jModelTest: Phylogenetic Model Averaging

Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae)

The genus Neocinnamomum is considered to be one of the most enigmatic groups in Lauraceae, mainly distributed in tropical and subtropical regions of Southeast Asia. The genus contains valuable oilseed and medicinal tree species. However, there are few studies on the genus Neocinnamomum at present, and its interspecific relationship is still unclear. In order to explore the genetic structure and evolutionary characteristics of the Neocinnamomum chloroplast genome and to resolve the species relationships within the genus, comparative genomic and phylogenetic analyses were performed on the whole chloroplast genome sequences of 51 samples representing seven Neocinnamomum taxa. The whole Neocinnamomum chloroplast genome size ranged from 150,753-150,956 bp, with a GC content of 38.8%-38.9%. A total of 128 genes were annotated within the Neocinnamomum chloroplast genome, including 84 protein coding genes, 8 rRNA genes, and 36 tRNA genes. Between 71-82 SSRs were detected, among which A/T base repeats were the most common. The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values > 0.004. Based on the whole chloroplast genome phylogenetic tree, the phylogenetic relationships among the seven Neocinnamomum taxa were determined. N. delavayi and N. fargesii were the most closely related species, and N. lecomtei was identified as the most basal taxon. In this study, the characteristics and sequence variation of the chloroplast genomes of seven Neocinnamomum taxa were revealed, and the genetic relationship among the species was clarified. The results of this study will provide a reference for subsequent molecular marker development and phylogenetic research of Neocinnamomum.

Morphological and Phylogenetic Characterization of Five Novel Nematode-Trapping Fungi (Orbiliomycetes) from Yunnan, China

Nematode-trapping fungi are widely studied due to their unique morphological structure, survival strategy, and potential value in the biological control of harmful nematodes. During the identification of carnivorous fungi preserved in our laboratory, five novel nematode-trapping fungi were established and placed in the genera Arthrobotrys and Drehslerella based on morphological and multigene (ITS, TEF, and RPB2) phylogenetic analyses. A. hengjiangensis sp. nov. and A. weixiensis sp. nov. are characterized by producing adhesive networks to catch nematodes. Dr. pengdangensis sp. nov., Dr. tianchiensis sp. nov., and Dr. yunlongensis sp. nov. are characterized by producing constricting rings. Morphological descriptions, illustrations, taxonomic notes, and phylogenetic analysis are provided for all new taxa; a key for Drechslerella species is listed; and some deficiencies in the taxonomy and evolution study of nematode-trapping fungi are also discussed herein.

Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition

In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.

Biogeographic diversification of Actaea (Ranunculaceae): Insights into the historical assembly of deciduous broad-leaved forests in the Northern Hemisphere

The deciduous broad-leaved forests (DBLFs) cover large temperate and subtropical high-altitude regions in the Northern Hemisphere. They are home to rich biodiversity, especially to numerous endemic and relict species. However, we know little about how this vegetation in the Northern Hemisphere has developed through time. Here, we used Actaea (Ranunculaceae), an herbaceous genus almost exclusively growing in the understory of the Northern Hemisphere DBLFs, to shed light on the historical assembly of this biome in the Northern Hemisphere. We present a complete species-level phylogenetic analysis of Actaea based on five plastid and nuclear loci. Using the phylogenetic framework, we estimated divergence times, ancestral ranges, and diversification rates. Phylogenetic analyses strongly support Actaea as monophyletic. Sections Podocarpae and Oligocarpae compose a clade, sister to all other Actaea. The sister relationship between sections Chloranthae and Souliea is strongly supported. Section Dichanthera is not monophyletic unless section Cimicifuga is included. Actaea originated in East Asia, likely the Qinghai-Tibet Plateau, in the late Paleocene (c. 57 Ma), and subsequently dispersed into North America in the middle Eocene (c. 43 Ma) via the Thulean bridge. Actaea reached Europe twice, Japan twice, and Taiwan once, and all these five colonization events occurred in the late Miocene-early Pliocene, a period when sea level dropped. Actaea began to diversify at c. 43 Ma. The section-level diversification took place at c. 27-37 Ma and the species-level diversification experienced accelerations twice, which occurred at c. 15 Ma and c. 5 Ma, respectively. Our findings suggest that the Northern Hemisphere DBLFs might have risen in the middle Eocene and further diversified in the late Eocene-Oligocene, middle Miocene and early Pliocene, in association with climatic deterioration during these four periods.

Genomic insights into the genetic basis of eagle-beak jaw, large head, and long tail in the big-headed turtle

The big-headed turtle (Platysternon megacephalum) is an endemic chelonian species in Asia. Unlike most other turtles in the world, P. megacephalum is characterized with eagle-beak jaw, large head, and long tail. Although these unique characteristics are well recognized, the underlying genetic basis remains largely elusive. Here, we performed comparative genomic analysis between P. megacephalum and other representative species, aiming to reveal the genetic basis of the unique morphological features. Our results revealed that the eagle-beak jaw is most likely enabled by combined effects of expansion of SFRP5, extraction of FGF11, and mutation of both ZFYVE16 and PAX6. Large head is supported by mutations of SETD2 and FGRF2 and copy number variations of six head circumference modulation-related genes (TGFBR2, Twist2, Rdh10, Gas1, Chst11, and SNAP25). The long tail is probably involved in a genetic network comprising Gdf11, Lin 28, and HoxC12, two of which showed a consistent expression pattern with a model organism (mice). These findings suggest that expansion, extraction, and mutation of those genes may have profound effects on unique phenotypes of P. megacephalum.

Morphological and molecular characterization of Contracaecum australe (Nematoda: Anisakidae) parasitizing Phalacrocorax brasilianus (Aves: Phalacrocoracidae) on the north coast of Brazil

For the first time in Brazil, Contracaecum australe is recorded parasitizing Phalacrocorax brasilianus (Aves, Suliformes, Phalacrocoracidae) from the Marine Extractive Reserve of Soure on Marajó Island, Brazilian Amazon. Its morphology revealed a body with a transversally striated cuticle, smooth or slightly cleft interlabia, lips with auricles, labial papillae, and conspicuous amphids. In males, the presence of the median papilla on the upper lip of the cloaca and spicules that reach almost half of the body of the parasite. These morphological characters, added to the number and distribution of the pre- and postcloacal papillae of the male specimens, and supported by the molecular phylogeny from the analysis of the ITS-1, 5.8S and ITS-2 genes, allowed the identification of these parasites.

Genetic Characterization of Echinococcus granulosus sensu stricto Isolated from Human Cysts from Sardinia, Italy

This study involved 20 patients affected by cystic echinococcosis (CE) who were referred to different hospitals of Sardinia (Italy) from 2017 to 2022. By means of a multidisciplinary approach, diagnosis was confirmed for CE in 18 patients and for different aetiologies in two subjects. Moreover, serology was positive for 15 subjects. Since multiple CE cysts were found in five patients, a total of 27 lesions were collected; however, only one for each patient was investigated for genetic characterization of E. granulosus s.s. DNA isolates. Our results included 15 fertile cysts that underwent DNA extraction and amplification by three different PCRs targeting nuclear (calreticulin) and mitochondrial genes (cox1 and nad5). DNA was sequenced, and by neighbour-joining phylogenetic trees we determined 10 G1 and five G3 genotypes previously reported in Sardinia. These sequences were used to construct a network, along with those circulating in Mediterranean areas. The haplotype network calculated on cox1 evidenced seven different haplotypes of the 15 isolates, with SAR2 the most represented, carried by seven cysts, and SAR17 never described in the Mediterranean area. Meanwhile, the nad5 sequences showed the most common haplotype as nd5SAR7, as well as two new haplotypes not previously described, nd5SAR13, isolated from a Sardinian patient, and nd5SAR14, isolated from a Romanian patient.

Phylogenetic analysis and temporal diversification of the tribe Alsineae (Caryophyllaceae) with the description of three new genera, Hesperostellaria, Reniostellaria and Torreyostellaria

Alsineae are one of the most taxonomically difficult tribes in Caryophyllaceae and consist of over 500 species distributed in the northern temperate zone. Recent phylogenetic results have improved our understanding on the evolutionary relationships among Alsineae members. Nevertheless, there are still some unresolved taxonomic and phylogenetic problems at the generic level, and the evolutionary history of major clades within the tribe was unexplored to date. In this study, we carried out phylogenetic analyses and divergence time estimation of Alsineae using the nuclear ribosomal internal transcribed spacer (nrITS) and four plastid regions (matK, rbcL, rps16, trnL-F). The present analyses yielded a robustly supported phylogenetic hypothesis of the tribe. Our results showed that the monophyletic Alsineae are strongly supported to be the sister of Arenarieae, and the inter-generic relationships within Alsineae were mostly resolved with strong support. Both molecular phylogenetic and morphological evidence supported the Asian species Stellaria bistylata and the two North American species Pseudostellaria jamesiana and Stellaria americana all should be recognized as new monotypic genera respectively, and three new genera Reniostellaria, Torreyostellaria, and Hesperostellaria were thereby proposed here. Additionally, molecular and morphological evidence also supported the proposal of the new combination Schizotechium delavayi. Nineteen genera were accepted within Alsineae and a key to these genera was provided. Molecular dating analysis suggested that Alsineae splitted from its sister tribe at ca. 50.2 million-years ago (Ma) during the early Eocene and began to diverge at ca. 37.9 Ma during the late Eocene, and divergent events within Alsineae occurred mainly since the late Oligocene. Results from the present study provide insights into the historical assembly of herbaceous flora in northern temperate regions.

Phylogeny and ultrastructure of Myxobolus rangeli n. sp. (Myxozoa, Bivalvulida), a histozoic parasite in Siluriformes fish from the Amazon region

A new species of Myxobolus parasitizing the arterial bulb and cardiac musculature of the freshwater fish Pimelodus ornatus Kner, 1858, from the Arari river in the municipality of Cachoeira do Arari, island of Marajó, Pará, Brazil, was described. In the present study, the observed prevalence of myxozoan parasites in the heart tissue of the hosts was 20% (6/30). The myxozoans observed had mature biconvex spores, slightly rounded, an anterior end with two pyriform polar capsules and a posterior end with very evident sporoplasm, measuring 8 ± 0.2 μmin length. The spore width was 5.8 ± 0.4 μm, with a thickness of 3.4 ± 0.2μm. The length of the polar capsules was 3.6 ± 0.3 μm and the width was 1.2 ± 0.2μm, with 6 to 7 turns of the polar filament. The divergences observed, regarding the morphometric and genetic structure of SSU rDNA, in relation to other Myxobolidae already described in the literature, confirm the description of the new species Myxobolus rangeli n. sp.

Xenasmatellales ord. nov. and Xenasmatellaceae fam. nov. for Xenasmatella (Agaricomycetes, Basidiomycota)

In the era of molecular phylogeny as dominant evidence in fungal taxonomy, the taxonomic framework of fungi adopted from morphological characteristics has been largely updated. Compared with other fungal groups, macrofungi underwent fewer updates at the order and higher level. In this study, the taxonomic placement of a poorly known macro-basidiomycetous genus Xenasmatella is studied. Phylogenetic and molecular clock analyses inferred from a seven-locus dataset support that the genus represents an order rank lineage. Accordingly, a monotypic order Xenasmatellales and a monotypic family Xenasmatellaceae are newly introduced for Xenasmatella within Agaricomycetes. The species diversity and relationships of Xenasmatella are further clarified with the aid of the phylogenetic analysis inferred from a four-locus dataset. In association with morphological characteristics, a new species Xenasmatella hjortstamii is described. Moreover, the distribution of Xenasmatella ailaoshanensis, X. gossypina, and X. wuliangshanensis previously known only from type localities in Yunnan Province, China are expanded. In addition, two unnamed single-specimen lineages of Xenasmatella from Victoria State, Australia and Sichuan, China are revealed, likely representing two potential new species of this genus. In summary, the current study updates the taxonomic framework of Agaricomycetes and provides a crucial supplement for comprehensively understanding the evolutionary history of this fungal class.

Novel Harzia ixtarensis Fungus on Annona cherimola Fruit in Mexico and Its Synergistic Relationship with Colletotrichum fragariae

Since 2005 in Íxtaro, Michoacán, symptoms of Harzia infection have been observed on immature Annona cherimola fruit with Colletotrichum fragariae-induced anthracnose lesions and mummified fruit. This study aimed to identify the Harzia sp. and evaluate its pathogenicity. Four isolates were obtained from fruit exhibiting symptoms, cultured in four types of agar under various conditions, and characterized based on concatenated internal transcribes spacer (ITS) + large subunit and ITS + small subunit sequences. Additionally, the isolates were compared with two CBS species (two-type strains and two isolates) of Harzia patula and H. tenella under the same conditions as the Harzia isolates, and all known Harzia spp. in culture were included in two phylogenetic analyses. H. ixtarensis sp. nov. was proposed. Compared with H. patula CBS isolate 121524 which was the most closely phylogenetically related species, H. ixtarensis was characterized by slower colony growth (white to salmonish-beige), different percentages of two forms of conidia (elongated and globose; unicellular and hyaline to subhyaline), and smaller conidia. The conidia mainly germinated with two hyaline tubes without an appressorium. In situ inoculations (1 × 10⁶ ml^-1 conidia suspension) of fruit showed that fruit with wounds developed larger lesions than those without wounds. Harzia inoculation on anthracnose lesions (induced by prior inoculation with C. fragariae) produced larger anthracnose lesions than C. fragariae alone. When C. fragariae or H. ixtarensis was inoculated alone, the lesion size was 51 and 99% smaller, respectively, indicating synergy between C. fragariae and H. ixtarensis. Thus, H. ixtarensis may have a parasitic-synergistic and necrotrophic lifestyle, and exhibited symptoms on anthracnose lesions.

Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil

To increase knowledge on Brevundimonas pathogens, we conducted in-depth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to β-lactams (penP, blaTEM-16, and blaBKC-1) and aminoglycosides [strA, strB, aac(6')-Ib, and aac(6')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas.

Species richness disparity in tropical terrestrial herbaceous floras: evolutionary insight from Collabieae (Orchidaceae)

Species richness is spatially heterogeneous even in the hyperdiverse tropical floras. The main cause of uneven species richness among the four tropical regions are hot debated. To date, higher net diversification rates and/or longer colonization time have been usually proposed to contribute to this pattern. However, there are few studies to clarify the species richness patterns in tropical terrestrial floras. The terrestrial tribe Collabieae (Orchidaceae) unevenly distributes in the tropical regions with a diverse and endemic center in Asia. Twenty-one genera 127 species of Collabieae and 26 DNA regions were used to reconstruct the phylogeny and infer the biogeographical processes. We compared the topologies, diversification rates and niche rates of Collabieae and regional lineages on empirical samplings and different simulated samplings fractions respectively. Our results suggested that the Collabieae originated in Asia at the earliest Oligocene, and then independently spread to Africa, Central America, and Oceania since the Miocene via long-distance dispersal. These results based on empirical data and simulated data were similar. BAMM, GeoSSE and niche analyses inferred that the Asian lineages had higher net diversification and niche rates than those of Oceanian and African lineages on the empirical and simulated analyses. Precipitation is the most important factor for Collabieae, and the Asian lineage has experienced more stable and humid climate, which may promote the higher net diversification rate. Besides, the longer colonization time may also be associated with the Asian lineages' diversity. These findings provided a better understanding of the regional diversity heterogeneity in tropical terrestrial herbaceous floras.

Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3 - 6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.

Retrospective Phylodynamic and Phylogeographic Analysis of the Human Papillomavirus 16 E6 Gene in the Mediterranean Region

Human papillomavirus 16 (HPV16) is considered to be strongly correlated with the development of cervical cancer. Among the 8 HPV16 genes, the E6 constitutes a remarkable marker to follow the evolutionary history and spatial phylodynamics of HPV16 in the Mediterranean basin. Thus, this work aims to decipher the major evolutionary events and crosstalks in the Mediterranean basin with a focus on Tunisian strains regarding the E6 oncogene. In this study, we first extracted the available and annotated Mediterranean strains of HPV16 E6 gene sequences (n = 155) from the NCBI nucleotide database. These sequences were aligned, edited, and used for the downstream phylogenetic analyses. Finally, a Bayesian Markov Chain Monte Carlo approach was applied to reconstruct the evolutionary history of HPV16 migration. Our results showed that the HPV circulating in Tunisia derived from a Croatian ancestor around the year 1987. This starting point spreads to most European countries to reach northern Africa through the Moroccan gateway in 2004.

Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications

BACKGROUND

Ceratostigma, a genus in the Plumbaginaceae, is an ecologically dominant group of shrubs, subshrub and herb mainly distributed in Qinghai-Tibet Plateau and North China. Ceratostigma has been the focal group in several studies, owing to their importance in economic and ecological value and unique breeding styles. Despite this, the genome information is limited and interspecific relationships within the genus Cerotastigma remains unexplored. Here we sequenced, assembled and characterized the 14 plastomes of five species, and conducted phylogenetic analyses of Cerotastigma using plastomes and nuclear ribosomal DNA (nrDNA) data.

RESULTS

Fourteen Cerotastigma plastomes possess typical quadripartite structures with lengths from 164,076 to 168,355 bp that consist of a large single copy, a small single copy and a pair of inverted repeats, and contain 127-128 genes, including 82-83 protein coding genes, 37 transfer RNAs and eight ribosomal RNAs. All plastomes are highly conservative and similar in gene order, simple sequence repeats (SSRs), long repeat repeats and codon usage patterns, but some structural variations in the border of single copy and inverted repeats. Mutation hotspots in coding (Pi values > 0.01: matK, ycf3, rps11, rps3, rpl22 and ndhF) and non-coding regions (Pi values > 0.02: trnH-psbA, rps16-trnQ, ndhF-rpl32 and rpl32-trnL) were identified among plastid genomes that could be served as potential molecular markers for species delimitation and genetic variation studies in Cerotastigma. Gene selective pressure analysis showed that most protein-coding genes have been under purifying selection except two genes. Phylogenetic analyses based on whole plastomes and nrDNA strongly support that the five species formed a monophyletic clade. Moreover, interspecific delimitation was well resolved except C. minus, individuals of which clustered into two main clades corresponding to their geographic distributions. The topology inferred from the nrDNA dataset was not congruent with the tree derived from the analyses of the plastid dataset.

CONCLUSION

These findings represent the first important step in elucidating plastome evolution in this widespread distribution genus Cerotastigma in the Qinghai-Tibet Plateau. The detailed information could provide a valuable resource for understanding the molecular dynamics and phylogenetic relationship in the family Plumbaginaceae. Lineage genetic divergence within C. minus was perhaps promoted by geographic barriers in the Himalaya and Hengduan Mountains region, but introgression or hybridization could not be completely excluded.

Taxonomy of Hyphodermella: a case study to show that simple phylogenies cannot always accurately place species in appropriate genera

The genus is a special and crucial taxonomic rank compared with others above the species level, because a species has to be placed in a certain genus instead of any other higher ranks. With more and more new species being described, the placements of their generic position are sometimes incorrect due to the simple phylogenies resulting from inappropriate sampling. Here, we focus on the taxonomy of a small wood-inhabiting fungal genus Hyphodermella. With the most comprehensive sampling to date, the phylogenetic position of Hyphodermella within Phanerochaetaceae is rearranged by employing the same ITS and nLSU regions as in previous studies and also the ITS, nLSU, rpb1, rpb2 and tef1α regions. Three species are excluded from Hyphodermella: H. poroides is placed in a newly introduced monotypic genus Pseudohyphodermella, while H. aurantiaca and H. zixishanensis are transferred to Roseograndinia. Hyphodermella suiae is described as a new species from South China and Vietnam. Keys to eight species in Hyphodermella and five in Roseograndinia are provided. Beyond solving the taxonomic issue of Hyphodermella itself, the current study also aims to suggest that all fungal taxonomists especially beginners should keep in mind to sample as many comprehensive taxa as possible in phylogenetic analyses.

Culture-Independent Single-Cell PacBio Sequencing Reveals Epibiotic Variovorax and Nucleus Associated Mycoplasma in the Microbiome of the Marine Benthic Protist Geleia sp. YT (Ciliophora, Karyorelictea)

Microbes in marine sediments constitute up to five-sixths of the planet's total biomass, but their diversity is little explored, especially for those forming associations with unicellular protists. Heterotrophic ciliates are among the most dominant and diversified marine benthic protists and comprise hotspot niches of bacterial colonization. To date, studies using culture-independent single-cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent, even for the most ubiquitous species. Here, we characterize the major bacterial groups associated with a representative marine benthic ciliate, Geleia sp. YT, collected directly from the coastal zone of Yantai, China. PacBio sequencing of the nearly full-length 16Sr RNA genes was performed on single cells of Geleia. Fluorescence in situ hybridization (FISH) analysis with genus-specific probes was further applied to locate the dominant bacterial groups. We identified a Variovorax-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host. We provide evidence of a nucleus-associated bacterium related to the human pathogen Mycoplasma, which appeared prevalently in the local populations of Geleia sp. YT for 4 months. The most abundant bacterial taxa associated with Geleia sp. YT likely represent its core microbiome, hinting at the important roles of the ciliate-bacteria consortium in the marine benthos. Overall, this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic ciliate and its symbioses.

Multiple Lineages of Hantaviruses Harbored by the Iberian Mole (Talpa occidentalis) in Spain

The recent detection of both Nova virus (NVAV) and Bruges virus (BRGV) in European moles (Talpa europaea) in Belgium and Germany prompted a search for related hantaviruses in the Iberian mole (Talpa occidentalis). RNAlater^®-preserved lung tissue from 106 Iberian moles, collected during January 2011 to June 2014 in Asturias, Spain, were analyzed for hantavirus RNA by nested/hemi-nested RT-PCR. Pairwise alignment and comparison of partial L-segment sequences, detected in 11 Iberian moles from four parishes, indicated the circulation of genetically distinct hantaviruses. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, demonstrated three distinct hantaviruses in Iberian moles: NVAV, BRGV, and a new hantavirus, designated Asturias virus (ASTV). Of the cDNA from seven infected moles processed for next generation sequencing using Illumina HiSeq1500, one produced viable contigs, spanning the S, M and L segments of ASTV. The original view that each hantavirus species is harbored by a single small-mammal host species is now known to be invalid. Host-switching or cross-species transmission events, as well as reassortment, have shaped the complex evolutionary history and phylogeography of hantaviruses such that some hantavirus species are hosted by multiple reservoir species, and conversely, some host species harbor more than one hantavirus species.

Global population genetic structure and lineage differentiation of the stable fly, Stomoxys calcitrans

The bloodsucking fly, Stomoxys calcitrans (Diptera: Muscidae), is a cosmopolitan pest that transmits potential pathogens mechanically. We conduct phylogeographic analyses of S. calcitrans to resolve its global population genetic structure for establishing baseline of molecular studies. Results from mitochondrial gene suggested that the major divergence of S. calcitrans predominantly occurred 0.32-0.47 million years ago (Mya) and the subsequent diversifications took place during 0.13-0.27 Mya. The Ethiopian region was deduced as the most likely origin of S. calcitrans and the Nearctic lineages were considered to have originated from Oriental or Palaearctic regions. Our results further revealed that each biogeographic region of S. calcitrans likely maintains its genetic specialty, and yet, those non-monophyletic relationships were possibly caused by ancestral retention, dispersal with mammals, long-distance migration, and the international livestock industries. Moreover, the three highly diverged Ethiopian lineages may be putative cryptic species that require clarification of their veterinary importance. Unravelling the genetic structure of stable fly and preventing gene flow among biogeographic regions through anthropogenic activities are thus pivotal in livestock industry administration, particularly genetic exchange among differentiated lineages that might lead to the consequence of ecological trait alterations.

Low genetic diversity and population structuring of Amblyomma hebraeum and Rickettsia africae from coastal and inland regions in the Eastern Cape Province of South Africa

Amblyomma hebraeum is the main vector of Rickettsia africae, the causative agent of African tick bite fever in southern Africa. Because pathogen dispersal is known to be influenced by tick adaptations to climate or host species, this study aimed to analyse the genetic diversity of A. hebraeum and R. africae infection of ticks collected from cattle in the Eastern Cape province of South Africa. DNA was extracted, amplified, and sequenced for the COI and ITS2 markers from A. hebraeum samples and the 17 kDa and ompA genes for rickettsial detection. Between six and ten haplotypes were identified from 40 COI and 31 ITS2 sequences; however, no population structuring was observed among sites (ΦST = 0.22, p < 0.05). All A. hebraeum isolates clustered with southern Africa GenBank isolates. Rickettsia africae was detected in 46.92% (95% CI = 41%-53%, n = 260) of ticks. All R. africae isolates clustered with strain PELE and Chucks, which were reported previously from South Africa. These results confirm that A. hebraeum populations are undergoing a recent population expansion driven by cattle movement, facilitating local and long dispersal events across the Eastern Cape province.

Oreocharis oriolus, a new species of Gesneriaceae in a sclerophyllous oak community from Yunnan, Southwest China

Oreocharis oriolus, a new species of Gesneriaceae in a sclerophyllous oak community from Yunnan, Southwest China, is described and illustrated. Morphologically, it resembles both O. forrestii and O. georgei, while it is distinct in combined characters of wrinkled leaves, peduncle and pedicel covered with whitish and egladular villous hairs, bract lanceolate and nearly glabrescent adaxially, and staminode absent. Molecular phylogenetic analysis based on nuclear ribosomal internal transcribed spacer (nrITS) and chloroplast DNA fragment (trnL-F) of 61 congeneric species also supported O. oriolus as a new species while it was nested with O. delavayi. It was currently assessed as 'Critically Endangered' (CR) regarding to its small-sized population and narrow distribution following the IUCN categories and criteria.

The identity of Tokays (Squamata: Gekkonidae: Gekko) from Hong Kong

The Tokay gecko (Gekko gecko), found throughout Southeast Asia and India, is a heavily harvested species of high commercial value. Recent studies have supported the elevation of the black morph of Tokay gecko, found only in southern China and northern Vietnam, to the species Gekko reevesii. Previous genetic studies focused on specimens of G. reevesii from southwestern populations. Hong Kong, in southeastern China, has native populations of G. reevesii. To verify the identity of G. reevesii in Hong Kong, we employed three mitochondrial genes (COI, Cytb & ND2) and constructed a matrilineal genealogy using other specimens from Guangxi (southwestern China) and northern Vietnam, as well as G. gecko from a wide range of Southeast Asian countries. Our study confirmed that G. reevesii occurs naturally in Hong Kong, but one exotic population of G. gecko, likely a translocation from international trade, was also revealed. Our study did not reject the species ranking of G. reevesii. Moreover, like previous studies, we recovered a paraphyletic G. gecko, which may reflect a species complex, hybridization or incomplete lineage sorting. More extensive sampling of the two species over a broader range of their asserted distribution together with the use of both mitochondrial and nuclear DNA are required to better investigate their biogeography.

The complete chloroplast genome sequence of a warm season ornamental grass, Cenchrus alopecuroides Thunb. 1794 (Poaceae)

Cenchrus alopecuroides Thunb. 1794 is a warm-season ornamental grass with glossy foliage and showy inflorescence, which is widely distributed from eastern Asia to Australia. Although this species is of great economic importance, little genomic sequence data are available. Here, we report the complete chloroplast genome sequence of C. alopecuroides, which provides valuable plastid genomic resources for further studies on this ornamental grass. The chloroplast genome of C. alopecuroides was 138,053 bp in length and exhibited a typical quadripartite structure, which comprised a pair of inverted repeat regions (22,331 bp) separated by a large (81,177 bp) and a small single copy (12,214 bp) region. In total, 110 unique genes were annotated in the chloroplast genome, containing 76 protein-coding genes, 30 transfer RNAs and four ribosomal RNAs. The overall GC content of the chloroplast genome was 38.6%. Phylogenetic analysis based on 11 whole-chloroplast genome sequences of Cenchrus species suggested that C. alopecuroides and C. compressus were sisters to each other and joint sisters to C. clandestinus.

Mitochondrial DNA and local ecological knowledge reveal two lineages of leatherback turtle on the beaches of Oaxaca, Mexico

Despite multiple conservation efforts of the Mexican government, the leatherback turtle is at serious risk of extinction. In this study, we investigated the possible presence of a genetic bottleneck that could prevent the recovery of this species and compared these findings with those of the olive ridley turtle, which is in true recovery. Our results confirmed that a demographic change occurred in the past and the presence of two different leatherback turtle lineages that diverged approximately 13.5 million years ago. Local ecological knowledge (LEK) also described the presence of these two lineages and warned that one is at higher risk of extinction than the other. Genetic analysis confirmed 124 mutations between the two lineages, and much lower genetic diversity in one lineage than the other. Our study highlights and substantiates the power of mixing LEK, environmental history, and genetics to better understand conservation challenges of highly threatened species such as the leatherback turtle. Moreover, we report a new lineage of the leatherback turtle which may represent a distinct species. Future studies should focus on morphological, ecological, biogeographical, evolutionary and conservation perspectives for the analysis of the new lineage.

Identification and pathogenicity of Aurifilum species (Cryphonectriaceae, Diaporthales) on Terminalia species in Southern China

The family of Cryphonectriaceae (Diaporthales) contains many important tree pathogens and the hosts are wide-ranging. Tree species of Terminalia were widely planted as ornamental trees alongside city roads and villages in southern China. Recently, stem canker and cracked bark were observed on 2-6 year old Terminalianeotaliala and T.mantaly in several nurseries in Zhanjiang City, Guangdong Province, China. Typical conidiomata of Cryphonectriaceae fungi were observed on the surface of the diseased tissue. In this study, we used DNA sequence data (ITS, BT2/BT1, TEF-1α, rpb2) and morphological characteristics to identify the strains from Terminalia trees. Our results showed that isolates obtained in this study represent two species of Aurifilum, one previously described species, A.terminali, and an unknown species, which we described as A.cerciana sp. nov. Pathogenicity tests demonstrated that both A.terminali and A.cerciana were able to infect T.neotaliala and two tested Eucalyptus clones, suggesting the potential for Aurifilum fungi to become new pathogens of Eucalyptus.

Phylogeny, Taxonomy and Evolutionary Trade-Offs in Reproductive Traits of Gomphoid Fungi (Gomphaceae, Gomphales)

Although functional ecology is a well-established field, our understanding of the evolutionary and ecological significance of the reproductive traits in macrofungi is still limited. Here, we reconstructed a phylogeny tree of gomphoid fungi in the narrower sense, including the species of the genera Gomphus and Turbinellus and used it to uncover the evolution of reproductive traits. Our analyses indicated that fungal fruit bodies and spores did not enlarge at a steady rate over time. Early gomphoid fungi essentially maintained their fruit body size, spore size and spore shape through the Mesozoic. In the Cenozoic, gomphoid fungi acquired significantly larger and more spherical spores by simultaneously expanding in length and width, with the fruit body size first decreasing and then enlarging. We argue that these trade-offs were driven by the effect of biological extinction and the dramatic climate changes of the Cenozoic. Gomphoid fungi initially increased in spore size and fruit body number as extinction survivors filled vacant niches. Both fruit bodies and spores eventually became larger as ecosystems saturated and competition intensified. One new species of Gomphus and nine new species of Turbinellus are described.

Complete Chloroplast Genome Determination of Ranunculus sceleratus from Republic of Korea (Ranunculaceae) and Comparative Chloroplast Genomes of the Members of the Ranunculus Genus

Ranunculus sceleratus (family: Ranunculaceae) is a medicinally and economically important plant; however, gaps in taxonomic and species identification limit its practical applicability. This study aimed to sequence the chloroplast genome of R. sceleratus from Republic of Korea. Chloroplast sequences were compared and analyzed among Ranunculus species. The chloroplast genome was assembled from Illumina HiSeq 2500 sequencing raw data. The genome was 156,329 bp and had a typical quadripartite structure comprising a small single-copy region, a large single-copy region, and two inverted repeats. Fifty-three simple sequence repeats were identified in the four quadrant structural regions. The region between the ndhC and trnV-UAC genes could be useful as a genetic marker to distinguish between R. sceleratus populations from Republic of Korea and China. The Ranunculus species formed a single lineage. To differentiate between Ranunculus species, we identified 16 hotspot regions and confirmed their potential using specific barcodes based on phylogenetic tree and BLAST-based analyses. The ndhE, ndhF, rpl23, atpF, rps4, and rpoA genes had a high posterior probability of codon sites in positive selection, while the amino acid site varied between Ranunculus species and other genera. Comparison of the Ranunculus genomes provides useful information regarding species identification and evolution that could guide future phylogenetic analyses.

Genetic diversity, distribution, and structure of Bemisia tabaci whitefly species in potential invasion and hybridization regions of East Africa

Outbreaks of whitefly, Bemisia tabaci species in East and Central Africa, have become increasingly prevalent during the previous 25 years and are responsible for driving the spread of plant-virus diseases, such as cassava mosaic disease and cassava brown steak disease. Epidemics of these diseases have expanded their ranges over the same period, spreading from Uganda into other sub-Saharan African countries. It was hypothesised that a highly abundant 'invader' population of B. tabaci was responsible for spreading these diseases from Uganda to neighbouring countries and potentially hybridising with the resident cassava B. tabaci populations. Here, we test this hypothesis by investigating the molecular identities of the highly abundant cassava B. tabaci populations from their supposed origin in Uganda, to the northern, central, eastern and coastal regions of Tanzania. Partial mitochondrial cytochrome oxidase I (mtCOI) barcoding sequences and nuclear microsatellite markers were used to analyse the population genetic diversity and structure of 2734 B. tabaci collected from both countries and in different agroecological zones. The results revealed that: (i) the putative SSA1 species is structured according to countries, so differ between them. (ii) Restricted gene flow occurred between SSA1-SG3 and both other SSA1 subgroups (SG1 and SG2), even in sympatry, demonstrating strong barriers to hybridization between those genotypes. (iii) Not only B. tabaci SSA1-(SG1 and SG2) was found in highly abundant (outbreak) numbers, but B. tabaci SSA1-SG3 and the Indian Ocean (IO) species were also recorded in high numbers in several sites in Tanzania. (iv) The SSA1-(SG1 and SG2) species was distributed in both countries, but in Tanzania, the B. tabaci IO and SSA1-SG3 species predominated. These data confirm that multiple, local Tanzanian B. tabaci species produce highly abundant populations, independent of the spread of the putative invasive B. tabaci SSA1-(SG1 and SG2) populations.

Insights into the Genetic Diversity of Leishmania (Viannia) panamensis in Panama, Inferred via Multilocus Sequence Typing (MLST)

Leishmaniasis is a disease caused by parasites of the genus Leishmania and transmitted by sand fly vectors. Tegumentary leishmaniasis is the most prevalent clinical outcome in Latin America, afflicting people from 18 countries. In Panama, the annual incidence rate of leishmaniasis is as high as 3000 cases, representing a major public health problem. In endemic regions, L. panamensis is responsible for almost eighty percent of human cases that present different clinical outcomes. These differences in disease outcomes could be the result of the local interplay between L. panamensis variants and human hosts with different genetic backgrounds. The genetic diversity of L. panamensis in Panama has only been partially explored, and the variability reported for this species is based on few studies restricted to small populations and/or with poor resolutive markers at low taxonomic levels. Accordingly, in this study, we explored the genetic diversity of sixty-nine L. panamensis isolates from different endemic regions of Panama, using an MLST approach based on four housekeeping genes (Aconitase, ALAT, GPI and HSP70). Two to seven haplotypes per locus were identified, and regional differences in the genetic diversity of L. panamensis were observed. A genotype analysis evidenced the circulation of thirteen L. panamensis genotypes, a fact that might have important implications for the local control of the disease.

Genomic characterization and Phylogenetic evolution of the canine parvoviruses in Iranian dogs, a nationwide study: CPV evolutionary analysis in Iran

Canine Parvo Virus 2(CPV-2) culminated in lots of fatalities in domestic dogs since its emergence in 1978. Mainly, it is responsible for severe hemorrhagic diarrhea, vomiting, and dehydration. CPV-2 has three main variants known 2a, 2b, and 2c. Due to the necessity of monitoring the evolutionary parameters of the virus, and also the lack of comprehensive study of CPV2 in Iran, this study is done for the first time in this country not only to characterize Iranian CPV genomes but also to study the evolutionary parameters and phylodynamics of CPV. The phylogenetic trees were constructed using the Maximum Likelihood (ML) method. By the use of the Bayesian Monte Carlo Markov Chain (BMCMC) method, evolutionary analysis and phylodynamics of the virus were investigated. Phylogenetic results showed that all Iranian isolates were classified in the CPV-2a variant. The central part of Iran was suggested to be the origin of the virus, especially the Alborz province. Before its prevalence throughout the country, the virus circulated in the central part, in Thran, Karaj, and Qom. Mutational analysis showed a positive selection pressure of CPV-2a. Investigating the evolutionary parameters of the virus proposed 1970 to be the date of birth of the virus, with a 95% credible interval between 1953 and 1987. The effective number of infections increased dramatically from 2012 to 2015, then faced a slightly decreasing trend from 2015 to 2019. A considerable up warding pattern was witnessed from the middle of 2019, which can be taken as a concern about the risk of vaccination failure.

Multi-loci phylogeny and morphological evidence support the recognition of Januaria (Spermacoceae, Rubiaceae), a new monospecific genus endemic to the North of Minas Gerais (Brazil)

Januaria is described as a new monospecific genus of Rubiaceae, based on material from Januária, northern Minas Gerais, Brazil. The new taxon is endemic to Brazil, occurring in a vegetation type that is known locally as "carrasco", in the southern limit of the Caatinga biome. Morphological (including palynological and SEM analyses) and molecular phylogenetic analyses based on nuclear (ETS, ITS) and plastid (atpB-rbcL, peth, rps16, trnL-trnF) sequence data were performed in the Spermacoce clade (tribe Spermacoceae). The molecular position and morphological features (a unique fruit dehiscence type, and pollen exine with simple reticulum) support Januaria as a new genus, with Mitracarpus as sister group, from which it differs principally in calyx morphology, corolla shape, and fruit dehiscence. Additionally, a further comparison with other morphologically similar genera is presented. We provide a formal description of Januaria, together with a distribution map and comments on its conservation. In addition, a discussion about the Brazilian endemics of the Spermacoce clade is given, also with a key to all the genera of this group present in the country.

Genome size estimation and its associations with body length, chromosome number and evolution in teleost fishes

Precise estimation of genome size (GS) is vital for various genomic studies, such as deciding genome sequencing depth, genome assembly, biodiversity documentation, evolution, genetic disorders studies, duplication events etc. Animal Genome Size Database provides GS of over 2050 fish species, which ranges from 0.35 pg in pufferfish (Tetraodon nigroviridis) to 132.83 pg in marbled lungfish (Protopterus aethiopicus). The GS of majority of the fishes inhabiting waters of Indian subcontinent are still missing. In present study, we estimated GS of 51 freshwater teleost (31 commercially important, 7 vulnerable and 13 ornamental species) that ranged from 0.58 pg in banded gourami (Trichogaster fasciata) to 1.92 pg in scribbled goby (Awaous grammepomus). Substantial variation in GS was observed within the same fish orders (0.64-1.45 pg in cypriniformes, 0.70-1.41 pg in siluriformes and 0.58-1.92 pg in perciformes). We examined the relationship between the GS, chromosome number and body length across all the fishes. Body length was found to be associated with GS, whereas no relationship was noticed between the GS and the chromosome number. The analysis using ancestral information revealed haploid chromosome number 25, 27 and 24 for the most recent common ancestor of cypriniformes, siluriformes and perciformes, respectively. The study led to generation of new records on GS of 43 fish species and revalidated records for 8 species. The finding is valuable resource for further research in the areas of fish genomics, molecular ecology and evolutionary conservation genetics.

A transcriptome-based phylogeny for Polynoidae (Annelida: Aphroditiformia)

Polynoidae is the most diverse radiation of Aphroditiformia and one of the most successful groups of all Annelida in terms of diversity and habitats colonized. With such an unmatched diversity, phylogenetic investigations have struggled to understand their evolutionary relationships. Previous phylogenetic analyses have slowly increased taxon sampling and employed methodologies, but despite their diversity and biological importance, large genomic sampling is limited. To investigate the internal relationships within Polynoidae, we conducted the first phylogenomic analyses of the group based on 12 transcriptomes collected from species inhabiting a broad array of habitats, including shallow and deep waters, as well as hydrothermal vents, anchialine caves and the midwater. Our phylogenomic analyses of Polynoidae recovered congruent tree topologies representing the clades Polynoinae, Macellicephalinae and Lepidonotopodinae. Members of Polynoinae and Macellicephalinae clustered in well supported and independent clades. In contrast, Lepidonotopodinae taxa were always recovered nested within Macellicephalinae. Though our sampling only covers a small proportion of the species known for Polynoidae, our results provide a robust phylogenomic framework to build from, emphasizing previously hypothesized relationships between Macellicephalinae and Lepidonotopodinae taxa, while providing new insights on the origin of enigmatic cave and pelagic lineages.

Comparative plastome genomics, taxonomic delimitation and evolutionary divergences of Tetraena hamiensis var. qatarensis and Tetraena simplex (Zygophyllaceae)

The Zygophyllum and Tetraena genera are intriguingly important ecologically and medicinally. Based on morphological characteristics, T. hamiensis var. qatarensis, and T. simplex were transferred from Zygophyllum to Tetraena with the least genomic datasets available. Hence, we sequenced the T. hamiensis and T. simplex and performed in-depth comparative genomics, phylogenetic analysis, and estimated time divergences. The complete plastomes ranged between 106,720 and 106,446 bp-typically smaller than angiosperms plastomes. The plastome circular genomes are divided into large single-copy regions (~ 80,964 bp), small single-copy regions (~ 17,416 bp), and two inverted repeats regions (~ 4170 bp) in both Tetraena species. An unusual shrinkage of IR regions 16-24 kb was identified. This resulted in the loss of 16 genes, including 11 ndh genes which encode the NADH dehydrogenase subunits, and a significant size reduction of Tetraena plastomes compared to other angiosperms. The inter-species variations and similarities were identified using genome-wide comparisons. Phylogenetic trees generated by analyzing the whole plastomes, protein-coding genes, matK, rbcL, and cssA genes exhibited identical topologies, indicating that both species are sisters to the genus Tetraena and may not belong to Zygophyllum. Similarly, based on the entire plastome and proteins coding genes datasets, the time divergence of Zygophyllum and Tetraena was 36.6 Ma and 34.4 Ma, respectively. Tetraena stem ages were 31.7 and 18.2 Ma based on full plastome and protein-coding genes. The current study presents the plastome as a distinguishing and identification feature among the closely related Tetraena and Zygophyllum species. It can be potentially used as a universal super-barcode for identifying plants.

Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

Circulation of four species of Anaplasmataceae bacteria in ticks in Harbin, northeastern China

Ticks play an important role in the evolution and transmission of Anaplasmataceae bacteria which are agents of emerging infectious diseases. In this study, a total of 1286 adult ticks belonging to five species were collected from cattle, goats, horses and vegetation in Harbin area, Heilongjiang province, northeastern China. The tick-borne Anaplasmataceae bacteria were identified by amplifying and sequencing the 16S rRNA (rrs) and heat shock protein-60 encoding (groEL) genes. The results showed that Ixodes persulcatus was dominant (38.8%, 499/1283) among the five tick species, and Anaplasmataceae bacteria were detected in all tick species with an overall prevalence of 7.4%. Four species of Anaplasmataceae bacteria (Anaplasma phagocytophilum, Anaplasma ovis, Anaplasma bovis, and "Candidatus Neoehrlichia mikurensis"), which are pathogenic to humans and/or animals, were identified from tick samples by phylogenetic analyzes of the rrs and groEL gene sequences. Interestingly, the cluster 1 strains were first identified in Asian, and a novel cluster was also detected in this study. These data revealed the genetic diversity of Anaplasmataceae bacteria circulating in ticks in Harbin area, highlighting the need to investigate these tick-borne pathogens and their risks to human and animal health.

Metabarcoding revealed a high diversity of Amphidomataceae (Dinophyceae) and the seasonal distribution of their toxigenic species in the Taiwan Strait

The dinophyte family Amphidomataceae includes the genera Azadinium and Amphidoma. Four of these species are known to produce azaspiracids, which are lipophilic phycotoxins accumulating in shellfish. The diversity and biogeography of Amphidomataceae is far from yet resolved. Here we performed a time series sampling of both water and sediments in the Taiwan Strait from Nov. 2018 to April 2021. Metabarcoding was performed to unveil the diversity of Amphidomataceae targeting internal transcribed spacer (ITS1) region and partial large subunit ribosomal DNA (LSU rDNA D1-D3), followed by quantitative PCR (qPCR) with modified primers for Az. poporum ribotypes. The diversity of Amphidomataceae was revealed from the water samples with the aid of ITS1 and LSU based molecular phylogeny. The LSU based approach detected only a few species. In contrast, ITS1 based dataset showed eight new Azadinium clades and several ZOTUs (zero-radius operational taxonomic units) grouping together with Am. languida. Moreover, eleven known Azadinium species including three ribotypes of Az. poporum and Az. dexteroporum, and two ribotypes of Az. spinosum, were detected. The latter two species have not been reported in China before. Among these toxigenic species, Az. poporum was relevantly abundant whereas others were rare. The maximum of 209 cells L ^-1 of Az. poporum ribotype A was estimated using qPCR nearby Quanzhou in Nov. 2018 and 172 cells L ¹ of Az. poporum ribotype B was detected far off coast in Apr. 2021. Metabarcoding on sediment samples revealed Az. poporum ribotypes B and C, but strains obtained with sediment incubation experiments yielded only ribotype B. Using qPCR about 0.2 cysts g ^-1 of Az. poporum ribotype B were quantified in May 2019 but cysts of Az. poporum ribotype C were not detected. Our results suggest that metabarcoding targeting ITS1 region is powerful to uncover the diversity of harmful dinophytes. Our results also highlight the rich diversity of Amphidomataceae and risk potential of azaspiracids in the Taiwan Strait and surrounding waters.

Phoxinus abanticus, a new species from the Lake Abant drainage in Türkiye (Teleostei: Leuciscidae)

Phoxinus abanticus, a new species, is described from the Lake Abant basin. It is distinguished from Phoxinus species in Türkiye and adjacent waters by the presence of fewer lateral line scales (60-69, vs. 75-91 in Phoxinus colchicus, 75-90 in Phoxinus strandjae); a deeper caudal peduncle (caudal peduncle depth: 1.8-2.3 times in length, vs. 2.4-2.9 in P. colchicus; 2.5-3.2 in P. strandjae); the absence of scales in the breast of males (vs. present); and ventral body reddish in nuptial colouration pattern for male (vs. brackish). The new species, P. abanticus, is also distinguished from its closest relative, P. strandjae, by a minimum of 3.40% genetic distance in the mtDNA cytochrome b (cyt b) gene.

Phylogeny of sea spiders (Arthropoda: Pycnogonida) inferred from mitochondrial genome and 18S ribosomal RNA gene sequences

The phylogeny of sea spiders has been debated for more than a century. Despite several molecular studies in the last twenty years, interfamilial relationships remain uncertain. In the present study, relationships within Pycnogonida are examined in the light of a new dataset composed of 160 mitochondrial genomes (including 152 new sequences) and 130 18S rRNA gene sequences (including 120 new sequences), from 141 sea spider morphospecies representing 26 genera and 9 families. Node congruence between mitochondrial and nuclear markers was analysed to identify the most reliable relationships. We also reanalysed a multilocus dataset previously published and showed that the high percentages of missing data make phylogenetic conclusions difficult and uncertain. Our results support the monophyly of most families currently accepted, except Callipallenidae and Nymphonidae, the monophyly of the superfamilies Ammotheoidea (Ammotheidae + Pallenopsidae), Nymphonoidea (Nymphonidae + Callipallenidae), Phoxichilidioidea (Phoxichilidiidae + Endeidae) and Colossendeoidea (Colossendeidae + Pycnogonidae + Rhynchothoracidae), and the sister-group relationship between Ammotheoidea and Phoxichilidioidea. We discuss the morphological evolution of sea spiders, identifying homoplastic characters and possible synapomorphies. We also discuss the palaeontological and phylogenetic arguments supporting either a radiation of sea spiders prior to Jurassic or a progressive diversification from Ordovician or Cambrian.

Lignin-Degrading Bacteria in Paper Mill Sludge

The effluents generated in the paper industry, such as black liquor, have a high content of lignin and other toxic components; however, they represent a source of lignin-degrading bacteria with biotechnological potential. Therefore, the present study aimed to isolate and identify lignin-degrading bacteria species in paper mill sludge. A primary isolation was carried out from samples of sludge present in environments around a paper company located in the province of Ascope (Peru). Bacteria selection was made by the degradation of Lignin Kraft as the only carbon source in a solid medium. Finally, the laccase activity (Um-L^-1) of each selected bacteria was determined by oxidation of 2,2'-azinobis-(3-etilbencenotiazolina-6-sulfonate) (ABTS). Bacterial species with laccase activity were identified by molecular biology techniques. Seven species of bacteria with laccase activity and the ability to degrade lignin were identified. The bacteria Agrobacterium tumefasciens (2), Klebsiella grimontii (1), and Beijeinckia fluminensis (1) were reported for first time. K. grimowntii and B. fluminensis presented the highest laccase activity, with values of 0.319 ± 0.005 UmL^-1 and 0.329 ± 0.004 UmL^-1, respectively. In conclusion, paper mill sludge may represent a source of lignin-degrading bacteria with laccase activity, and they could have potential biotechnological applications.

Bioclimatic Origin Shapes Phylogenetic Structure of Tirmania (Pezizaceae): New Species and New Record from North Africa

The phylogenetic relationships among Tirmania were investigated using the internal transcribed spacer (ITS) and large subunit (LSU) regions of the nuclear-encoded ribosomal DNA (rDNA) and compared with morphological and bioclimatic data. The combined analyses of forty-one Tirmania samples from Algeria and Spain supported four lineages corresponding to four morphological species. Besides the two previously described taxa, Tirmania pinoyi and Tirmania nivea, here we describe and illustrate a new species, Tirmania sahariensis sp. nov., which differs from all other Tirmania by its distinct phylogenetic position and its specific combination of morphological features. We also present a first record of Tirmania honrubiae from North Africa (Algeria). Our findings suggest that restrictions imposed by the bioclimatic niche have played a key role in driving the speciation process of Tirmania along the Mediterranean and Middle East.

Time-calibrated phylogenies reveal mediterranean and pre-mediterranean origin of the thermophilous vegetation of the Canary Islands

BACKGROUND AND AIMS

The Canary Islands have strong floristic affinities with the Mediterranean Basin. One of the most characteristic and diverse vegetation belts of the archipelago is the thermophilous woodland (between 200 and 900 m.a.s.l.). This thermophilous plant community consists of many non-endemic species shared with the Mediterranean Floristic Region together with Canarian endemic species. Consequently, phytogeographic studies have historically proposed the hypothesis of an origin of the Canarian thermophilous species following the establishment of the summer-dry mediterranean climate in the Mediterranean Basin around 2.8 million years ago.

METHODS

Time-calibrated phylogenies for 39 plant groups including Canarian thermophilous species were primarily analysed to infer colonization times. In particular, we used 26 previously published phylogenies together with 13 new time-calibrated phylogenies (including newly generated plastid and nuclear DNA sequence data) to assess whether the time interval between stem and crown ages of Canarian thermophilous lineages postdates 2.8 Ma. For lineages postdating this time threshold, we additionally conducted ancestral area reconstructions to infer the potential source area for colonization.

KEY RESULTS

A total of 43 Canarian thermophilous lineages were identified from 39 plant groups. Both mediterranean (16) and pre-mediterranean (9) plant lineages were found. However, we failed to determine the temporal origin for 18 lineages because a stem-crown time interval overlaps with the 2.8-Ma threshold. The spatial origin of thermophilous lineages was also heterogeneous, including ancestral areas from the Mediterranean Basin (nine) and other regions (six).

CONCLUSIONS

Our findings reveal an unexpectedly heterogeneous origin of the Canarian thermophilous species in terms of colonization times and mainland source areas. A substantial proportion of the lineages arrived in the Canaries before the summer-dry climate was established in the Mediterranean Basin. The complex temporal and geographic origin of Canarian thermophilous species challenges the view of the Canary Islands (and Madeira) as a subregion within the Mediterranean Floristic Region.

Phylogeny and biogeography of Tiliacoreae (Menispermaceae), a tribe restricted to tropical rainforests

BACKGROUND AND AIMS

Modern tropical rainforests house the highest biodiversity of Earth's terrestrial biomes and are distributed in three low-latitude areas. However, the biogeographical patterns and processes underlying the distribution of biodiversity among these three areas are still poorly known. Here, we used Tiliacoreae, a tribe of pantropical lianas with a high level of regional endemism, to provide new insights into the biogeographical relationships of tropical rainforests among different continents.

METHODS

Based on seven plastid and two nuclear DNA regions, we reconstructed a phylogeny for Tiliacoreae with the most comprehensive sampling ever. Within the phylogenetic framework, we then estimated divergence times and investigated the spatiotemporal evolution of the tribe.

KEY RESULTS

The monophyletic Tiliacoreae contain three major clades, which correspond to Neotropical, Afrotropical and Indo-Malesian/Australasian areas, respectively. Both Albertisia and Anisocycla are not monophyletic. The most recent common ancestor of Tiliacoreae occurred in Indo-Malesia, the Afrotropics and Neotropics in the early Eocene, then rapidly diverged into three major clades between 48 and 46 Ma. Three dispersals from Indo-Malesia to Australasia were inferred, one in the middle Eocene and two in the late Oligocene-late Miocene, and two dispersals from the Afrotropics to Indo-Malesia occurred in the late Eocene-Oligocene.

CONCLUSIONS

The three main clades of Anisocycla correspond to three distinct genera [i.e. Anisocycla sensu stricto and two new genera (Georgesia and Macrophragma)]. Epinetrum is a member of Albertisia. Our findings highlight that sea-level fluctuations and climate changes in the Cenozoic have played important roles in shaping the current distribution and endemism of Tiliacoreae, hence contributing to the knowledge on the historical biogeography of tropical rainforests on a global scale.

The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa

The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.

Phylogenetic and host-parasite relationship analyses of Henneguya caquetaia sp. nov (Myxosporea: Myxobolidae) infecting an Amazonian cichlid fish

The present study describes a new species of Henneguya infecting the ornamental fish Caquetaia spectabilis from the Brazilian Amazon. Fish specimens were collected where the Tapajós and Amazon rivers merge, municipality of Santarém in the State of Pará, Brazil. Infections were intense, with several plasmodia spread on the opercula, fins and eye. Phylogenetic characterization and host-parasite relationship studies of the new Henneguya species used a combination of small subunit ribosomal DNA (ssrDNA) and morphological (photonic and transmission electron microscopy) analyses. Plasmodia were white round to ellipsoidal measuring up to 1.8 mm. The myxospores body measured 20.5 ± 3.9 (15-27) in length, 7.9 μm (6.2-10.8) in width, 6.7 μm (6.0-7.6) in thickness, 20.5 μm (14.4-32.3) in caudal appendages length, and 40.6 μm (34.2-54.6) in total length. The two polar capsules were elongated and equal in size, measuring 4.3 μm (3.3-5.4) in length and 2.1 μm (1.3-2.8) in width. Histological analysis revealed the parasite development in connective tissues of the fins, eyes and opercula. The skin of the fins and opercula presented detachment of the epidermis, however, no inflamatory infiltrate was observed. In the eye were observed inflammatory infiltratate in the epithelium and stroma of the cornea. Ultrastructure analysis showed the connective tissue capsule composed by an inner cellular layer with fibroblasts and outer layer where collagen fibers arranged transversely yet interspersed by layers of fibers arranged longitudinally. Numerous invaginations and extensive pinocytotic channels were observed in the plasmodial membrane. A layer of microfilament-like microfilament-like material was observed in the ectoplasm area and along to the internal surface of the plasmodial membrane. Generative cells and early stages of sporogenesis were seen more internally. The ssrDNA based phylogeny showed the South American species grouped in two lineages and the new species arises in a well-sustained subclade as sister branch of the clade composed by Henneguya spp. parasites of cichlids fish.

Beyond species loss: How anthropogenic disturbances drive functional and phylogenetic homogenization of Neotropical dung beetles

Anthropogenic activities drive tropical forest loss and biodiversity decay. However, few studies have addressed how the biodiversity response varies between disturbance-adapted species (i.e., winners) and those highly susceptible to disturbance (i.e., losers), or whether such responses differ between the taxonomic, functional, or phylogenetic dimensions of diversity. Understanding these dynamics can help prevent or buffer biotic homogenization processes. Using a meta-analytical approach with dung beetles as model organisms, we evaluated how anthropogenic habitat disturbances influence the multiple diversity dimensions of winner and loser species relative to conserved forest sites in the Neotropics. Habitats were organized according to a disturbance gradient ranging from second-growth forests, shaded agroforestry, lowly-shaded agroforestry, living fences, and pastures. Our database included 30 studies, from which we calculated nine metrics divided into three alfa diversity aspects: richness, evenness, and divergence. We also evaluated the beta-diversity response to disturbance and forest protection. All dimensions of dung beetle diversity decreased significantly with increasing disturbance levels, with phylogenetic diversity showing the highest losses, whereas evenness metrics increased in second-growth forests and agroforestry systems. Loser dung beetles showed high diversity loss as well as functional and phylogenetic clustering, reflecting a pervasive biotic homogenization in the most severely disturbed habitats, whereas winner species were insensitive to anthropogenic disturbances. Beta diversity increased significantly with disturbance and forest protection. Our study showed that heavy disturbances erode and homogenized all diversity dimensions of loser dung beetles. However, second-growth forests and agroforestry systems mitigated diversity loss and homogenization processes by favoring the coexistence between functional and phylogenetically distant species and maintaining assemblages compositionally similar to those in conserved forests, highlighting their importance for conservation. We encourage natural resource managers to consider protection of disturbed off-reserve forests in management schemes as these are essential for maintaining biodiversity in an increasingly anthropized world.

Detection of the Xanthi Chryso-like Virus in New Geographical Area and a Novel Arthropod Carrier

Here, we report on a serendipitous finding of a chryso-like virus associated with Culex pipiens mosquitos in the course of study aimed to detect and characterize West Nile virus (WNV) circulating in mosquitos in Serbia, Southern Europe. Upon initial detection of unexpected product in a PCR protocol for partial WNV NS5 gene amplification, further confirmation and identification was obtained through additional PCR and Sanger sequencing experiments. Bioinformatic and phylogenetic analysis identified the obtained sequences as Xanthi chryso-like virus (XCLV). The finding is particular for the fact that it associates XCLV with a new potential vector species and documents a novel geographical area of its distribution.

Evolution and Classification of Musaceae Based on Male Floral Morphology

Classification of the banana family (Musaceae) into three genera, Musa, Ensete and Musella, and infrageneric ranking are still ambiguous. Within the genus Musa, five formerly separated sections were recently merged into sections Musa and Callimusa based on seed morphology, molecular data and chromosome numbers. Nevertheless, other key morphological characters of the genera, sections, and species have not been clearly defined. This research aims to investigate male floral morphology, classify members of the banana family based on overall similarity of morphological traits using 59 banana accessions of 21 taxa and make inferences of the evolutionary relationships of 57 taxa based on ITS, trnL-F, rps16 and atpB-rbcL sequences from 67 Genbank and 10 newly collected banana accessions. Fifteen quantitative characters were examined using principal component analysis and canonical discriminant analysis and 22 qualitative characters were analyzed by the Unweighted Pair Group Method with an Arithmetic Mean (UPGMA). The results showed that fused tepal morphology, median inner tepal shape and length of style supported the three clades of Musa, Ensete and Musella, while shapes of median inner tepal and stigma classified the two Musa sections. In conclusion, a combination of morphological characters of male flowers and molecular phylogenetics well support the taxonomic arrangement within the banana family and the Musa genus and assist in selection of characters to construct an identification key of Musaceae.

Those Nematode-Trapping Fungi That are not Everywhere: Hints Towards Soil Microbial Biogeography

The existence of biogeography for microorganisms is a raising topic in ecology and researchers are employing better distinctions between single species, including the most rare ones, to reveal potential hidden patterns. An important volume of evidence supporting heterogeneous distributions for bacteria, archaea and protists is accumulating, and more recently a few efforts have targeted microscopic fungi. We propose an insight into this latter kingdom by looking at a group of soil nematode-trapping fungi whose species are well-known and easily recognizable. We chose a pure culture approach because of its reliable isolation procedures for this specific group. After morphologically and molecularly identifying all species collected from 2250 samples distributed in 228 locations across Yunnan province of China, we analyzed occurrence frequencies and mapped species, genera, and richness. Results showed an apparent cosmopolitan tendency for this group of fungi, including species richness among sites. However, only four species were widespread across the region, while non-random heterogeneous distributions were observed for the remaining 40 species, both in terms of statistical distribution of species richness reflected by a significant variance-to-mean ratio, as well as in terms of visually discernible spatial clusters of rare species and genera on the map. Moreover, several species were restricted to only one location, raising the question of whether endemicity exists for this microbial group. Finally, environmental heterogeneity showed a marginal contribution in explaining restricted distributions, suggesting that other factors such as geographical isolation and dispersal capabilities should be explored. These findings contribute to our understanding of the cryptic geographic distribution of microorganisms and encourage further research in this direction.