Bayesian Phylogenetic Analyses Research Articles

Molecular Detection and Genotyping of Chlamydia psittaci in Birds in Buenos Aires City, Argentina

Chlamydia psittaci is a bacterium that infects several species of birds and mammals. It is the causal agent of avian chlamydiosis and psittacosis in humans and it is globally distributed. Chlamydia psittaci is one of the main zoonotic pathogens transmitted by birds. In Argentina, there has been limited research on the prevalence and genetic variability of C. psittaci. The aim of this study was to detect and genotype C. psittaci using molecular techniques in birds living in Buenos Aires City, Argentina, during the period 2012–2015. A descriptive, observational, retrospective and cross-sectional study was carried out. A total of 983 bird samples submitted for diagnosis of avian chlamydiosis were analyzed. The frequency of C. psittaci was 12.54% and 7.89% in Psittaciformes and Columbiformes, respectively. A 348 bp region of the ompA gene was sequenced in positive samples. Molecular genotyping was performed through a Bayesian phylogenetic analysis. Of the 983 bird samples, 83 were positive for C. psittaci and 44 could be sequenced. The genotypes found were A, B, and E. Despite the high levels of host specificity, we found six psittacids with genotype B and one pigeon with genotype A, reflecting the affiliative interaction between Psittaciformes and Columbiformes. This study represents the first survey reporting the presence of C. psittaci in birds within the largest and most populous city in Argentina.

Elymus multiramosus (Poaceae), a new species from the north-western Qinghai-Tibetan Plateau, China

A new species from China, Elymus multiramosus Y.C. Zhang, sp. nov. is described and illustrated herein, based on morphological characters and molecular phylogenetic analysis. The taxonomic descriptions of E. multiramosus and the comparison with related species are presented. The taxonomic distinctiveness of this new species was inferred by Maximum Likelihood (ML) analysis and Bayesian phylogenetic analysis, based on the complete chloroplast genome sequence. It is assigned to the Elymus section and bears similarity to Elymus nutans Griseb. However, it can be easily distinguished from other species by its compound spike, in contrast to the simple spike inflorescence typical of those species. The compound spike is characterised by rhachillas that are extended at the base of the main axis, giving rise to 3–6 mini-spike-like branches. Notably, these branches significantly increase in length from the top towards the bottom of the compound spike. In the molecular phylogeny, Elymus multiramosus from Qinghai, north-western China, is phylogenetically positioned as a distinct lineage. The lineage comprising Elymus sinosubmuticus from Sichuan, east of the Tibetan Plateau and Elymus nutans from the Himalayas forms a sister group to Elymus multiramosus, suggesting that these three species share a common ancestor that is distinct from the lineage leading to Elymus atratus from Gansu, north of the Tibetan Plateau.

Comprehensive phylogenomic analysis of Zika virus: Insights into its origin, past evolutionary dynamics, and global spread

BackgroundZika virus (ZIKV), a Flaviviridae family member, has been linked to severe neurological disorders. Despite detailed studies on recent outbreaks, the early evolutionary history of ZIKV remains partially unclear. This study elucidates ZIKV origin and evolutionary dynamics, focusing on recombination events, early lineage diversification, and virus spread across continents. MethodsWe assessed recombination using multiple methods. We conducted Bayesian phylogenetic analyses to understand the evolutionary relationships and timing of key diversification events. Model selection was carried out to determine the most appropriate evolutionary model for our dataset. ResultsOur phylogenies revealed recent recombination between Singaporean and African lineages, indicating the co-circulation of diverse lineages during outbreaks. Thailand was identified as a crucial hub in the spread across Asia. The phylogenetic analysis suggests that the ZIKV lineage dates back to the eleventh century, with the first significant diversification occurring in the nineteenth century. The timing of the re-introduction of the Asian lineage into Africa and the delay between probable introduction and outbreak onset were also determined. ConclusionsThis study provides novel insights into ZIKV's origin and early evolutionary dynamics, highlighting Thailand's role in the spread of the virus in Asia and recent recombination events between distant lineages. These findings emphasize the need for continuous surveillance and a better understanding of ZIKV biology to forecast and mitigate future outbreaks.

A panoramic view of the molecular epidemiology, evolution, and cross-species transmission of rosaviruses

Rosavirus is a newly discovered member of the family Picornaviridae that was initially detected in wild rodents and subsequently in children with diarrhoea. Nevertheless, there is a significant gap in our understanding of the geographical distribution, phylogenetic relationships, evolutionary patterns, and transmission of rosaviruses. To address these issues, we analysed 434 rodents and shrews from five different species that were collected in southern China. Using PCR screening of faecal samples, we detected rosaviruses in Norway rats (Rattus norvegicus) and identified two previously undocumented host species: tanezumi rats (Rattus tanezumi) and Asian house shrews (Suncus murinus). Rosaviruses were particularly common in these animals, with an overall prevalence rate of 32.49% (141/434). For genetic and evolutionary analyses, we selected six representative positive samples to amplify the complete genomes of rosaviruses. Bayesian phylogenetic analysis suggested that our sequences clustered within the genus Rosavirus, where genotype B sequences are the closest relatives. The elevated nonsynonymous-to-synonymous ratios observed in rosavirus B may be attributed to relaxed selection pressures driven by virus spillover events. On the basis of the available data, it is hypothesized that the genus Rosavirus may have originated from Norway rats around the year 1339. In summary, these findings provide valuable insights into the complex evolutionary history of rosaviruses and underscore the urgent need for ongoing surveillance of this virus.

DNA sequencing reveals higher taxonomic diversity of coralline algae (Corallinales and Hapalidiales, Rhodophyta) in the tropical western North Atlantic that complicates ecological studies

Abstract Understanding of non-geniculate coralline algal (NGCA) diversity, prevalence, and distribution in the tropical western North Atlantic is currently limited by reliance on morphological and anatomical features that are inadequate for species identifications. Reef surveys from two study sites, the Florida Keys (Florida, USA) and Roatán (Honduras), provided prevalence data for the main benthic organisms as well as relative abundance for NGCA genera. NGCA collected during these surveys and from additional sites and depths were identified using DNA sequences from two plastid genes, psbA and rbcL, and two nuclear genes, SSU and LSU, and supported by morphological and anatomical descriptions. Bayesian and Maximum Likelihood phylogenetic analyses, along with species delimitation and genetic distance methods, resolved 11 genera within two orders. Within the Corallinales, the genera Dawsoniolithon, Porolithon and Spongites each had one species, Harveylithon and Lithophyllum had two, Titanoderma three, Hydrolithon four, Neogoniolithon eight, and an unknown genus within the subfamily Neogoniolithoideae had 11 putative species. Within the Hapalidiales, the genera Phymatolithon and Roseolithon each had one species. This study reinforces the inability of morphological and anatomical features to distinguish NGCA species in the tropical western North Atlantic, resulting in substantial underestimations of species richness and diversity.

Tuber cumberlandense and T. canirevelatum, two new edible Tuber species from eastern North America discovered by truffle-hunting dogs

ABSTRACT Ectomycorrhizal fungi in the genus Tuber form hypogeous fruiting bodies called truffles. Many Tuber species are highly prized due to their edible and aromatic ascomata. Historically, there has been attention on cultivating and selling European truffle species, but there is growing interest in cultivating, wild-harvesting, and selling species of truffles endemic to North America. North America has many endemic Tuber species that remain undescribed, including some that have favorable culinary qualities. Here, we describe two such Tuber species from eastern North America. Maximum likelihood and Bayesian phylogenetic analyses of ITS (internal transcribed spacer), tef1 (translation elongation factor 1-alpha), and rpb2 (second largest subunit of RNA polymerase II) sequences were used to place these species within a phylogenetic context. We coupled these data with morphological analyses and volatile analyses based on gas chromatography–mass spectrometry. Tuber cumberlandense, sp. nov. (previously referred to as Tuber sp. 66), is a member of the Rufum clade that has been opportunistically harvested for commercial sale from T. melanosporum orchards across eastern North America. Tuber canirevelatum, sp. nov. belongs in the Macrosporum clade and thus far is only known from eastern Tennessee, USA. Both new species were discovered with the assistance of trained truffle dogs. The volatile profiles of T. canirevelatum and T. cumberlandense were measured in order to characterize aromas based on the chemical compounds produced by these fungi. Ascomata from both species were enriched in acetone, dimethyl sulfide, 1-(methylthio)-1-propene, and 1-(methylthio)propane. In this work, we celebrate and encourage the use of trained truffle-hunting dogs for fungal biodiversity discovery and research.

Molecular phylogenetic and biogeographic evidence of Lepidagathis Willd. (Acanthaceae, Barlerieae) focusing on Indian endemics.

Lepidagathis Willd., a genus belonging to the Acanthaceae family, is primarily distributed in tropical and subtropical regions worldwide, encompassing approximately 153 species. While considerable morphological research has been conducted on Lepidagathis, it has not completely dispelled taxonomic ambiguities and conflicting interpretations. Molecular analysis emerges as a valuable tool for resolving these taxonomic uncertainties, but the availability of nucleotide sequence data for Lepidagathis has been limited thus far. This study delivers a phylogenetic analysis of Lepidagathis species, utilizing both chloroplast and nuclear regions. The results of Bayesian Inference and Maximum Likelihood phylogenetic analyses consistently segregate the studied Lepidagathis species into two principal clades, denoted as Clade A and Clade B. Notably, this analysis firmly positions the Indian endemic Lepidagathis within Clade A, supported by robust statistical evidence. Furthermore, our biogeographical analysis strongly suggests that the origin of Lepidagathis might be traced back to Eurasia. This research establishes a foundational molecular phylogeny of Lepidagathis, offering valuable insights for future taxonomic investigations. Additionally, it sheds light on the evolutionary history and biogeographical origins of the Lepidagathis genus.

A phylogenetic study of South-Western Tibetic

Abstract This study performs primary data collection, transcription, and cognate coding for eight South West Tibetic languages (Lowa, Gyalsumdo, Nubri, Tsum, Yohlmo, Kagate, Jirel, and Sherpa). This includes partial cognate coding, which analyses linguistic relations at the morpheme level. Prior resources and inferences are leveraged to conduct a Bayesian phylogenetic analysis. This helps estimate the extent to which the historical relationships between the languages represent a tree-like structure. We argue that small-scale projects like this are critical to wider attempts to reconstruct the cultural evolutionary history of Sino-Tibetan and other families.

Elucidating the Mitogenomic Blueprint of Pomadasys perotaei from the Eastern Atlantic: Characterization and Matrilineal Phylogenetic Insights into Haemulid Grunts (Teleostei: Lutjaniformes).

The parrot grunt fish, Pomadasys perotaei, has a limited distribution in the Eastern Atlantic Ocean and is an important species in marine capture fisheries across several West African countries. Despite its ecological and economic significance, the mitogenomic information for this species is lacking. This study utilized next-generation sequencing to generate the de novo mitogenome of P. perotaei from Eastern Atlantic. The resulting mitogenome is 16,691 base pairs and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and an AT-rich control region (CR). Most of the PCGs exhibit nonsynonymous (Ka) and synonymous (Ks) substitution rates of less than '1', indicating strong negative selection across haemulid fishes. The control region of Pomadasys species contains four conserved domains, as seen in other teleost's, with polymorphic nucleotides that can be used to study population structures through the amplification of short mitochondrial gene fragments. Additionally, Bayesian phylogenetic analysis based on PCGs revealed a non-monophyletic clustering pattern of Pomadasys within the haemulid matrilineal tree. Overall, the structural characterization and phylogenetic analysis enhance our understanding of the genetic composition and evolutionary history of Pomadasys species from the Indo-West Pacific and Eastern Atlantic Oceans.

On the importance of assessing topological convergence in Bayesian phylogenetic inference.

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the effective sample size and to investigate trace graphs of the sampled parameters. A major limitation of these approaches is that they are developed for continuous parameters and therefore incompatible with a crucial parameter in these inferences: the tree topology. Several recent advancements have aimed at extending these diagnostics to topological space. In this reflection paper, we present two case studies-one on Ebola virus and one on HIV-illustrating how these topological diagnostics can contain information not found in standard diagnostics, and how decisions regarding which of these diagnostics to compute can impact inferences regarding MCMC convergence and mixing. Our results show the importance of running multiple replicate analyses and of carefully assessing topological convergence using the output of these replicate analyses. To this end, we illustrate different ways of assessing and visualizing the topological convergence of these replicates. Given the major importance of detecting convergence and mixing issues in Bayesian phylogenetic analyses, the lack of a unified approach to this problem warrants further action, especially now that additional tools are becoming available to researchers.

Mitochondrial DNA patterns describe the evolutionary history of the bonnethead shark Sphyrna tiburo (Linneus 1758) complex in the western Atlantic Ocean.

The apparent lack of physical barriers in the marine realm has created the conception that many groups have a constant gene flow. However, changes in ocean circulation patterns, glacial cycles, temperature, and salinity gradients are responsible for vicariant events in many fish species, including sharks. The bonnethead shark, Sphyrna tiburo, is an endangered small coastal shark species. Although considerable efforts have recently been undertaken, little remains known about the possible biogeographic scenario that can explain its actual distribution within the western Atlantic (WA). Here, we used 599 mitochondrial sequences to assess the phylogeographic structure and implement Bayesian phylogenetic analyses to obtain divergence times and reconstruct the ancestral geographic range. This allowed us to infer processes responsible for the diversification of S. tiburo into major divergent lineages. Our results indicated that S. tiburo in the WA represents three independent lineages, with Brazilian samples differentiated into a distinct genetic cluster. The posterior probability of ancestral range analysis indicated that the species likely originated in the northern region (Carolina Province and the southern Gulf of Mexico), where it colonized southward through the uplifting of the Central American Isthmus (CAI). The Northern and Caribbean genetic clusters appear to have arisen from the intensification of the Loop Current, which currently flows northward passing the Yucatan Peninsula, Gulf of Mexico, and east Florida. Following initial colonization, the Northeastern Brazil group differentiated from the Caribbean region due to the sediment and freshwater discharge of the Amazon-Orinoco Plume. Thus, the evolutionary history of the S. tiburo complex can be explained by a combination of dispersal and vicariance events that occurred over the last ~5 million years (MY). We established and confirmed the species and population limits, demonstrating that the Amazon-Orinoco Plume constitutes a significant dispersal barrier for coastal sharks. Finally, we discuss some recommendations for the conservation of the bonnethead shark.

Bioinformatic identification of monkeypox virus phylogenetic gene trees that are representative of its whole-genome phylogenetic tree.

Phylogenetic analysis based on whole-genome sequences is the gold standard for monkeypox virus (MPXV) phylogeny. However, genomic epidemiology capability and capacity are lacking or limited in resource poor countries of sub-Saharan Africa. Therefore, these make real-time genome surveillance of MPXV virtually impossible. We hypothesized that phylogenetic analysis based on single, conserved genes will produce phylogenetic tree topology consistent with MPXV whole-genome phylogeny, thus serving as a reliable proxy to phylogenomic analysis. In this study, we analyzed 62 conserved MPXV genes and showed that Bayesian phylogenetic analysis based on five genes (OPG 066/E4L, OPG068/E6R, OPG079/I3L, OPG145/A18R, and OPG150/A23R) generated phylogenetic trees with 72.2-96.3% topology similarity index to the reference phylogenomic tree topology. Our results showed that phylogenetic analysis of the identified five genes singly or in combination can serve as surrogate for whole-genome phylogenetic analysis, and thus obviates the need for whole-genome sequencing and phylogenomic analysis in regions where genomic epidemiology competence and capacity are lacking or unavailable. This study is relevant to evolution and genome surveillance of MPXV in resource limited countries.

Quantifying the effects of the mitochondrial genome on milk production traits in dairy cows: empirical results and modelling challenges

Significant advances in livestock traits have been achieved primarily through selection strategies targeting variation in the nuclear genome, with little attention given to mitogenome variation. We analyzed the influence of the mitogenome on milk production traits of Holstein cattle in Croatia based on strategically generated next-generation sequencing data for 109 cows pedigree-linked to 7115 milk production records (milk, fat and protein yield) from 3006 cows (first 5 lactations). Since little is known about the biology of the relationship between mitogenome variation and production traits, our quantitative genetic modeling was complex. Thus, the proportion of total variance explained by mitogenome inheritance was estimated using 5 different models: (1) cytoplasmic model with maternal lineages (CYTO), (2) haplotypic model with mitogenome sequences (HAPLO), (3) amino acid model with unique amino acid sequences (AMINO), (4) evolutionary model based on a phylogenetic analysis using Bayesian Evolutionary Analysis Sampling Trees phylogenetic analysis (EVOL), and (5) mitogenome SNP model (SNPmt). The polygenic autosomal and X chromosome additive genetic effects based on pedigree were modeled, together with the effects of herd-year-season interaction, permanent environment, location, and age at first calving. The estimated proportions of phenotypic variance explained by mitogenome in 4 different models (CYTO, HAPLO, AMINO, and SNPmt) were found to be substantial given the size of mitogenome, ranging from 5% to 7% for all 3 milk traits. At the same time, a negligible proportion of the phenotypic variance was explained by mitogenome with the EVOL model. Similarly, in all models, no proportion of phenotypic variance was explained by the X chromosome. Although our results should be confirmed in other dairy cattle populations, including a large number of sequenced mitogenomes and nuclear genomes, the potential of utilizing mitogenome information in animal breeding is promising, especially as the acquisition of complete genome sequences becomes cost-effective.

Transmission network of Hepatitis C virus subtype 2a in Huazhou County, Shaanxi Province, China

BackgroundHuazhou County has one of the highest rates of hepatitis C virus (HCV) infection incidence and prevalence in Shaanxi Province, northwest China. Understanding the characteristics of HCV transmission patterns in this area could help guide targeted prevention strategies. This study employed phylogenetic analysis and the construction of a molecular transmission network of HCV-infected people in Huazhou County to describe the predominant strains of HCV and identify factors associated with onward transmission.MethodsWhole blood samples were obtained from HCV RNA-positive individuals for sequencing of the non-structural protein 5B region. A maximum-likelihood (ML) phylogenetic tree was constructed to determine HCV subgenotypes, and Bayesian phylogenetic analysis was employed to estimate the evolutionary history. The transmission network was constructed using the ML phylogenetic tree and pairwise distances. Logistic regression was used to identify factors associated with clustering in the transmission network.ResultsML phylogenetic analysis confirmed that the 61 sequences analyzed in the study belonged to subtype 2a. Bayesian phylogenetic analysis showed that the majority of subtype 2a sequences originated in the northwest of China and had descended approximately 8 to 20 years before sampling. Overall, 26.2% of participant sequences were grouped into phylogenetic network clusters. Multivariate logistic regression showed that individuals who had a history of blood transfusions and were living in Shi Village, Huazhou County, were more likely to form clusters within the transmission network.ConclusionHCV transmission in Huazhou County was predominantly associated with subtype 2a. Having a history of blood transfusions and living in residential Shi Village, Huazhou County, were factors associated with a high risk of HCV infection transmission. Prioritizing targeted interventions for these patient groups may help to prevent further infections.

Molecular Epidemiology and Phyloevolutionary Analysis of Porcine Parvoviruses (PPV1 through PPV7) Detected in Replacement Gilts from Colombia.

Eight porcine parvovirus (PPV) species, designated as PPV1 through PPV8, have been identified in swine. Despite their similarities, knowledge about their distribution and genetic differences remains limited, resulting in a gap in the genetic classification of these viruses. In this study, we conducted a comprehensive analysis using PPV1 to PPV7 genome sequences from Colombia and others available in the GenBank database to propose a classification scheme for all PPVs. Sera from 234 gilts aged 180 to 200 days were collected from 40 herds in Colombia. Individual detection of each PPV (PPV1 through PPV7) was performed using end-point PCR. Complete nucleotide (nt) sequencing was performed on the PPV1 viral protein (VP), and near-complete genome (NCG) sequencing was carried out for novel porcine parvoviruses (nPPVs) (PPV2 through PPV7). Phylogenetic analyses were conducted by comparing PPV1-VP sequences to 94 available sequences and nPPVs with 565 NCG, 846 nPPV-VP, and 667 nPPV-nonstructural protein (NS) sequences. Bayesian phylogenetic analysis was used to estimate substitution rates and the time to the most recent common ancestor for each PPV. The highest prevalence was detected for PPV3 (40.1%), followed by PPV5 (20.5%), PPV6 (17%), PPV1 (14.5%), PPV2 (9.8%), PPV4 (4.2%), and PPV7 (1.3%). Notably, all tested sera were negative for PPV8 genomes. An analysis of the PPV1-VP sequences revealed two main clades (PPV1-I and PPV1-II), with the sequences recovered in this study grouped in the PPV1-II clade. Comparative analysis showed significant genetic distances for PPV2 to PPV7 at the NCG (>6.5%), NS (>6.3%), and VP (>7.5%) regions, particularly when compared to equivalent regions of PPV genomes recovered worldwide. This study highlights the endemic circulation of nPPVs in Colombian pig herds, specifically among gilts. Additionally, it contributes to the phylogenetic classification and evolutionary studies of these viruses. The proposed method aims to categorize and divide subtypes based on current knowledge and the genomes available in databanks.

Mitochondrial phylogenomics reveals the sister relationship between the endogean Mediterranean raymondionymine weevils and the remaining 51,000+ Curculionidae (Coleoptera)

The tribe Raymondionymini has long been neglected in phylogenetic studies. The tribe is characterized by uncertain monophyly, fluctuating taxonomic status, and a composition prone to instability. All raymondionymine weevils are wingless and have eyes either completely absent or, rarely, consisting of a single ommatidium. With body lengths predominantly below three millimeters, they inhabit deep soil environments and are infrequently collected. The core of this tribe comprises nine genera distributed in Europe and around the Mediterranean region and encompassing 76 species, while six additional genera include 17 species distributed in USA (California), Mexico, Ecuador, Venezuela, Russian Far East, and Madagascar. Here, we present eight new mitogenomes, complemented by one publicly available, encompassing all but two Mediterranean genera of raymondionymine weevils. We used publicly available Curculionoidea mitogenomes to compile an all-inclusive dataset with 391 terminals and a reduced dataset with 61 terminals representing main families of Curculionoidea and subfamilies within Curculionidae. Our maximum likelihood and Bayesian phylogenetic analyses, employing both DNA and amino acids datasets under alternative partition schemes, consistently produced congruent phylogenies. Our results show that the Mediterranean raymondionymines form a strongly supported clade, and their easternmost and morphologically distinct genus Ubychia is sister to the rest of them. Most notably, our results consistently recover a sister relationship between the clade of Mediterranean raymondionymine weevils and a clade encompassing all remaining Curculionidae. Consequently, we propose a revision of weevil taxonomy: (i) Our target group is removed from the non-monophyletic subfamily Brachycerinae; (ii) this clade is resurrected to its former subfamily level within Curculionidae, as the subfamily Raymondionyminaestat. rev; (iii) the nine Mediterranean genera Alaocephala, Alaocyba, Coiffaitiella, Derosasius, Ferreria, Raymondiellus, Raymondionymus, Tarattostichus, and Ubychia compose Raymondionyminaestat. rev; (iv) and non-Mediterranean genera Alaocybites, Bordoniola, Gilbertiola, Homosomus, Neoubychia, and Schizomicrus are considered as “incertae sedis” pending further phylogenetic corroboration. We hypothesize that the remaining Brachycerinae and the non-Mediterranean representatives within Raymondionyminae constitute a series of species-poor early-diverging lineages representing currently unrecognized subfamilies of Curculionidae.

Bayesian phylogeographic inference of wheat yellow mosaic virus in China and Japan suggests that the virus migration history coincided with historical events

Wheat yellow mosaic virus (WYMV) is one of the most serious viral pathogens causing reductions in wheat yield in East Asia. We investigated the phylodynamics of WYMV by analysing the CP, VPg and P1 genes to understand the origin and dispersal of the virus. A Bayesian phylogenetic analysis revealed that the most recent common WYMV ancestor occurred in approximately 1742 (95% credibility interval, 1439–1916) CE (Common Era), and the evolutionary rates of the VPg, CP and P1 genes were 6.669 × 10−4 (95% credibility interval: 4.575 × 10−4–8.927 × 10−4), 2.468 × 10−4 (95% credibility interval: 1.667 × 10−4–3.338 × 10−4) and 5.765 × 10−5 (95% credibility interval: 3.285 × 10−6–1.252 × 10−4), respectively. Our phylogeographic analysis indicated that the WYMV population may have originated in Henan Province, China, first spreading to Japan in the mid-19th century and stopping after the Japanese surrender in World War II. The second wave spread to Japan from Shandong Province, China, in approximately 1977, a few years after the establishment of diplomatic relations between China and Japan. Before the founding of the People's Republic of China, Henan Province was the emigration centre of WYMV in East Asia, and after the late 20th century, Jiangsu and Shandong Provinces were also the virus emigration centres in East Asia. In addition, there were two migration pathways from Japan to Jiangsu and Shandong Provinces, China, in approximately 1918 and approximately 1999 respectively. Our results suggest that the wide spread of WYMV in East Asia is strongly related to human factors.

A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and ‘archaic’ South American ungulates

Abstract Ever since the discovery of Macrauchenia patachonica by Charles Darwin in 1834, the affinities of litopterns—a group of extinct South American Native Ungulates (SANUs)—have been elusive. In particular, the interfamilial relationships and timing of the familial diversification within the order Litopterna have not been addressed with adequate taxon and character sampling, and modern phylogenetic methods. We address these issues using a new morphological matrix of 703 dental and mandibular characters, scored for the earliest litopterns alongside early SANUs of other orders (Astrapotheria, Notoungulata, Pyrotheria, and Xenungulata). We also included members of families that have been often included within Litopterna, such as Didolodontidae, Protolipternidae, Indaleciidae, and Notonychopidae, the last two sometimes grouped in the order Notopterna. We conducted maximum parsimony and undated and tip-dated Bayesian phylogenetic analyses. Our results indicate that (1) didolodontids, protolipternids, and kollpaniines should be considered early SANUs, but not particularly closely related to any order, (2) Indaleciidae and Notonychopidae usually form a monophyletic group (Notopterna), and (3) Litopterna is a monophyletic unit composed of four families [Adianthidae, Anisolambdidae (subfamilies Anisolambdinae and Sparnotheriodontinae), Macraucheniidae, Proterotheriidae], and tentatively the notoptern families Indaleciidae and Notonychopidae with a probable origin ~64.0 Mya in the Early Palaeocene.

Paronatrema davidbowiei n. sp. (Trematoda: Syncoeliidae), a new parasite of the pelagic thresher (Alopias pelagicus) and its phylogenetic relationships within the suborder Hemiurata Skrjabin & Guschanskaja, 1954

A new species of hemiurid trematode found on the gills and in the aorta of the pelagic thresher Alopias pelagicus from the eastern Pacific, off Costa Rica, is described based on an integrative taxonomic approach that includes the use of light and scanning electron microscopy, and 28S rDNA sequencing. Phylogenetic analysis was also performed to explore, for the first time, the relationships of a member of the subfamily Otiotrematinae within the suborder Hemiurata. Paronatrema davidbowiei n. sp. can be distinguished from the congeners by having tegumental spines on the dorsal surface of the forebody, papillae on the oral sucker, and different morphology or number of testicular follicles. BLAST analysis revealed that sequences of Paronatrema davidbowiei n. sp. had the highest degree of similarity with Hirudinella spp. (Hirudinellidae). Results from Maximum Likelihood and Bayesian phylogenetic analyses, returning trees with the exact same topology and strong branch support, distinguished between the two superfamilies included in the suborder Hemiurata: Azygioidea and Hemiuroidea. Our analysis placed the new species in a clade with Copiatestes filiferus, the only existing sequence of the family Syncoeliidae.

Vicariant speciation resulting from biogeographic barriers in the Australian tropics: The case of the red-cheeked dunnart (Sminthopsis virginiae).

Global biodiversity loss continues unabated, and in Australia, the rate of recent mammal extinctions is among the worst in the world. Meanwhile, the diversity among and within many endemic mammal species remains undescribed. This information is crucial to delineate species boundaries and thus inform decision-making for conservation. Sminthopsis virginiae (the red-cheeked dunnart) is a small, dasyurid marsupial found in four disjunct populations around the northern coast of Australia and New Guinea. There are three currently recognized subspecies, each occupying a distinct geographic location. Sminthopsis v. virginiae occurs in Queensland, S. v. rufigenis is distributed across New Guinea and the Aru Islands, and S. v. nitela has populations in the Top End of the Northern Territory and the Kimberley region of Western Australia. Previous molecular work has suggested the current subspecies definitions are not aligned with DNA sequence data, though the sampling was limited. We undertook a comprehensive genetic and morphological review of S. virginiae to clarify relationships within the species. This included mitochondrial (CR, 12S, and cytb) and nuclear (omega-globin, IRBP, and bfib7) loci, and morphometric analysis of skulls and whole wet-preserved specimens held in museums. Maximum Likelihood and Bayesian phylogenetic analyses resolved samples into two distinct clades, demarcated by the Gulf of Carpentaria in Australia's north. Sminthopsis. v. nitela was consistently separated from S. v. virginiae and S. v. rufigenis, based on the overall body and skull size and craniodental features, while S. v. virginiae and S. v. rufigenis were more difficult to distinguish from each other. Thus, we redescribed S. virginiae, recognizing two species, S. nitela (raised from subspecies) and S. virginiae (now comprising the subspecies S. v. virginiae and S. v. rufigenis). This study highlights the importance of recognizing cryptic mammal fauna to help address the gap in our knowledge about diagnosing diversity during a time of conservation crisis.