Distinct Evolutionary Lineages Research Articles

Molecular phylogenetic studies on Trigonella section Ellipticae (Trifolieae, Fabaceae) from India utilising nrDNA (ITS) and cpDNA (trnL–trnF & petL–psbE)

This study highlights the critical importance of species delimitation in biodiversity conservation, focusing on the poorly understood Indian Trigonella species, with focus on T. sect. Ellipticae. Despite their ecological and socio-economic significance, these species, primarily found in the northwest Himalayas, have been inadequately catalogued and preserved. Adapted to harsh, dry environments, T. sect. Ellipticae exhibits morphological traits that complicate traditional species delimitation due to significant overlap among species boundaries. To address these challenges, we integrated molecular sequence data (nrDNA ITS and cpDNA (trnL–trnF & petL–psbE)) with morphological analysis, confirming the monophyly of Trigonella and revealing distinct evolutionary lineages within T. sect. Ellipticae. While nrDNA ITS sequences alone proved insufficient for resolving species relationships, phylogenetic investigations utilizing plastid data identified three distinct clades, enhancing taxonomic clarity. The study also suggests that observed morphological variations in T. cachemiriana may be due to phenotypic plasticity rather than distinct evolutionary lineages. We propose a new combination, T. emodi var. gracilis, to better represent the diversity within this group. Overall, this research underscores the necessity of combining molecular and morphological approaches for effective species delimitation, contributing to broader biodiversity conservation efforts in India, where many species remain inadequately catalogued. As the urgency for conservation increases, refining taxonomic frameworks is essential for ensuring that conservation strategies are based on accurate biological data.

Phylogenomic analyses of the Listeriaceae family support species reclassification and proposal of a new family and new genera.

The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.

Functional and phylogenetic structure of mammals along elevational gradients in the Central and East Himalayas

BackgroundMountain ecosystems are critical hotspots of global biodiversity, yet the dynamics of community assembly along their elevational gradients are not well understood. This gap is primarily due to the complexity of environmental and biotic interactions that influence species distribution and community structure. Although extensive research has been conducted on certain taxa, such as small mammals and bats, comprehensive studies encompassing entire mammal assemblages are lacking. Our research aims to bridge this gap by examining the taxonomic, phylogenetic, and functional diversity, as well as the assemblage structures of mammal communities across elevational gradients in the Central and East Himalayas, exploring how diverse ecological and evolutionary processes impact community assembly.MethodsWe analyzed mammal elevational diversity patterns using species richness, functional diversity (FD), and phylogenetic diversity (PD). We compared the observed values of community structure, such as mean pairwise phylogenetic distance (MPD) and mean pairwise functional distance (MFD), with null-model corrected effect sizes to identify patterns and processes of community assembly. Using structural equation modeling and hierarchical partitioning, we investigated the relationships between climate, productivity, and various facets of diversity, describing the organization of each component across different elevations.ResultsTaxonomic, functional, and phylogenetic diversity generally decreased with elevation but showed varied patterns such as mid-elevation peaks, low-elevation plateaus, or monotonic declines across different regions. Richness-controlled functional diversity increased towards mid-low elevations and decreased at higher elevations in both regions, whereas richness-controlled phylogenetic diversity lacked consistent patterns. Phylogenetic structures tended to cluster from mid to high elevations, indicating closer relationships than those observed in random communities, likely due to significant environmental turnover near tree lines. Functional structure showed greater clustering at high elevations and increased over-dispersion at lower elevations, suggesting that species are more functionally similar than expected at higher elevations and more diverse at lower elevations. Our results revealed that environmental factors, evolutionary histories, and trait-driven ecological processes collectively shape species richness along these gradients.ConclusionsOur results showed incongruent community structures across phylogenetic and functional diversity. Generally, functional traits are closely linked to environmental conditions, reducing the chance of observing traits that are misaligned with their surroundings. Species with similar ecological roles or distinct evolutionary lineages often show convergent adaptations to highland environments. Additionally, our findings emphasize that community assembly varies with the biogeography and diversification history of individual mountain ranges, complicating the development of a generalized theory. Using multiple measures is important for accurate community structure assessments and effective conservation planning, as variable elevational patterns exist across different diversity dimensions.

A new brown rot disease of plum caused by Mucor xinjiangensis sp. nov. and screening of its chemical control.

A novel species of Mucor was identified as the causal agent of a brown rot of Prunus domestica (European plum), widely grown in the south of Xinjiang, China. This disease first appears as red spots after the onset of the fruits. With favorable environmental conditions, fruit with infected spots turn brown, sag, expand, wrinkle, and harden, resulting in fruit falling. Fungal species were isolated from infected fruits. A phylogenetic analysis based on internal transcribed spacer (ITS) regions and the large subunit (LSU) of the nuclear ribosomal RNA (rRNA) gene regions strongly supported that these isolates made a distinct evolutionary lineage in Mucor (Mucoromycetes, Mucoraceae) that represents a new taxonomic species, herein named as Mucor xinjiangensis. Microscopic characters confirmed that these strains were morphologically distinct from known Mucor species. The pathogenicity of M. xinjiangensis was confirmed by attaching an agar disk containing mycelium on fruits and re-isolation of the pathogen from symptomatic tissues. Later, fourteen fungicides were selected to determine the inhibitory effect on the pathogen. Further, results showed that difenoconazole had the best effect on the pathogen and the strongest toxicity with the smallest half maximal effective concentration (EC50) value, followed by a compound fungicide composed of difenoconazole with azoxystrobin, mancozeb, prochloraz with iprodione, pyraclostrobin with tebuconazole, and trifloxystrobin with tebuconazole and ethhylicin. Present study provides the basis for the prevention and control of the novel plum disease and its pathogen.

Fungal Bioluminescence: Past, Present, and Future

The complex and diverse phenomenon of fungal bioluminescence has captured human curiosity. Nevertheless, in the field of studies, there are not many attempts made particularly to reveal the new species of these interesting fungi. This study comprehensively reviews the diversity, distribution, evolution, bioluminescence mechanisms, ecological roles, and potential applications of these fungi. Most importantly, we also present an updated list of the reported bioluminescent fungi (122) so far identified from five distinct evolutionary lineages worldwide—Armillaria, Eoscyphella, Lucentipes, Mycenoid, and Omphalotus—mainly in tropical and subtropical areas. Bioluminescent fungi are descended from the last common ancestor of the Mycenoid and the Marasmioid clades of Agaricales, which have been maintained for at least 160 million years of evolution. We underscore the potential for future research to understand the ecological role of bioluminescent fungi, inspiring hope and optimism for the future of this field.

Patterns in Genome-Wide Codon Usage Bias in Representative Species of Lycophytes and Ferns.

The latest research shows that ferns and lycophytes have distinct evolutionary lineages. The codon usage patterns of lycophytes and ferns have not yet been documented. To investigate the gene expression profiles across various plant lineages with respect to codon usage, analyze the disparities and determinants of gene evolution in primitive plant species, and identify appropriate exogenous gene expression platforms, the whole-genome sequences of four distinct species were retrieved from the NCBI database. The findings indicated that Ceratopteris richardii, Adiantum capillus-veneris, and Selaginella moellendorffii exhibited an elevated A/U content in their codon base composition and a tendency to end with A/U. Additionally, S. capillus-veneris had more C/G in its codons and a tendency to end with C/G. The ENC values derived from both ENC-plot and ENC-ratio analyses deviated significantly from the standard curves, suggesting that the codon usage preferences of these four species were primarily influenced by genetic mutations and natural selection, with natural selection exerting a more prominent influence. This finding was further supported by PR2-Plot, neutrality plot analysis, and COA. A combination of RSCU and ENC values was used as a reference criterion to rank the codons and further identify the optimal codons. The study identified 24 high-frequency codons in C. richardii, A. capillus-veneris, and Diphasiastrum complanatum, with no shared optimal codons among the four species. Arabidopsis thaliana and Ginkgo biloba exhibited similar codon preferences to the three species, except for S. moellendorffii. This research offers a theoretical framework at the genomic codon level for investigating the phylogenetic relationships between lycophytes and ferns, shedding light on gene codon optimization and its implications for genetic engineering in breeding.

Molecular analysis reveals the evolutionary distinctiveness of the Silver-backed Chevrotain within the genus Tragulus

Abstract The Silver-backed Chevrotain (Tragulus versicolor), a mammal endemic to the unique coastal arid ecosystem in south-central Vietnam, is an enigmatic mouse deer with little information available about its ecology and evolutionary history. The recent rediscovery of the species provides a rare opportunity to clarify its taxonomy and phylogenetic relationship within the genus Tragulus. In this study, we sequenced the complete mitochondrial cytochrome b gene for samples of T. versicolor and T. kanchil from Vietnam. Our molecular results show that the species forms a distinct evolutionary lineage sister to all other species in the genus, confirming the earlier hypothesis based on morphological evidence. However, further research is needed to assess the genetic diversity of the species and design appropriate conservation measures. As the species has not been secured over much of its range, it is recommended that the population in Nui Chua National Park, the only one covered by a protected area, be prioritized for conservation actions. Conserving the species in this unique and imperiled ecosystem will also benefits a suite of locally endemic and threatened species of fauna and flora.

Taxonomic revision of the formerly monotypic orchid genus Dactylostalix

The Calypsoinae orchid genus Dactylostalix, previously considered a monotypic genus endemic to Japan and the Russian Far East (the Kuril Islands and Sakhalin Island), is now redefined to encompass two species. This reclassification is based not only on the examination of type specimens and literature but also on molecular data. While Pergamena uniflora has long been regarded as a synonym of Dactylostalix ringens, it is distinguishable by its shorter scape, smaller flower, less spotted tepals, drooping sepals and lateral petals, labellum with smaller, narrowly triangular to ovate lateral lobes, more distinct keels on the adaxial surface of the lip, and a slender column with a smaller stigma and weakly developed clinandrium. We propose the new combination Dactylostalix uniflora, recognizing it as a distinct species within the genus Dactylostalix. Phylogenetic analysis utilizing genome-wide markers has also demonstrated that the two species are genetically distinct. Our findings, obtained through the integration of morphological data and molecular phylogenetics, indicate that D. uniflora represents a distinct evolutionary lineage from D. ringens. Examination of type specimens has led us to conclude that Calypso japonica, Dactylostalix maculosa, and Dactylostalix ringens f. punctatus are junior synonyms of D. ringens. Additionally, we designate the lectotypes for P. uniflora (= D. uniflora), C. japonica, and D. maculosa.

Distinct evolutionary lineages of Schistocephalus parasites infecting co-occurring sculpin and stickleback fishes in Alaska.

Sculpins (coastrange and slimy) and sticklebacks (ninespine and threespine) are widely distributed fishes cohabiting 2 south-central Alaskan lakes (Aleknagik and Iliamna), and all these species are parasitized by cryptic diphyllobothriidean cestodes in the genus Schistocephalus. The goal of this investigation was to test for host-specific parasitic relationships between sculpins and sticklebacks based upon morphological traits (segment counts) and sequence variation across the NADH1 gene. A total of 446 plerocercoids was examined. Large, significant differences in mean segment counts were found between cestodes in sculpin (mean = 112; standard deviation [s.d.] = 15) and stickleback (mean = 86; s.d. = 9) hosts within and between lakes. Nucleotide sequence divergence between parasites from sculpin and stickleback hosts was 20.5%, and Bayesian phylogenetic analysis recovered 2 well-supported clades of cestodes reflecting intermediate host family (i.e. sculpin, Cottidae vs stickleback, Gasterosteidae). Our findings point to the presence of a distinct lineage of cryptic Schistocephalus in sculpins from Aleknagik and Iliamna lakes that warrants further investigation to determine appropriate evolutionary and taxonomic recognition.

Reclassification of a reveromycin-producer and the proposals of Actinacidiphila reveromycinica sp. nov. and Actinacidiphila acidipaludis comb. nov.

Streptomyces sp. SN-593, a reveromycin producer, was previously thought to belong to the genus Streptomyces based on its morphological and chemotaxonomic characteristics. In this paper, we re-considered its taxonomic position according to the current criteria. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain belongs to the genus Actinacidiphila. In multilocus sequence and phylogenomic analyses, the strain SN-593 represented a distinct evolutionary lineage within this genus, and its closest neighbor was A. yanglinensis. Digital DNA-DNA hybridization indicated that the strain shares less than 32% DNA-DNA relatedness with the type strains of closely related species, confirming this strain is a novel genomospecies. According to its phenotypic distinctiveness from the closest neighbor, we propose Actinacidiphila reveromycinica sp. nov. for the strain SN-593T. Additionally, as Streptomyces acidipaludis belonged to the genus Actinacidiphila in these analyses, it should be transferred to the genus, for which Actinacidiphila acidipaludis comb. nov. is proposed.

Morphological and molecular evidence for considering Xylocopa nigrocincta as the senior synonym of Xylocopa suspecta (Apidae: Xylocopini)

Xylocopa nigrocincta Smith, 1854, and Xylocopa suspecta Moure & Camargo, 1988, are two nominal species within the subgenus Neoxylocopa and have a sympatric geographic distribution in South America. While X. nigrocincta is recognized by the presence of reddish metasomatic bands, X. suspecta is entirely black. Although morphologically distinct in terms of metasomal band colour, other morphological characters suggest that both species could be the same evolutionary entity and therefore synonymous. The aim of this research was to review both nigrocincta and suspecta morphotypes using an integrative approach (morphological and molecular) to evaluate if they are truly two different evolutionary lineages. Females of both species were obtained from field collections and museums, representing a large part of their morphotype distribution. Additional diagnostic characters of the external morphology were investigated, such as metasomal band colour, metasomal punctuation, wing colours, and apical regions of the basitibial plate. Mitochondrial gene sequences (COI and CytB) were used for phylogenetic reconstructions. Our results showed that both nigrocincta and suspecta morphotypes are undistinguished based on morphology, although the metasomal band colour, together with the geographic distribution, revealed the presence of three distinct morphogroups, including an intermediate one with a variable number of reddish bands. Nonetheless, the three morphogroups are not supported by molecular data and therefore represent intra-specific variations. In conclusion, our results do not support the hypothesis that the two nominal species are distinct evolutionary lineages, and we propose a synonym between X. nigrocincta and X. suspecta.

Subspecies inflation hampers conservation efforts: a case study on wall lizards

Abstract The common practice of using subspecies as conservation targets raises the question of whether efforts are focused on preserving conspicuous components of the species’ phenotypic variability rather than evolutionarily significant units. To address this question, in this study we performed a comprehensive morphological and genetic assessment on all the subspecies of wall lizard described for the Aeolian Archipelago (Italy) to determine whether they represent distinct evolutionary lineages and/or discrete phenotypic partitions. Further, we applied a monophyly test to 70 subspecies belonging to seven wall lizard species occurring in Italy, based on our results and on previous phylogeographic studies. We found that none of the Aeolian subspecies represents a distinct evolutionary lineage, despite some morphological differentiation of island populations across the archipelago, suggesting a very recent origin of island populations and of the observed phenotype variation. Across seven wall lizard species, tests revealed that lizard subspecies rarely (< 9% of cases) match evolutionary units. This study demonstrates that intraspecific taxonomy of wall lizards is a poor predictor of phylogeographic partitions and evolutionary units, and therefore of limited use (if not dangerous) for defining conservation and management units. A better approach would be relying on the integration of genomic and phenotypic data to assess the evolutionary significance and conservation value of phenotypic and genetic units within species.

Is resource specialization the key?: some, but not all Red Crossbill call types associate with their key conifers in a diverse North American landscape

Red Crossbills (Fringillidae: Loxia curvirostra) are finches specialized to pry open cones and extract seeds of coniferous trees. Within the species, variable bill morphology may provide more efficient foraging on some species of conifers than others. Subgroups also have distinctly different contact calls often given in flight (hereafter, call types). Variable morphology and discrete call types suggest the existence of distinct evolutionary lineages. Because coniferous trees produce seeds on irregular and unpredictable schedules, crossbills wander widely in search of food. The key conifer hypothesis suggests that each call type diverged by specializing on a single conifer species to maximize foraging efficiency, while other hypotheses have emphasized geographic isolation as a driver of lineage divergence. To quantify the degree to which call types occur with specific conifer species, we surveyed Red Crossbills in five ecoregions of western and central Oregon, USA, an area with high conifer diversity. Two of five call types (Types 5 and 10) were encountered in only one ecoregion and associated with their hypothesized key conifers. Three others (Types 2, 3, and 4) were found to wander widely and did not exclusively align geographically with their presumed key conifer species. Whereas types 2 and 3 were sometimes associated with their proposed key conifers, they wandered widely during our 2-year study and occurred with a wide variety of conifers. Type 4 was not significantly associated with its key conifer and also wandered widely during our study. Relationships of call types with key conifers were weaker in the winter and spring, when Types 3 and 4 were frequently encountered in hard-coned pines rather than their soft-coned key conifer species. In our study area, the key conifer hypothesis was strongly supported only for call type 10 as that call type was not encountered away from the coastal range of Sitka Spruce (Picea sitchensis). We found mixed support for the key conifer hypothesis based on our measure of geographic associations of crossbills with a diverse array of coniferous tree species. In most cases we observed, crossbills wandered widely and associated with multiple species of conifers.

How many lineages are there of the stingrays genus Hypanus (Myliobatiformes: Dasyatidae) and why does it matter?

Abstract Stingrays genus Hypanus currently encompasses nine valid species from the Atlantic and Pacific oceans, though the phylogenetic relationships amongst some of them were based on a single mitochondrial gene and did not involve all putative Hypanus species. To address the monophyly of the genus and its relationship to other Dasyatinae genera, we sequenced the whole mitochondrial genomes of all species that supposedly belong to this genus and representatives of Dasyatinae, Neotrygoninae, and, as an outgroup, Fontitrygon (Urogymninae). Based on phylogenetic analyses, Hypanus is the sister-genus to all other Dasyatinae, and this subfamily is closely-related to Neotrygoninae within the family Dasyatidae. The species F. geijskesi is closely related to H. guttatus rather than to its congeners and should be allocated to Hypanus as H. geijskesi for the genus monophyly. After lineage delimitation analyses, we identified three species complexes composed of H. americanus, H. guttatus, and H. say, with two distinct evolutionary lineages within each, leaving the genus with 13 evolutionary units, of which six are currently under threat and only H. sabinus is of least concern. The urgency in identifying these new lineages lies in the fact they might already be under threat before being formally described.

Animal evolution at the ocean’s water-air interface

Innovation is a key to evolutionary success and entrance into novel ecosystems.1 Species that float freely at the ocean's surface, termed obligate neuston (also called pleuston, here referred to simply as neuston), include highly specialized taxa from distinct evolutionary lineages that evolved floating morphologies.2 In 1958, Soviet scientist, A.I. Savilov,3 stated that floating animal species are derived from benthic ancestors, rather than species from the adjacent pelagic zone, and that floating morphologies are homologous to benthic attachment structures. To test Savilov's hypothesis, we constructed molecular phylogenies and ancestral states for all major floating groups for which molecular data were available. Our results reveal that four of the five clades examined arose directly from a substrate-attached ancestor, although that substrate was not necessarily the benthos, as Savilov stated, and instead included epibiotic and rafting ancestors. Despite their diverse evolutionary origins, floating animals use gas-trapping mechanisms to remain at the surface,4,5,6 and many of these gas-trapping structures appear to be homologous to substrate attachment structures. We also reconstruct the trophic habits of floating mollusks and their sister species, revealing that prey preference remains conserved upon entering the ocean's surface ecosystem. Colonization of the ocean's surface seems to have occurred through successive evolutionary steps from the seafloor. Our results suggest that these steps often included transitions through epibiotic (where species attach to other living organisms) or rafting (where species attach to floating debris) habits. The water-air interface, despite its unique properties, may, in some ways, be just another substrate.

Tardigrade Augean stables—a challenging phylogeny and taxonomy of the family Ramazzottiidae (Eutardigrada: Hypsibioidea)

Abstract Tardigrade taxonomy is most often hindered by prevalent outdated species descriptions, lack of integrative redescriptions, scarce genetic information, and fragmentary sampling. Here, we diagnose the problems obscuring phylogenetic inference and the taxonomy of the cosmopolitan family Ramazzottiidae. We carried out the most extensive phylogenetic analysis of this family to date, with a considerable influx of new genetic data from poorly sampled regions of the world. We found two new distinct evolutionary lineages defined by distinct morphological traits (dorsal cuticular sculpturing and/or body shape), characterized by restricted geographic distributions, and we delineated them as new species complexes: the Neotropical Ramazzottius baumanni complex and the Afro-Oriental Ramazzottius szeptyckii complex. Nevertheless, we could not confidently ascertain the taxonomic status of both complexes due to: (i) the current state of the ramazzottiid taxonomy, with outdated and/or imprecise species descriptions with heterogeneous terminology and, in many cases, without accounting for intraspecific variation; (ii) the missing genetic information for key taxa; and (iii) the possible lack of monophyly of Cryoconicus and Ramazzottius as suggested by our results. In addition to diagnosing the problems of ramazzottiid phylogeny and systematics, we also propose possible solutions that could accelerate the progress in our understanding of the evolution of this group.

Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus.

Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.

Almost half of the Gymnura van Hasselt, 1823 species are unknown: Phylogeographic inference as scissors for cutting the hidden Gordian knot and clarify their conservation status

AbstractGymnurid rays are found in tropical, subtropical, and temperate regions around the world, where they are associated with sandy or muddy bottoms in coastal areas, being easily distinguished from other rays by the width of the disc. In recent years, the systematics of this family have been revised extensively. However, there has been no comprehensive molecular review of the family based on an adequate sample of species and localities, which may have obscured the presence of distinct evolutionary lineages. The present study was based on samples of 12 of the 13 valid species of the genus Gymnura, which were used for a multilocus reconstruction of the evolutionary history of the family Gymnuridae. Our results indicate the existence of several cryptic gymnurid lineages, within the species Gymnura micrura, Gymnura lessae, Gymnura altavela, and Gymnura poecilura. Also, we indicate that only half of the species that compose the genus are known, as well their conservation status. The analyses also indicate that the gymnurids originated during the Paleocene, with events of dispersal and vicariance occurring through the formation of oceanographic barriers, and species diversification peaking during the Oligocene and Miocene. The results of the present study reinforce the need for a comprehensive revision of the systematics of the family, in particular, the widely distributed species that are considered valid taxa, but may, in fact, represent different cryptic species. The inadequate classification of this cryptic diversity may have negative implications for the development of effective conservation measures.

Coastal dwarf variants of the red swamp Banksia (Proteaceae) represent parallel ecotypic evolution rather than a divergent evolutionary lineage of single origin

Abstract Morphological variation is common within widely distributed plant species and often raises interesting taxonomic and evolutionary questions. We sampled eight typical inland populations and two coastal dwarf populations of Banksia occidentalis to assess whether the coastal variant warrants taxonomic recognition. Genomic (single nucleotide polymorphisms) and morphometric analyses were undertaken to assess the variation within and between variants. Genetically, the coastal populations were more closely related to geographically adjacent populations of the typical variant than they were to each other, indicating that each coastal population has originated independently. Morphologically, the coastal populations also did not represent a cohesive phenotypic group, with both falling outside the range of variation for the typical variant, but also not overlapping each other. Wide morphological, but not genomic, variation was identified along a coastal–inland transect. Combined, these data indicate that the morphological variation in these coastal populations is the result of parallel ecotype evolution from experiencing similar environmental conditions and does not represent the diversification of a distinct evolutionary lineage that would have warranted taxonomic recognition. Our study highlights the consequences of strong selection pressures in marginal environments and provides fascinating insight to the long evolutionary history of the flora in this ancient Australian landscape.

Shumkonia mesophila gen. nov., sp. nov., a novel representative of Shumkoniaceae fam. nov. and its potentials for extracellular polymeric substances formation and sulfur metabolism revealed by genomic analysis.

A microaerophilic, mesophilic, chemoorganoheterotrophic bacterium, designated Y-P2T, was isolated from oil sludge enrichment in China. Cells of the strain were Gram-stain-negative, non-motile, non-spore-forming, rod-shaped or slightly curved with 0.8-3.0µm in length and 0.4-0.6µm in diameter. The strain Y-P2T grew optimally at 25°C (range from 15 to 30°C) and pH 7.0 (range from pH 6.0 to 7.5) without NaCl. The major cellular fatty acids were C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The main polar liquids of strain Y-P2T comprised phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The respiratory quinone was Q-10. Acetate and H2 were the fermentation products of glucose. The DNA G + C content was 66.0%. Strain Y-P2T shared the highest 16S rRNA gene sequence similarity (90.3-90.6%) with species within Oceanibaculum of family Thalassobaculaceae in Rhodospirillales. Phylogenetic analyses based on 16S rRNA gene sequences and genomes showed that strain Y-P2T formed a distinct evolutionary lineage within the order Rhodospirillales. On the basis of phenotypic, phylogenetic and phylogenomic data, we propose that strain Y-P2T represents a novel species in a novel genus, for which Shumkonia mesophila gen. nov., sp. nov., within a new family Shumkoniaceae fam. nov. The type strain is Y-P2T (= CCAM 826T = JCM 34766T).