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Publications related to Phylogenetics (10,000)
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Osteology plays an indispensable role in understanding the normal patterns of different species, serving as the foundation for zoological understanding. Mazama nana is well-known in Brazil; however, basic morphological descriptions of the species are scarce, while Subulo gouazoubira, currently revalidated as Mazama gouazoubira, is also prevalent in...
Article
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The study intended to inspect the prevalence of the infection in pregnant woman (Toxoplasma gondii acute and chronic stage of parasite) by rapid test and making a genetic tree after analyzing number of samples with PCR technique. This study integrated (100) blood samples taken from pregnant women in Baghdad Governorate from private laboratories and...
Article
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Although environmental enrichment procedures have demonstrated their benefit to non-human animals in zoos and aquariums, the field has given little attention to phylogenetic variables that might affect their efficacy. Recently, research with loggerhead sea turtles Caretta caretta has demonstrated that they have true colour vision and that colours m...
Article
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diversity quantifies the change in taxonomic and phylogenetic composition between areas. It can be partitioned into two additive components (turnover and nestedness). Geographic distance, which reflects dispersal limitation, and climatic distance, which reflects environmental filtering, are major drivers of β‐diversity, but few studies have assesse...
Article
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Changes in land use and climate directly impact species populations. Species with divergent characteristics may respond differently to these changes. Therefore, understanding species’ responses to environmental changes is fundamental for alleviating biodiversity loss. However, the relationships between land use changes, climate changes, species' in...
Article
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The rapid early diversification of arthropods has made understanding internal relationships within the group fiendish. Particularly unresolved is the origin of Euchelicerata, a clade consisting of the Prosomapoda (comprising the extant Xiphosura and Arachnida and the extinct Chasmataspidida, Eurypterida and synziphosurines) and the extinct Offacoli...
Article
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The Barremian-aged Wessex Formation of the Isle of Wight, UK, offers a globally significant glimpse into the sauropod dinosaur faunas of the early Cretaceous. These deposits have yielded specimens of several neosauropod lineages, such as rebbachisaurids, titanosauriforms (including some of the earliest titanosaur remains), and possible flagellicaud...
Poster
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COLE TCH (2024) Phylogénie des ÉPICÉAS (Picea) © Cole 2024 (CC-BY) • arbre phylogénétique hypothétique des espèces du genre Picea basé sur Shao et al. (2019) et Feng et al. (2019) • longueur des branches arbitraires, et non représentatives du temps • informations géographiques de POWO (Plants of the World Online)
Poster
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The grasshopper genus Italopodisma is strictly endemic to the central Appennines and includes nine species and five subspecies with scattered populations distributed from Sibillini Mountains to the Matese Massif. All populations are mainly present in ecosystems at high elevation (1600-2800 m-asl), such as grasslands, alpine meadows and rocky areas....
Poster
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COLE TCH (2024) Phylogénie des SAPINS (Abies) © Cole 2024 (CC-BY) • arbre phylogénétique hypothétique des espèces du genre Abies basé sur des données du transcriptome de Wei et al. (2024) • longueur des branches arbitraires, et non représentatives du temps • informations géographiques de POWO (Plants of the World Online)
Article
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Pittosporum roimata Gemmill & S.N. Carter (Pittosporaceae, Apiales) was established in 2018 as an endemic species confined to the Poor Knights Islands group, off the eastern coastline of Northland Aotearoa / New Zealand. The new species was distinguished from P. cornifolium A. Cunn. on the basis of vegetative characters (leaf length, width, petiole...
Article
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Universal Single Copy Orthologs (USCOs), as a set of markers of nearly universal single copy genes, show a superiority in phylogenomic inference. Here, we developed a Bench-marking Universal Single Copy Orthologs (BUSCOs) dataset, neuropterida_odb10, tailored for Neuropterida, based on high-quality genome assemblies and transcriptome data, comprisi...
Article
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Deconica is a relatively small genus, with only 90 names recorded in previous research. In this study, four new species of Deconica have been identified based on morphological and phylogenetic evidence from subtropical regions of China. This represents the first discovery of new species of Deconica in China. Morphologically, D. austrosinensis is ch...
Preprint
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Common bean ( Phaseolus vulgaris L.) is a legume pulse crop that provides significant dietary and ecosystem benefits globally. We investigated two key traits, determinacy and photoperiod sensitivity, that are integral to its management and crop production, and that were early selected during the domestication of both Mesoamerican and Andean gene po...
Conference Paper
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The results showed that the genetic structure of Weatherfish in Croatia is uniform, with no deeper structure or division. Phylogenetic reconstruction resulted in the soft polytomy, which indicates recent and rapid emergence of all haplotypes from a common ancestor. Although the genetic diversity of Weatherfish in Croatia is small, diversity is p...
Poster
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COLE TCH (2024) Phylogénie d es CUPRESSACEAE (CupPP) © Cole 2024 (CC-BY) • arbre phylogénétique hypothétique basé sur des données de Stull et al. 2021 et Liu et al. 2022 • longueur des branches arbitraires, et non représentatives du temps • nombres d‘espèces et distribution géographique à partir de POWO (Plants of the World Online)
Article
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The paternally inherited Y chromosome is highly informative of genetic ancestry, therefore making it useful in studies of population history. In Finland, two Y-chromosomal haplogroups reveal the major substructure of the population: N1a1 enriched in the northeast and I1a in the southwest, suggested to reflect eastern and western ancestry contributi...
Article
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Avian pathogenic Escherichia coli strains (APEC) are responsible for major economic losses in poultry farms. The use of antibiotics has led to the emergence of resistant bacteria having direct impact on the food industry. In order to evaluate the resistance of 191 Tunisian APEC strains, we determined the antimicrobial resistance profile of these ba...
Poster
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COLE TCH (2024) Phylogénie des PINS (Genus Pinus) © Cole 2024 (CC-BY) • arbre phylogénétique hypothétique des espèces du genre Pinus basé sur des données transcriptomes de Jin et al. (2021) • longueur des branches arbitraires, et non représentatives du temps • informations géographiques de POWO (Plants of the World Online)
Article
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Phylogenetic indexes summarize the evolutionary information within a given assemblage pool based on the topology and branch lengths of a hypothesized phylogenetic tree. However, different historical contingencies experienced by these assemblages can unevenly distribute evolutionary information through time and over the phylogeny. ‘treesliceR' is an...
Article
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During a survey of microfungi associated with forest plants, four specimens related to Kirschsteiniothelia were collected from decaying wood in Guizhou, Hainan and Yunnan Provinces, China. Kirschsteiniothelia species have sexual and asexual forms. They are commonly found as saprophytes on decaying wood and have been reported as disease-causing path...
Article
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A new species of pseudionine parasite is described from the deep-sea shrimp Notostomus gibbosus A. Milne-Edwards, 1881, collected in the Gulf of Mexico, the first record of a bopyrid parasitizing any member of the family Acanthephyridae Spence Bate, 1888. Morphological and molecular data are provided to support the inclusion of the new species and...
Article
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Basidiomata belonging to the genus Candolleomyces were collected from plains of Punjab, Pakistan, and characterized based on morpho-anatomical and phylogenetic analyses. In phylograms nrITS & nrLSU regions were used to ascertain exact positions of our new taxa in this genus. Three novel taxa, Candolleomyces granulosis, C. pabbiensis and C. umbonatu...
Article
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The role of sociality in the demography of animals has become an intense focus of research in recent decades. However, efforts to understand the sociality–demography nexus have hitherto focused on single species or isolated taxonomic groups. Consequently, we lack generality regarding how sociality associates with demographic traits within the Anima...
Article
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The β and β′ subunits of the RNA polymerase (RNAP) are large proteins with complex multi‐domain architectures that include several insertional domains. Here, we analyze the domain organizations of RNAP‐β and RNAP‐β′ using sequence, experimentally determined structures and AlphaFold structure predictions. We observe that lineage‐specific insertional...
Article
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As defining various taxonomic ranks, especially at and within a specific level, can often be difficult, we used an evolutionarily young group of Central Asian beetles, the genus Anoplistes, to examine the limits between species, subspecies and ecotype. The molecular data (COI genetic distance, haplotype network and species delimitation) and detaile...
Article
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Many parasites can alter the behavior of their hosts in a manner beneficial to the parasite (parasitic manipulations). Obviously, examples of non-manipulative parasites also exist, however, their number might be underestimated because of publication bias. Trematodes from the Diplostomidae family that infect fish eyes are often considered manipulato...
Article
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Aim Changes in landscape configuration significantly impact ecosystems and the services they provide, including disease regulation for both humans and wildlife. Land use conversion usually favors disturbed‐adapted species, which are often known reservoirs of zoonotic parasites, thereby potentially escalating spillover events (i.e., the transmission...
Article
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Here I explore the biological relevance, origin and meaning of the concept of cladogram (rooted, directed branching diagrams representing the hypothesized phylogenetic relationships among the terminal taxa under study) and argue that cladograms do not necessarily entail synapomorphies, but synapomorphies are required to test and ultimately falsify...
Preprint
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In a balanced lethal system, half of the reproductive output always succumbs. A clear example is observed in Triturus newts, which contain two distinct versions of chromosome 1. Developmental arrest occurs in Triturus embryos with two copies of the same chromosome 1 version, but not in those that possess two different versions, suggesting that each...
Preprint
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NEAT1 and MALAT1 are the only two lncRNAs that utilise the tRNA-processing machinery for their maturation, coded very close to each other yet differing in function and evolutionary conservation. Here, we identified NEAT1 and MALAT1 orthologs in 545 mammals and studied their conservation patterns to gain functional insights. In the functional basis...
Article
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The geographic distribution and systematics of many groups of insects are still understudied across large geographic areas of the Iberian Peninsula. This lack of knowledge and the fact that many species have a complex evolutionary history due to the existence of "refugia within refugia" have hindered the taxonomic description of the true biodiversi...
Article
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Junipers are one of the most diverse groups of gymnosperms today. They are adapted to arid areas of the world. In this study, we analysed the chemical composition of the leaf n-alkanes of 170 individuals belonging to Juniperus communis subsp. communis, J. communis var. saxatilis, J. deltoides and J. mac-rocarpa from the Balkans. Localities with at...
Article
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Utricularia sect. Utricularia contains 36 recognised species world-wide, including the recently described U. adamsii from northern Australia. We here present a molecular phylogeny of subgenus Utricularia representing most Australian species based on sequences of two plastid markers and nuclear ITS. We provide molecular evidence for hybridization ev...
Article
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Background and aims Understanding the eco-evolutionary processes that govern leaf elemental composition in subtropical regions with diverse forest landscapes remains a challenge. Here, we investigated the phylogenetic and environmental regulation of leaf elemental composition in subtropical forests. Methods We sampled surface soils and leaves from...
Article
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Plant-specific APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factors are involved in the regulation of genes associated with the growth and developmental processes of numerous plants. Although AP2/ERF proteins from other species have been intensively studied, no studies have been reported on the AP2/ERF family of Luffa cylindrica, an...
Preprint
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Cooperation, the mutual benefit that individuals of different species obtain when they interact together, is ubiquitous in nature. Despite their importance, most of all current ecological theories have been formalized focusing on negative interactions such as competition or predation. The role of cooperation, or other types of positive interactions...
Article
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The pollen morphology of the Rosaceae was investigated using light microscopy, despite its systematic implications. The main aim of this study was to verify the taxonomic significance of the pollen traits studied in 25 species and collected from different localities in Swat district, northern Khyber Pakhtunkhwa, Pakistan. In the present study, we h...
Article
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Hand, foot, and mouth disease (HFMD), a common childhood infection caused by enterovirus, poses a serious public health concern in China. We collected and analyzed epidemiological data on 62,133 HFMD cases in Shenyang City, Liaoning Province, from 2013 to 2023. The average annual incidence was 76.12 per 100,000 person-years; 99.45% of cases were mi...
Article
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Understanding the global variation of plant strategies is essential for unravelling eco-evolutionary processes and ecosystem functions. Variation in ten fundamental aboveground and fine-root traits is summarised in four dimensions, the first of which relates to aboveground plant size. However, there is no consensus about how root size fits within t...
Article
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The invasion of Cydalima perspectalis (Walker, 1859) (Lepidoptera, Crambidae) poses a significant threat to European ecosystems and North American ornamentals. In an effort to identify potential biological control agents from the native habitats of C. perspectalis, a field survey was conducted from 2022 to 2024 in South Korea. During the survey, a...
Article
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The well-characterized edible and medicinal bamboo mushroom is Phallus indusiatus, a Chinese bamboo mushroom with long white indusium (skirt). To date, scientists have found more than five species of bamboo mushrooms in Thailand, containing bamboo mushrooms with long white, short white, and several colored skirts. Still, most of them are unidentifi...
Article
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Birds are among the organisms most impacted by plant invasions, the effects of which are particularly conspicuous during the breeding season. Birds can incorrectly assess the suitability of large, invasive hogweeds Heracleum sp. in south‐eastern Poland when selecting nesting sites early in spring when the developing invaders do not yet differ subst...
Article
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Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional...
Article
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Interferons (IFNs) stimulate the expression of numerous IFN-stimulating genes via the Janus kinase-signal transducers and activators of the transcription (JAK-STAT) signaling pathway, which plays an important role in the host defense against viral infections. In mammals, including humans and mice, a substantial number of IFN-stimulated genes (ISGs)...
Article
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Delimitation of allopatric populations into species remains subjective and largely arbitrary. Many cold-adapted species from the sub-Arctic and Central and Southern European Mountain systems provide excellent models to study allopatry problem due to their patchy distributions. The same concerns many Holarctic species, which frequently show varying...
Preprint
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Since Carl Linnaeus introduced the binomial nomenclature system in the 18th century, zoological classification has experienced significant transformations. While Linnaeus’ taxonomy provided a foundational structure based on morphological traits, advancements in evolutionary theory, genetics, and molecular biology have revolutionized the way organis...
Article
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During a survey of saprobic fungal niches in Southwestern China, eighteen ascomycetous collections of Nigrograna (Nigrogranaceae, Pleosporales, Dothideomycetes) were found on dead branches of medicinal plants. These taxa were characterized and identified based on morphological and culture characteristics, and phylogenetic analyses of a combined the...
Poster
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COLE TCH (2023) Filogenia de los MAMÍFEROS VIVOS © Cole 2023 (CC-BY) Spanish version of: Cole (2023) Phylogeny of MAMMALS (MamPP) • números de especies de IUCN Red List 2023, Vers. 2022-2: 27 ordens, ~6000 especies (EX 85, CR 233, EN 550, VU 557) • filogenia de los placentarios: OʼLeary MA et al. (2013) Science 339: 662–667; filogenia de los marsup...
Article
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Maize is a major crop, feed, and industrial material. Caffeic acid-O-methyltransferase (COMT) is a methylase closely associated with lignin biosynthesis and plant growth and resistance. In this study, we identified the COMT gene (ZmCOMT) family in maize and further analyzed its phylogenetic evolution, subcellular localization, and its function in r...
Article
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Numerous studies in humans have shown that altruism may influence mate choice decisions, highlighting its potential role as a sexual signal. Whether using altruism as a signal is an adaptation, however, remains largely unresolved. In this review, we aim to investigate the adaptive nature of altruism as a sexual signal by constructing a comprehensiv...
Article
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Background The global pandemic caused by SARS‐CoV‐2 has underlined the significance of strict genomic surveillance to track virus evolution and the possible emergence of new variants, particularly in densely populated countries like Bangladesh. This study outlines a strategic framework of genomic surveillance to track the evolution of the virus in...
Article
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In 2018, an adult male of a small-sized Tube-nosed Bat (Chiroptera: Vespertilionidae: Murina) was captured at an arid cave located on the Qinghai–Tibet Plateau in Yushu City, Qinghai Province, China. Despite external morphological similarities with those of M. harpioloides and M. chrysochaetes, the individual in question displays explicit cranioden...
Article
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We describe a new species, Chrysosplenium insularis J.E.Jang, K.H.Lee & H.Y.Gil, belonging to the family Saxifragaceae, from the southern islands of the Republic of Korea. Chrysosplenium insularis is morphologically similar to C. japonicum (Maxim.) Makino but can be distinguished by fairly persistent bulbils, green to yellowish-green sepals, four s...
Article
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While flowering plants have diversified in virtually every terrestrial clime, climate constrains the distribution of individual lineages. Overcoming climatic constraints may be associated with diverse evolutionary phenomena including whole genome duplication (WGD), gene‐tree conflict, and life‐history changes. Climatic shifts may also have facilita...
Article
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Opatrini Brullé, 1832 is the most species-rich tribe in the subfamily Blaptinae Leach, 1815. In this study, a preliminary phylogenetic relationship among 14 species of five genera of Opatrini is hypothesized based on mitochondrial gene (COI) fragment. Based on the phylogenetic topology and the results of three molecular species delimitation analyse...
Article
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Extensive research into bat flight mechanisms has highlighted the complex functional and evolutionary dynamics of their wing structures, yet the anatomical details of certain wing muscles remain elusive. In particular, the intramembranous plagiopatagiales proprii muscles, located within the plagiopatagium—an area of the wing lacking direct joint co...
Article
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In humans, interactions with objects are often embedded in communicative exchanges. Objects offer unique affordances to explore, carry functions and hold cultural relevance, which can shape children’s interactions and communication. Research indicates that the use of artificial objects, such as certain toys, helps promote pre-linguistic communicati...
Article
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Two new species of Agaricales, Deconica flavum and Entocybe roseoalbus, are described from Mount Tianmu, Zhejiang Province, Eastern China. Two new species are distinct and monophyletic based on morphology and phylogenetic analyses. Deconica flavum differs from other Deconica species in that the pileus is brow shallow in the center and stipe with ye...
Article
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The relationship between biodiversity and ecosystem function is crucial for understanding the structure and processes of subtropical forest ecosystems. However, the extent to which biodiversity influences subtropical forest biomass remains unclear. This study applies Bayesian causal inference to explore causal relationships between forest Abovegrou...
Article
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The highly pathogenic avian influenza 2.3.4.4b H5 viruses have been a cause for concern recently, as they have been responsible for continuous outbreaks since 2021. In China, the H5N6 subtype has been predominantly circulating in domestic poultry but has rarely been detected in wild birds over the past 3 years. In December 2023, novel reassortant 2...
Article
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Polymyxin antibiotics B and colistin are considered drugs of last resort for the treatment of multi-drug and carbapenem-resistant Gram-negative bacteria. With the emergence and dissemination of multi-drug resistance, monitoring the use and resistance to polymyxins imparted by mobilised colistin resistance genes (mcr) is becoming increasingly import...
Article
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The current representatives of the family Natrialbaceae within the class Halobacteria were subjected to phylogenetic, phylogenomic, and comparative genomic analyses. The current species of Halobiforma and Halomontanus were found to be related to those of Natronobacterium and Natronoglomus, respectively. According to the cutoff value of average amin...
Article
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Two new species of Neooxyartes Ho, 2018 are described from Central Vietnam: N. minimus sp. nov. from Kon Ka Kinh National Park and N. neohiraseoides sp. nov. from Chu Yang Sin National Park. A new genus Mycovartes gen. nov. is described to accommodate Oxyartes vietnamensis Ho, 2018 resulting into the new combination Mycovartes vietnamensis (Ho,...
Article
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Hatching synchronisation is widespread in oviparous taxa. It has been demonstrated that many species use sounds to coordinate synchronous hatching, being widespread among archosaurs (birds and crocodilians). Recent studies have shown that some turtle species produce vocalisations from within the egg, but the role of this behaviour in synchronising...
Article
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Reptiles are one of the most diverse groups of vertebrates in the world that are distributed in almost all ecosystems. Many of these studies have focused on exploring their diversity patterns across different environments; and recent studies on reptile alpha and beta diversity have incorporated a multifaceted approach into their analysis to have mo...
Article
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New distribution records and a redescription are presented for Caperhantus cicurius (Fabricius, 1787), a diving beetle endemic to the Cape region of South Africa, which is only distantly related to other Afrotropical dytiscids. We show that the species is much more widely distributed than previously recognized and present details of occupied habita...
Preprint
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The establishment of the symmetry axis is crucial for the development of all organisms. In insects, this process begins early in oogenesis with the correct distribution of the mRNAs and proteins in the oocyte. One of the proteins that contribute to organizing this distribution is Capicua (Cic). Cic has been studied in Drosophila melanogaster oogene...
Article
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Natural rubber production currently relies heavily on a single species, Hevea brasiliensis, underscoring the urgent need to identify alternative sources to alleviate the strain on natural rubber production.