribution records. We...
Article
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Darwin’s naturalization hypothesis predicts successful alien invaders to be distantly related to native species, whereas his pre-adaptation hypothesis predicts the opposite. It has been suggested that depending on the invasion stage (that is, introduction, naturalization and invasiveness), both hypotheses, now known as Darwin’s naturalization conun...
Article
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Dicephalospora is a genus of Helotiaceae (Helotiales) that presently comprises 14 species, all of which were collected from Asia. The current study describes three additional species and a collection from Chiang Rai and Chiang Mai Provinces, Thailand. The new fungi were identified based on morphological characteristics coupled with phylogenetic ana...
Poster
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COLE TCH, MEDAN D (2022) FILOGENIA de las FABACEAE, Spanish version of: COLE TCH (2022) FABACEAE PHYLOGENY POSTER • selección de 97 géneros destacados de la familia de las legumbres con ejemplos de especies importantes y ampliamente difundidas • árbol basado en datos de filotranscriptómica nuclear de Zhao et al. 2021 • seis subfamilias, con ca. 20....
Article
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The early evolution of thyreophoran dinosaurs is thought to have occurred primarily in northern continents since most evidence comes from the Lower and Middle Jurassic of Europe and North America. The diversification into stegosaurs and ankylosaurs is obscured by a patchy fossil record comprising only a handful of fragmentary fossils, most with unc...
Article
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The holobiont concept places emphasis on the strict relationship between a host and its associated microbiome, with several studies supporting a strong effect of the quality of the microbiome on the host fitness. The generalities of the holobiont have been questioned for several invertebrates, including zooplankton. Here we assess the role of host...
Article
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Background Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island’s population and became a critical threat to public health. Methods We conducted a genomic surveillance study through a partnership...
Article
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Solar salterns are an ideal model for extreme environments since they contain a halophilic microorganisms that must adapt to these conditions. In North Sinai, these environments have not gotten much attention. However, the focus of our investigation was on the salterns' waters and saline soil. The study of this microflora showed that it had a lot o...
Article
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Mountain systems offer excellent opportunities to understand β‐diversity patterns and the processes driving them. However, β‐diversity patterns and the underlying mechanisms that lead to dissimilarity in mountain amphibian communities across elevational gradients remain elusive. We aimed to evaluate how amphibian communities respond to environmenta...
Article
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Contact zones are considered as windows into the evolutionary process, allowing identification of factors influencing the evolutionary forces. Here, we combined phylogenetic and morphometric analyses to explore the evolutionary process affecting the taxonomic pattern of two subspecies of Testudo graeca ( T. g. buxtoni and T. g. zarudnyi ) across th...
Article
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The genus Cottus contains more than 60 species that are common in freshwater bodies of northern Eurasia and North America. Despite the abundance of species, this genus has been insufficiently studied in Eastern European rivers and lakes. The new taxon Cottus cyclophthalmus sp. nov. was found in the Neman/Nemunas and Venta river systems (Baltic Sea...
Article
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(1) The focus on floral functional traits and their variability has been significantly lower than when compared to other plant organs. Here, we focused on the variability of four novel floral chemical traits. We aimed to assess the level of interspecific variability of total non-structural carbohydrates (TNC) and total phenolic compounds (TPh) in t...
Poster
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COLE TCH, LEANDRO TD (2022) FILOGENIA das FABACEAE • Portuguese version of: COLE TCH (2022) FABACEAE PHYLOGENY POSTER • seleção de 97 gêneros proeminentes da família dos legumes, legumes, com exemplos de espécies relevantes e de ocorrência ampla • árvore filogenética baseada em dados de transcriptomas nucleares de Zhao et al. 2021 • seis subfamília...
Chapter
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Dərman bitkilərinə olan tələbatın sürətlə artması və müxtəlif səbəblərdən onların ayrı-ayrı növlərinin ehtiyatının azalması əczaçılıq elmi qarşısında mövcud bitki ehtiyatlarının səmərəli istifadə edilməsi və ehtiyatları azalmış dərman bitkilərini əvəz edə biləcək yeni bitki növlərinin axtarışı kimi vacib vəzifələri qoyur. Yeni bitki növlərinin axta...
Article
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Hierodulinae is a species-rich mantid subfamily, with some species bearing a notable leaf-like pronotum. However, the evolutionary pattern and taxonomic significance of the leaf-like pronotum are largely unknown. Here, we present a phylogenomic analysis of the Hierodulinae genera Rhombodera Burmeister, 1838, and Hierodula Burmeister, 1838 based on...
Conference Paper
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Most evolutionary-oriented deep generative models do not explicitly consider the underlying evolutionary dynamics of biological sequences as it is performed within the Bayesian phylogenetic inference framework. In this study, we propose a method for a deep variational Bayesian generative model (EvoVGM) that jointly approximates the true posterior o...
Article
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We used molecular data to address species delimitation in a species complex of the parmelioid genus Canoparmelia and compare the pharmacological properties of the two clades identified. We used HPLC_DAD_MS chromatography to identify and quantify the secondary substances and used a concatenated data set of three ribosomal markers to infer phylogenet...
Article
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Across herbivorous insect clades, species richness and host-use diversity tend to positively covary. This could be because host-use divergence drives speciation, or because it raises the ecological limits on species richness. To evaluate these hypotheses, we performed phylogenetic path model analyses of the species diversity of Nearctic aphids. Her...
Preprint
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SARS-CoV-2 Omicron BA.2.75 emerged in May 2022. BA.2.75 is a BA.2 descendant but is phylogenetically different from BA.5, the currently predominant BA.2 descendant. Here, we showed that the effective reproduction number of BA.2.75 is greater than that of BA.5. While the sensitivity of BA.2.75 to vaccination- and BA.1/2 breakthrough infection-induce...
Article
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The use of molecular data to study the evolutionary history of organisms has revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies, more and more genetic sequence data are available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limi...
Article
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Karst caves are oligotrophic environments that appear to support a high diversity of fungi. Studies of fungi in Thailand’s caves are limited. During a 2019 exploration of the mycobiota associated with soil samples from a karst cave, namely, Phu Pha Phet in the Satun UNESCO Global Geopark in Satun Province, southern Thailand, two previously undescri...
Article
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Migliozzi V., Donato G. (2022). Amanita section Vaginatae in Lazio. First contribution. Institution of Amanita griseocaerulea sp. nov., description of Amanita fulvoides and Amanita huijsmanii. Only recently, thanks to phylogenetic investigations in the ITS region, a complete knowledge of the diversity of Amanita sect. Vaginatae in Europe has begun...
Preprint
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The ability of predicting upcoming events or conditions in advance offers substantial selective advantage to living beings. The most successful systematic tool for fairly reliable prognoses is the use of dynamical causal models in combination with memorised experience. Surprisingly, causality is a fundamental but rather controversially disputed con...
Article
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A black coral, Bathypathes thermophila Chimienti, sp. nov. is described from the Saudi Arabian coasts of the Gulf of Aqaba and north Red Sea (Neom area) using an integrated taxonomic approach. The morphological distinctiveness of the new species is confirmed by molecular analyses. The species thrives in warm and high salinity waters typical of the...
Article
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The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of euka...
Article
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Over half of all crocodylians are threatened with extinction, with many species considered to be functionally extinct throughout their historical ranges. How such losses impact crocodylian functional diversity (FD) and its conservation is poorly understood, but can be investigated using measurable traits. Where such information is unavailable, phyl...
Article
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Iteroparous species may reproduce at many different ages, resulting in a reproductive dispersion that affects the damping of population perturbations, and varies among life histories. Since generation time (Tc$$ {T}_c $$) is known to capture aspects of life‐history variation, such as life‐history speed, does Tc$$ {T}_c $$ also determine reproductiv...
Article
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A novel endophyte, Parathyridaria ephedrae sp. nov. (Thyridariaceae) was isolated from the stem of Ephedra gerardiana growing in Kargil district of Union territory Ladakh, India. Detailed micromorphological investigations revealed that this isolate differs from previously described Parathyridaria species by having 1–3 wart-like prominent papillae,...
Article
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Background Hand, foot, and mouth disease (HFMD) is a common child infectious disease caused by more than 20 enterovirus (EV) serotypes. In recent years, enterovirus A71 (EV-A71) has been replaced by Coxsackievirus A6 (CV-A6) to become the predominant serotype. Multiple EV serotypes co-circulate in HFMD epidemics, and this study aimed to investigate...
Article
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Hymenophyllum chamaecyparicola T.C.Hsu & Z.X.Chang, a new filmy fern species (Hymenophyllaceae) has been described from Taiwan and illustrated based on morphological and phylogenetic evidence. Although the new species resembles members in the subgenus Mecodium, namely H. wrightii, our plastid phylogeny has revealed that it is genetically distant fr...
Article
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Aquatic hyphomycetes are key microbial decomposers of allochthonous organic matter in freshwater ecosystems. Although their importance in carbon flow and food webs in streams is widely recognized, there are still gaps in our understanding of their molecular diversity and distribution patterns. Our study utilized the growing database of ITS rDNA bar...
Article
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The evolution and diversity of the supergroup Amoebozoa is complex and poorly understood. The supergroup encompasses predominantly amoeboid lineages characterized by extreme diversity in phenotype, behavior and genetics. The study of natural selection, a driving force of diversification, within and among species of Amoebozoa will play a crucial rol...
Article
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This paper reports the first occurrence of Lasiodiplodia theobromae in Brazil nut (Bertholletia excelsa). Cankers were found on branches of 3-year-old Brazil nut plants in Belém, Pará, Brazil. The symptomatic plants displayed reddish vascular lesions. The pathogen was identified using morphological and phylogenetic analyses. Koch’s postulates were...
Article
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Carbohydrate-binding modules (CBMs) are important substrate-binding domains that are mainly contained within carbohydrate-active enzymes. To elucidate the mechanism of enzyme-carbohydrate recognition and to promote the process of enzymatic engineering, it is important to explore more potential CBMs. However, the information and analytic tools of CB...
Article
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Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiver...
Article
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Deciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multiple Myeloma patients during up to 14 years. Applying imaging-guided sampling we observe three evolutionary patterns, including relapse driven...
Article
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The genus Acer is widespread throughout the northern temperate zone, and many species within the genus are of ecological and economical importance. Here we report the newly sequenced chloroplast genome of Acer pubipetiolatum var. pingpienense. This chloroplast genome has a total length of 156,730 bp, and contains a pair of inverted repeats (IRs, 26...
Article
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Аннотация. Хасанов Б.А. Фузариозный вилт хлопчатника и современные методы идентификации грибов из рода Fusarium Link. Узбекский биологический журнал, 2013, № 4, с. 18-24. Вилт средневолокнистого хлоачатника (Gossypium hirsutum L.), возбудителем которого являетя гриб Fusarium oxysporum f. sp. vasinfectum, является серьёзным заболеванием, широко расп...
Preprint
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The Uto-Aztecan language family is one of the largest language families in the Americas. However, there has been considerable debate about its origin and how it spread. Here we use Bayesian phylogenetic methods to analyze lexical data from 34 Uto-Aztecan varieties and 2 Kiowa-Tanoan languages. We infer the age of Proto-Uto-Aztecan to be around 4,10...
Article
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This study aimed to examine the use of role-taking constructions in two micro-community sign languages (SLs): Yucatec Maya SL (YMSL), and Soure SL. Various role-taking types were quantified and changes in gaze direction were annotated on data regarding these two SLs. The results showed (i) a greater diversity of role-taking produced in YMSL, includ...
Article
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Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2...
Article
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Species of Arthrinium s. l. are usually known as endophytes, pathogens or saprobes occurring on various hosts and substrates and are characterised by globose to subglobose, sometimes irregular, dark brown and smooth-walled or finely verruculose conidia, always with a truncate basal scar. Currently, Arthrinium s. l. contains two phylogenetically dis...
Preprint
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Root nodule symbiosis (RNS) allows plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. RNS is a complex trait requiring coordination from both the plant host and the bacterial symbiont, and pinpointing the evolutionary origins of root nodules is critical for understanding the gene...
Article
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Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bul...
Article
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Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely related...
Article
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Here, we report the genomic characterization of two siphophages, named hairong and ZY21, that infect the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. The genome sequences of hairong (112,842 bp) and ZY21 (112,006 bp) were determined. Global sequence comparison showed that hairong, ZY21, and two phages of the genus Nickievirus...
Poster
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The genus Pewenomyces was recently described based on Pewenomyces kutranfy, a fungal pathogen that causes cankers on branches and stems of Araucaria araucana in Chile. This genus resides in the Coryneliaceae, a relatively small Family, and its morphology resembles those of species in the closely related genera Caliciopsis and Hypsotheca. During the...
Article
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Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capabl...
Article
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As a result of an ongoing survey of microfungi associated with garden and ornamental plants in Qijing, Yunnan, China, several saprobic fungal taxa were isolated from Magnolia grandiflora. Both morphological and combined SSU, LSU, ITS, tef1, and rpb2 locus phylogenetic analyses (maximum-likelihood and Bayesian analyses) were carried out to identify...