Bayesian Phylogenetic Analyses Research Articles

Epidemiology and phylodynamics of multiple clades of H5N1 circulating in domestic duck farms in different production systems in Bangladesh.

Waterfowl are considered to be natural reservoirs of the avian influenza virus (AIV). However, the dynamics of transmission and evolutionary patterns of AIV and its subtypes within duck farms in Bangladesh remain poorly documented. Hence, a cross-sectional study was conducted in nine districts of Bangladesh between 2019 and 2021, to determine the prevalence of AIV and its subtypes H5 and H9, as well as to identify risk factors and the phylodynamics of H5N1 clades circulating in domestic duck farms. The oropharyngeal and cloacal swab samples were tested for the AIV Matrix gene (M-gene) followed by H5, H7, and H9 subtypes using rRT-PCR. The exploratory analysis was performed to estimate AIV and its subtype prevalence in different production systems, and multivariable logistic regression model was used to identify the risk factors that influence AIV infection in ducks. Bayesian phylogenetic analysis was conducted to generate a maximum clade credibility (MCC) tree and the maximum likelihood method to determine the phylogenetic relationships of the H5N1 viruses isolated from ducks. AIV was detected in 40% (95% CI: 33.0-48.1) of the duck farms. The prevalence of AIV was highest in nomadic ducks (39.8%; 95% CI: 32.9-47.1), followed by commercial ducks (24.6%; 95% CI: 14.5-37.3) and backyard ducks (14.4%; 95% CI: 10.5-19.2). The H5 prevalence was also highest in nomadic ducks (19.4%; 95% CI: 14.0-25.7). The multivariable logistic regression model revealed that ducks from nomadic farms (AOR: 2.4; 95% CI: 1.45-3.93), juvenile (AOR: 2.2; 95% CI: 1.37-3.61), and sick ducks (AOR: 11.59; 95% CI: 4.82-32.44) had a higher risk of AIV. Similarly, the likelihood of H5 detection was higher in sick ducks (AOR: 40.8; 95% CI: 16.3-115.3). Bayesian phylogenetic analysis revealed that H5N1 viruses in ducks belong to two distinct clades, 2.3.2.1a, and 2.3.4.4b. The clade 2.3.2.1a (reassorted) has been evolving silently since 2015 and forming at least nine subgroups based on >90% posterior probability. Notably, clade 2.3.4.4b was introduced in ducks in Bangladesh by the end of the year 2020, which was genetically similar to viruses detected in wild birds in Japan, China, and Africa, indicating migration-associated transmission of an emerging panzootic clade. We recommend continuing AIV surveillance in the duck production system and preventing the intermingling of domestic ducks with migratory waterfowl in wetlands.

First Report of Mulberry Rust Caused by Cerotelium fici on Morus nigra in Brazil.

Leaf rust caused by Cerotelium fici (Cast.) Arth. is the main disease affecting Moraceae family plants, such as Ficus and Morus species (Galleti and Rezende 2016; Srikantaswamy et al. 2006). In August 2020, rust symptoms were observed in 100% of mulberry (Morus nigra L.) trees in an experimental orchard (Piracicaba, SP, Brazil; 22°42'28"S, 47°37'42"W). Mulberry leaves with high rust severity became yellowish and fell-off prematurely. Pustules were light brown with yellowish halo and presented mean size of 0.9 mm2. Uredinial paraphyses (n = 50) measured 42.2 ± 0.67 µm long with wall uniformly ca 0.6-1.1 μm thick. Urediniospores were brownish, echinulate, globoid to broadly ellipsoid, and measured 27.1 ± 0.29 × 21.0 ± 0.27 µm with a wall thickness of 0.6 ± 0.01 µm (n = 100). The morphology of the urediniospores observed in this study was similar to that reported in the literature for C. fici on Morus alba and Ficus spp. (Gupta et al. 1994; McKenzie 1986; Hennen et al. 2005). We used a low-coverage genome-skimming approach to retrieve genetic information of the rRNA cluster and the mtDNA. Genomic DNA was extracted from 3-4 mg of stored urediniospores at -80 °C, macerated in liquid nitrogen, using a modified cetyl trimethylammonium bromide extraction procedure (Lo Piccolo et al. 2012), and sequenced with 150-bp paired-end reads on Illumina NovaSeq 6000 System. Raw data, (45,761,957 X 2 reads) were assembled with SPAdes v3.15.1 (Bankevich et al., 2012) and the output used to create a custom BLAST database. Loci used for the phylogenetic analyses were identified by BLASTn using, as a query, sequences of C. fici from Ficus sp. from Australia publicly available: Accession No. MH047210.1 for the rRNA and MW036502.1 for COX3. The retrieved sequences were deposited in GenBank under accession numbers OM296992 and OP797407 for the partial rRNA cluster and COX3, respectively. The Bayesian inference phylogenetic analysis of the three concatenate loci (18S, 28S, and COX3) revealed that the isolate obtained in this study (MN1) was clustered in a well-supported clade with C. fici type species. Pathogenicity tests were conducted using mulberry potted plants under greenhouse conditions (25 ± 5 °C). The urediniospores suspension (5 × 104 urediniospores ml-1) with 0.05% Tween 20 was sprayed with an airbrush on fully expanded leaves until run-off. As a control, mulberry plants were sprayed with distilled water and kept under the same conditions. Inoculated and mock-inoculated plants were kept in a dark moist chamber at 23 °C (± 2 °C) for 24 h. After this period, plants were moved to the greenhouse. The experimental design was completely randomized with five replicates, each replicate consisted of one potted plant and the experiment was performed twice. At 12 days post-inoculation, all inoculated plants showed rust symptoms identical to those observed in the field, whereas control plants had no symptoms. The first symptoms were small pustules on the abaxial surface of fully expanded leaves. Small chlorotic lesions were observed on the adaxial leaf surface, which evolved into necrotic lesions. The pathogen was re-inoculated into potted plants, where it was maintained through monthly inoculations. To our knowledge, this is the first report of mulberry rust on M. nigra in Brazil. As mulberry leaves are the only natural food for silkworm (Bombyx mori L.), rust poses a significant threat to the sericulture industry because the disease can decrease production and quality of mulberry foliage.

Acynodon adriaticus from Villaggio del Pescatore (Campanian of Italy): Anatomical and chronostratigraphic integration improves phylogenetic resolution in Hylaeochampsidae (Eusuchia)

The hylaeochampsid crocodylomorph Acynodon adriaticus, from the uppermost Cretaceous ‘Villaggio del Pescatore’ site, belongs to an early diverging lineage in Eusuchia. Here an additional specimen, MCSNT 57031, is osteologically and osteohistologically described in detail. After integrating this morphological information together with the recent chronostratigraphic recalibration of the site to the lower–middle Campanian, the tip-dated Bayesian phylogenetic analysis recovers this taxon in a monophyletic clade with the Spanish Acynodon iberoccitanus. Conflicting results from the maximum parsimony and Bayesian analyses, and discussion on the intraspecific variability between the specimens assigned to A. adriaticus, highlights the need for a detailed morphological description and integration with an updated phylogenetic scaffold, in order to resolve the monophyly of the genus Acynodon and the relationships of these branches of early diverging eusuchians. The curious discrepancy between morpho- and osteo-skeletal maturity suggest unique ecomorphological adaptations in this Campanian crocodylomorph.

Morphological and molecular description of Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) from the Manchurian wapiti Cervus elaphus xanthopygus.

Dictyocaulus xanthopygus sp. nov. (Nematoda: Trichostrongyloidea) was isolated from the lungs of the Manchurian wapiti in Primorsky kray, Russia. The newly described species exhibits morphological characteristics of Dictyocaulus but is distinct from congeneric species based on morphological (lengths of body and esophagus, distances from the anterior end to nerve ring and to excretory pore, the thickness of the buccal capsule, etc.) and molecular features. High levels of genetic divergence as well as Bayesian phylogenetic analyses based on 18S rRNA nuclear and cox1 mitochondrial genes supported the independence of Dictyocaulus xanthopygus sp. nov. Secondary structures of helix 39 of 18S rRNA were identical, while ES9 adjacent to the helix has a unique conformation for newly described worms. Energy-efficient conformational rearrangements of rRNA secondary structures can be applicable in studies on the pathogenesis, epidemiology, taxonomy and evolutionary biology of parasites. Additionally, bracketed dichotomous keys to six valid species of Dictyocaulus were prepared.

Global molecular evolution and phylogeographic analysis of barley yellow dwarf virus based on the cp and mp genes

Barley yellow dwarf virus (BYDV) has caused considerable losses in the global production of grain crops such as wheat, barley and maize. We investigated the phylodynamics of the virus by analysing 379 and 485 nucleotide sequences of the genes encoding the coat protein and movement protein, respectively. The maximum clade credibility tree indicated that BYDV-GAV and BYDV-MAV, BYDV-PAV and BYDV-PAS share the same evolutionary lineage, respectively. The diversification of BYDV arises from its adaptability to vector insects and geography. Bayesian phylogenetic analyses showed that the mean substitution rates of the coat and movement proteins of BYDV ranged from 8.327 × 10− 4 (4.700 × 10− 4–1.228 × 10− 3) and 8.671 × 10− 4 (6.143 × 10− 4–1.130 × 10− 3) substitutions/site/year, respectively. The time since the most recent common BYDV ancestor was 1434 (1040–1766) CE (Common Era). The Bayesian skyline plot (BSP) showed that the BYDV population experienced dramatic expansions approximately 8 years into the 21st century, followed by a dramatic decline in less than 15 years. Our phylogeographic analysis showed that the BYDV population originating in the United States was subsequently introduced to Europe, South America, Australia and Asia. The migration pathways of BYDV suggest that the global spread of BYDV is associated with human activities.

Molecular Characteristics of Enterovirus B83 Strain Isolated from a Patient with Acute Viral Myocarditis and Global Transmission Dynamics.

This study determined the global genetic diversity and transmission dynamics of enterovirus B83 (EV-B83) and proposed future disease surveillance directions. Blood samples were collected from a patient with viral myocarditis, and viral isolation was performed. The complete genome sequence of the viral isolate was obtained using Sanger sequencing. A dataset of 15 sequences (from three continents) that had sufficient time signals for Bayesian phylogenetic analysis was set up, and the genetic diversity and transmission dynamics of global EV-B83 were analyzed using bioinformatics methods, including evolutionary dynamics, recombination event analysis, and phylogeographic analysis. Here, we report the complete genome sequence of an EV-B83 strain (S17/YN/CHN/2004) isolated from a patient with acute viral myocarditis in Yunnan Province, China. All 15 EV-B83 strains clustered together in a phylogenetic tree, confirming the classification of these isolates as a single EV type, and the predicted time for the most recent common ancestor appeared in 1998. Recombinant signals were detected in the 5'-untranslated region and 2A-3D coding regions of the S17 genome. The phylogeographic analysis revealed multiple intercontinental transmission routes of EV-B83. This study indicates that EV-B83 is globally distributed. Our findings add to the publicly available EV-B83 genomic sequence data and deepen our understanding of EV-B83 epidemiology.

Subgrouping in a ‘dialect continuum’: A Bayesian phylogenetic analysis of the Mixtecan language family

AbstractSubgrouping language varieties within dialect continua poses challenges for the application of the comparative method of historical linguistics, and similar claims have been made for the use of Bayesian phylogenetic methods. In this article, we present the first Bayesian phylogenetic analysis of the Mixtecan language family of southern Mexico and show that the method produces valuable results and new insights with respect to subgrouping beyond what the comparative method and dialect geography have provided. Our findings reveal potential new subgroups that should be further investigated. We show that some unexpected groupings raise important questions for phylogenetics and historical linguistics about the effects of different methods of primary data gathering and organization that should be considered when interpreting subgrouping results.

Visualizing incompatibilities in phylogenetic trees using consensus outlines.

Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis. A consensus tree is often used to summarize what the trees have in common. Consensus networks were introduced to also allow the visualization of the main incompatibilities among the trees. However, in practice, such networks often contain a large number of nodes and edges, and can be non-planar, making them difficult to interpret. Here, we introduce the new concept of a phylogenetic consensus outline, which provides a planar visualization of incompatibilities in the input trees, without the complexities of a consensus network. Furthermore, we present an effective algorithm for its computation. We demonstrate its usage and explore how it compares to other methods on a Bayesian phylogenetic analysis of languages using data from a published database and on multiple gene trees from a published study on water lilies.

A new species of the Cyrtodactylusbrevipalmatus group (Squamata, Gekkonidae) from Tak Province, northwestern Thailand.

An integrative taxonomic analysis was used to delimit and diagnose a new species of the Cyrtodactylusbrevipalmatus group from Tak Province in western Thailand. Although Bayesian phylogenetic analyses place C.denticulatussp. nov. within the brevipalmatus group, the new species is neither nested within nor is it the sister species of any other species in the brevipalmatus group. Furthermore, based on the mitochondrial NADH dehydrogenase subunit 2 gene (ND2) and adjacent tRNAs, it bears an uncorrected pairwise sequence divergence of 7.87-21.94% from all other species in the brevipalmatus group. Cyrtodactylusdenticulatussp. nov. is differetiated from all other species in the brevipalmatus group by having a number of unique charateristics such as denticulate ventrolateral body folds and ventrolateral subcaudal ridges, characters not seen in any other species of the group (n = 51 individuals). Additionally, based on a multiple factor anlaysis, C.denticulatussp. nov. does not overlap with any other species in multivariate space. The discovery of C.denticulatussp. nov. underscores the unrealized diversity of upland ecosystems across Thailand and the urgent need for increased exploration and conservation of these unique imperiled montane refugia, especially in this era of climate change.

SNP data reveals the complex and diverse evolutionary history of the blue-ringed octopus genus (Octopodidae: Hapalochlaena) in the Asia-Pacific

The blue-ringed octopus species complex (Hapalochlaena spp.), known to occur from Southern Australia to Japan, currently contains four formally described species (Hapalochlaena maculosa, Hapalochlaena fasciata, Hapalochlaena lunulata and Hapalochlaena nierstraszi). These species are distinguished based on morphological characters (iridescent blue rings and/or lines) along with reproductive strategies. However, the observation of greater morphological diversity than previously captured by the current taxonomic framework indicates that a revision is required. To examine species boundaries within the genus we used mitochondrial (12S rRNA, 16S rRNA, cytochrome c oxidase subunit 1 [COI], cytochrome c oxidase subunit 3 [COIII] and cytochrome b [Cytb]) and genome-wide SNP data (DaRT seq) from specimens collected across its geographic range including variations in depth from 3 m to >100 m. This investigation indicates substantially greater species diversity present within the genus Hapalochlaena than is currently described. We identified 10,346 SNPs across all locations, which when analysed support a minimum of 11 distinct clades. Bayesian phylogenetic analysis of the mitochondrial COI gene on a more limited sample set dates the diversification of the genus to ∼30 mya and corroborates eight of the lineages indicated by the SNP analyses. Furthermore, we demonstrate that the diagnostic lined patterning of H. fasciata found in North Pacific waters and NSW, Australia is polyphyletic and therefore likely the result of convergent evolution. Several “deep water” (>100 m) lineages were also identified in this study with genetic convergence likely to be driven by external selective pressures. Examination of morphological traits, currently being undertaken in a parallel morphological study, is required to describe additional species within the complex.

Molecular networks reveal complex interactions with MSM in heterosexual women living with HIV-1 who play peripheral roles in Guangzhou, China

BackgroundWith the number of newly diagnosed HIV-positive heterosexual women increasing yearly, it is urgent to understand HIV-1 transmission among heterosexual women in Guangzhou, China. MethodsHIV-1 pol sequences were obtained from people living with HIV-1 during 2008 to 2017 in Guangzhou, China. A molecular network was constructed using HIV-1 TRAnsmission Cluster Engine with 1.5% genetic distance. Potential linkage and centrality metric were measured with Cytoscape. Transmission pathways between heterosexual women and men who have sex with men (MSM) were determined using Bayesian phylogenetic analysis. ResultsIn the network, 1799 (62.6%) MSM, 692 (24.1%) heterosexual men and 141 (4.9%) heterosexual women formed 259 clusters. Molecular clusters including MSM and heterosexuals were more likely to form larger networks (P<0.001). Nearly half of the heterosexual women (45.4%) were linked to heterosexual men and 17.7% to MSM, but only 0.9% of MSM were linked to heterosexual women. Thirty-three (23.4%) heterosexual women linked to at least one MSM node and were in peripheral role. Compared to general heterosexual women, the proportion of heterosexual women linked to MSM infected with CRF55_01B (P<0.001) and CRF07_BC (P<0.001) was higher than that of other subtypes, and the proportion diagnosed between 2012 and 2017 (P = 0.001) was higher than that in 2008–2012. In MCC trees, 63.6% (21/33) of the heterosexual women differentiated from the heterosexual evolutionary branch, while 36.4% (12/33) differentiated from the MSM evolutionary branch. ConclusionHeterosexual women living with HIV-1 were mainly linked to heterosexual men and were in peripheral positions in the molecular network. The role of heterosexual women in HIV-1 transmission was limited, but the interaction between MSM and heterosexual women were complex. Awareness of the HIV-1 infection status of sexual partners and active HIV-1 detection are needed for women.

Phylogenetic assessment of the halophilic Australian gastropod Coxiella and South African Tomichia resolves taxonomic uncertainties, uncovers new species and supports a Gondwanan link

Genetic and morphological data have suggested a Gondwanan connection between the three non-marine aquatic gastropod genera Coxiella Smith, 1894, Tomichia Benson, 1851 and Idiopyrgus Pilsbry, 1911. These genera have recently been included in the family Tomichiidae Wenz, 1938, however, further assessment of the validity of this family is warranted. Coxiella is an obligate halophile that occurs in Australian salt lakes while Tomichia occurs in saline and freshwater environments in southern Africa and Idiopyrgus is a freshwater taxon from South America. Despite their novel evolutionary and ecological characteristics, Coxiella, Tomichia and Idiopyrgus are poorly studied, and the lack of a contemporary taxonomic framework restricts our ability to assess the risk of declining habitat quality to these gastropods. We used data from mitochondrial (COI and 16S) and nuclear (28S and 18S) genes in 20 species from all three genera to undertake the most comprehensive phylogenetic test of the Tomichiidae to date. Bayesian and Maximum Likelihood phylogenetic analyses of a concatenated dataset (2974 bp) of all four genes strongly supported a monophyletic Tomichiidae. The COI analysis (n = 307) identified 14 reciprocally monophyletic lineages in Coxiella that comprised eight of the nine currently described species and at least six putative new species. Four distinct genetic clades of species with somewhat distinctive morphologies were found, each of which may constitute a distinct genera. In addition, four species of Tomichia were identified, including three described and one putatively new species. Current species descriptions of Coxiella do not account for the range of morphological variation observed within most described species, and although morphology is reasonably effective at delineating between clades, it is of limited use when trying to separate closely related Coxiella species. The improved understanding of the taxonomy and diversity of Tomichia and especially Coxiella will underpin future studies and conservation planning for these taxa.

Unravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.

The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance. A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis. The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621. Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.

Corrigendum to: 'Spatial evolution of human cultures inferred through Bayesian phylogenetic analysis' (2023) by Takahashi and Ihara.

Corrigendum to: 'Spatial evolution of human cultures inferred through Bayesian phylogenetic analysis' (2023) by Takahashi and Ihara.

RESURRECTION OF PLESIOCREADIUM WINFIELD, 1929 (DIGENEA: MACRODEROIDIDAE) WITH PHYLOGENETIC ANALYSES AND SUPPLEMENTAL OBSERVATIONS OF ITS TYPE SPECIES FROM RIVERS IN ARKANSAS, MISSISSIPPI, NEW YORK, AND TENNESSEE.

We herein resurrect and emend PlesiocreadiumWinfield, 1929 (Digenea: Macroderoididae) and provide a supplemental description of its type species, Plesiocreadium typicumWinfield, 1929, based on adult specimens collected from the intestine of bowfins, Amia calva Linnaeus, 1766 (Amiiformes: Amiidae), captured in the L'Anguille River (Mississippi River Basin, Arkansas), Big Lake (Pascagoula River Basin, Mississippi), Chittenango Creek (Oneida Lake, New York), and Reelfoot Lake (Tennessee River Basin, Tennessee). Plesiocreadium spp. (Pl. typicum and Plesiocreadium flavum [Van Cleave and Mueller, 1932] n. comb.) differ from other macroderoidids by having a dorsoventrally flat forebody, ceca that extend posteriad beyond the testes and that do not form a cyclocoel, testes that are greater than one-half of maximum body width, a cirrus sac that is dorsal to the ventral sucker and arches dextrad or sinistrad, a uterine seminal receptacle, asymmetrical vitelline fields that remain separated anteriorly and posteriorly and that extend anteriad to the level of the ventral sucker, and an I-shaped excretory vesicle. Bayesian phylogenetic analyses (ITS2 and 28S) recovered monophyletic Plesiocreadium sensu stricto (as defined herein) sister to Macroderoides trilobatusTaylor, 1978 and that clade sister to the remaining macroderoidids, with sequences ascribed to species of Macroderoides Pearse, 1924 recovered as paraphyletic. We regard Macroderoides parvus (Hunter, 1932) Van Cleave and Mueller, 1934, M. trilobatus, and RauschiellaBabero, 1951 as incertae sedis. Arkansas, New York, and Tennessee comprise new locality records for Pl. typicum.

Low Genetic Diversity in the Highly Morphologically Diverse Sida fallax Walp. (Malvaceae) Throughout the Pacific1

Sida fallax Walp. (‘ilima) (Malveae, Malvoideae, Malvaceae) is native to the Pacific area and is broadly distributed throughout this region. Sida fallax is the most widespread and variable taxon of Malvaceae in the Hawaiian Islands and it occurs with diverse morphological forms and in different habitats from Hawai‘i Island to Midway Atoll. The low elevation and mountain ecotypes are two extreme ecological forms of S. fallax with many intermediate morphological types existing between these extreme ecotypes in the Hawaiian Islands. The range of morphological and ecological diversity in Sida fallax suggests that this species requires further biosystematics investigation. The purpose of this study was two-fold. First, explore the genetic diversity among S. fallax populations throughout its native range in the Pacific region to assess if it is a single species or potentially multiple cryptic species; second, investigate the biogeographic origin of S. fallax. To do this, Sida fallax was sampled throughout the Hawaiian Islands and in different parts of the Pacific region. Bayesian phylogenetic analyses based on nuclear (ITS and ETS) and chloroplast regions (psbA–trnH) were carried out. Results indicate that there is very little sequence-level variation in this species throughout its distribution and phylogenetic analysis clearly demonstrated that Sida fallax is a single species throughout the Pacific region and the different forms of Hawaiian S. fallax are not genetically distinct at the sequence level. Although the pattern of dispersal of S. fallax is not clear, an American origin is most likely.

Identification of a novel HIV-1 second-generation circulating recombinant form (CRF136_0107) among men who have sex with men in China.

To investigate the molecular epidemiology of HIV-1 in Heilongjiang, China, and try to spot signs of new circulating recombinant form (CRF) in this region. A molecular epidemiological study was conducted in Heilongjiang, China during 2011-2020. Plasma samples were collected from three HIV-1 positive patients. The near full-length genome sequences (NFLGs) of a novel circulating recombinant form (CRF) were then obtained and subjected to phylogenetic analysis using Mega 7.0.26. Recombination analysis was performed by the jumping profile Hidden Markov Model (jpHMM). Finally, the origin time of this novel CRF was inferred using the Bayesian phylogenetic analysis in Beast v1.10.4. The three NFLGs formed a distinct monophyletic cluster in the neighbor-joining (NJ) tree. Recombination analysis revealed that the recombinant genome was composed of five segments derived from CRF01_AE, subtypes B, and C, but further confirmed to be a second-generation recombinant form of CRF01_AE/CRF07_BC by a comparison of genome maps and subregion phylogenetic analysis and therefore designated as CRF136_0107. With Bayesian phylogenetic analysis, CRF136_0107 was estimated to originate around 2010-2011. A novel HIV-1 CRF01_AE/CRF07_BC second-generation CRF called CRF136_0107 was identified among men who have sex with men (MSM) in Heilongjiang, a northeast province of China.

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes.

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

A MORPHOLOGICAL AND MOLECULAR REVIEW OF THE TAXONOMY OF THE TRIFOLIUM DEPAUPERATUM SPECIES COMPLEX

The amphitropical Trifolium depauperatum Desv. species complex (Fabaceae) is a group of closely related clovers with a disjunct native distribution in Chile and western North America. Based on the most recent treatment by Vincent and Isely in 2012, the species complex includes two species, one of which contains three varieties. Historically, the taxonomy of this species complex has been unstable; therefore, we performed a morphological and molecular analysis from herbarium specimens and fresh tissue to further explore taxonomic delimitations. Multivariate and cluster analyses were performed on the morphological data. Bayesian and Maximum Parsimony phylogenetic analyses were performed on the molecular data. Both data sets support the recognition of four taxa: T. depauperatum var. depauperatum, T. depauperatum var. amplectens (Torr. & A.Gray) Rattan, T. depauperatum var. truncatum (Greene) J.S.Martin ex Isely, and T. hydrophilum Greene. We designate three new lectotypes and one epitype, and provide a key to taxa, synonymy, descriptions, and distributional information for each.

A giant raptor (Aves: Accipitridae) from the Pleistocene of southern Australia

The giant accipitrid Dynatoaetus gaffae gen. et sp. nov. is described from existing and newly collected material. Initial fossil remains were collected from Mairs Cave (Flinders Ranges, South Australia) in 1956 and 1969, and comprised a sternum, distal humerus and two ungual phalanges. A further 28 bones from this individual—including the neurocranium, vertebrae, furculum, and additional wing and leg bones, most of which were incomplete—were discovered at the site in 2021. This allowed identification of additional fossils from the same species in collections from Cooper Creek (Lake Eyre Basin, SA), Victoria Fossil Cave (Naracoorte, SA) and Wellington Caves (Wellington, NSW). Dynatoaetus has variable similarity across elements to those of living species in the Perninae, Gypaetinae, Circaetinae and Aegypiinae. Parsimony and Bayesian phylogenetic analyses of combined morphological and DNA data resolved it as the immediate sister-group to the Aegypiinae within the Circaetinae + Aegypiinae clade. The robust and eagle-like morphology of the lower hindlimbs suggest that the species was a predator, rather than a scavenger, and thus functionally similar to large circaetines such as the Philippine Eagle Pithecophaga jefferyi. Furthermore, this new species is the largest known bird of prey from Australia, much larger than the modern Wedge-Tailed Eagle Aquila audax. It is outsized in Australasia only by female Hieraaetus moorei (the extinct Haast’s Eagle from New Zealand). It is inferred to have been Australia’s top terrestrial avian predator during the Pleistocene, ranging from arid inland Australia to the more temperate coast, and likely became extinct around the time of the megafaunal mass extinction which peaked around 50 Ka. Its extinction in the late Pleistocene, along with the recently described scavenging vulture Cryptogyps lacertosus, marked a distinct decline in the diversity and function of Australia’s raptor guild.