Genus-level Taxonomy Research Articles

Enigmas no longer: using ultraconserved elements to place several unusual hawk taxa and address the non-monophyly of the genusAccipiter(Accipitriformes: Accipitridae)

AbstractHawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genus Accipiter) are not monophyletic. Here, we combine a large new dataset obtained from ultraconserved elements, generated from whole genome sequencing of 134 species, with publicly available legacy markers (i.e. a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 237 extant or recently extinct species. Our densely sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly of Accipiter and provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups.

Systematic revision of the ant subfamily Leptanillinae (Hymenoptera, Formicidae).

The genus-level taxonomy of the ant subfamily Leptanillinae (Hymenoptera: Formicidae) is here revised, with the aim of delimiting genus-level taxa that are reciprocally monophyletic and readily diagnosable based upon all adult forms. This new classification reflects molecular phylogenetics and is informed by joint consideration of both male and worker morphology. Three valid genera are recognized in the Leptanillinae: Opamyrma, Leptanilla (= Scyphodonsyn. nov., Phaulomyrma, Leptomesites, Noonillasyn. nov., Yavnellasyn. nov.), and Protanilla (= Anomalomyrmasyn. nov., Furcotanilla). Leptanilla and Protanilla are further divided into informal, monophyletic species groups. Synoptic diagnoses are provided for all genera and informal supraspecific groupings. In addition, worker-based keys to all described species within the Leptanillinae for which the worker caste is known are provided; and male-based keys to all species for which males are known, plus undescribed male morphospecies for which molecular data are published. The following species are described as new: Protanillawallaceisp. nov., Leptanillaacherontiasp. nov., Leptanillabelantansp. nov., Leptanillabethyloidessp. nov., and Leptanillanajaphallasp. nov.

Systematic studies on some West African species of the Tribe Bauhinieae (Cercidioideae)

The tribe Bauhinieae is the largest and most taxonomically complex group within the subfamily Cercidoideae. They possess the most distinguishable morphological features but are the most variable group. Here, we explore the phylogenetic relationship of the tribe Bauhinieae using morphological, anatomical and molecular data (ITS, rbcL, trnL-F, ITS+rbcL+trnL-F). Relationships inferred from morphological, anatomical and molecular data revealed congruent result, a non-monophyletic Bauhinia and Piliostigma group. The leaf epidermal shape in all Bauhinia species examined are polygonal with straight cell walls except B. tomentosa, which has an undulating cell wall. Stomatal types observed vary between the two genera studied. Bauhinia species has paracytic stomata while Piliostigma species exhibited hemiparacytic stomata. Dendrogram generated revealed the interrelationship between the species at a distance value of 80. Bayesian analysis revealed a high resolution of species and posterior probability. The strict consensus tree for all the tested gene regions revealed a polyphyletic Bauhina divided into three major clades. The Piliostigma group exhibited a paraphyletic and polyphyletic relationship within the Bauhinia group at high support values. B tomentosa exhibited a closer relationship with Piliostigma species. These results support the proposition to divide members of the large Bauhinia s.s group into subclades. This study has attempted to elucidate the unresolved species and genus level taxonomy of the tribe Bauhinieae. However, more variable gene regions in addition to broader species sampling should be considered for further phylogenetic patterns of this taxon.

Physical activity and diet associations with the gut microbiota in the Coronary Artery Risk Development in Young Adults (CARDIA) study

BackgroundGut microbiota may influence metabolic pathways related to chronic health conditions. Evidence for physical activity and diet influences on gut microbial composition exists, but data from diverse population-based cohort studies are limited. ObjectivesWe hypothesized that gut microbial diversity and genera are associated with physical activity and diet quality. MethodsData were from 537 participants in the Coronary Artery Risk Development in Young Adults (CARDIA) Study, a prospective cohort, who attended the year 30 follow-up examination (2015–2016; aged 47–61 y; 45% Black race/55% White race; 45% men/55% women). The 16S ribosomal RNA marker gene was sequenced from stool DNA, and genus-level taxonomy was assigned. Within-person microbial diversity (α-diversity) was assessed with Shannon diversity index and richness scores; between-person diversity (β-diversity) measures were generated with principal coordinates analysis (PCoA). Current and long-term physical activity and diet quality measures were derived from data collected over 30 y of follow-up. Multivariable-adjusted regression analysis controlled for: sociodemographic variables (age, race, sex, education, and field center), other health behaviors (smoking, alcohol consumption, and medication use), and adjusted for multiple comparisons with the false discovery rate (<0.20). ResultsBased on PCoA β-diversity, participants’ microbial community compositions differed significantly (P < 0.001), with respect to both current and long-term physical activity and diet quality. α-Diversity was associated only with current physical activity (positively) in multivariable-adjusted analysis. Multiple genera (n = 45) were associated with physical activity and fewer with diet (n = 5), including positive associations with Lachnospiraceae UCG-001 and Ruminococcaceae IncertaeSedis with both behaviors. ConclusionsPhysical activity and diet quality were associated with gut microbial composition among 537 participants in the CARDIA study. Multiple genera were associated with physical activity. Physical activity and diet quality were associated with genera consistent with pathways related to inflammation and short-chain fatty acid production.

Genus-level, trait-based multimetric diatom indices for assessing the ecological condition of rivers and streams across the conterminous United States

Taxonomic inconsistency in species-level identifications has constrained use of diatoms as biological indicators in aquatic assessments. We addressed this problem by developing diatom multimetric indices (MMIs) of ecological condition using genus-level taxonomy and trait-based autecological information. The MMIs were designed to assess river and stream chemical, physical and biological condition across the conterminous United States. Trait-based approaches have the advantage of using both species-level and genus-level data, which require less effort and expense to acquire than traditional species-based approaches and eliminate the persistent taxonomic biases introduced over vast geographic extents. For large-extent assessment programs that require multiple taxonomic laboratories to process samples, such as the United States Environmental Protection Agency’s (U.S. EPA’s) National Rivers and Streams Assessment (NRSA), the trait approach can eliminate discrepancies in species-level identification or nomenclature that hinder diatom data interpretation. We developed trait-based MMIs using NRSA data for each of the three large ecoregions across the U.S. - the East, Plains, and West. All three MMIs performed well in discriminating least-disturbed from most-disturbed sites. The MMI for the East had the greatest discrimination ability, followed by MMIs for the Plains and West, respectively. The performance of the MMIs was comparable to that observed in existing NRSA fish and macroinvertebrate MMIs. Our research shows that trait-based diatom indices constructed on genus-level taxonomy can be effective for large-scale assessments, and may also allow programs such as NRSA to assess trends in freshwater condition retrospectively, by revisiting older diatom datasets. Moreover, our genus-based approach facilitates including of diatoms into other assessment programs that have limited monitoring resources.

Single-Strand Conformation Polymorphism Fingerprint Method for Dictyostelids.

Dictyostelid social amoebae are a highly diverse group of eukaryotic soil microbes that are valuable resources for biological research. Genetic diversity study of these organisms solely relies on molecular phylogenetics of the SSU rDNA gene, which is not ideal for large-scale genetic diversity study. Here, we designed a set of PCR–single-strand conformation polymorphism (SSCP) primers and optimized the SSCP fingerprint method for the screening of dictyostelids. The optimized SSCP condition required gel purification of the SSCP amplicons followed by electrophoresis using a 9% polyacrylamide gel under 4°C. We also tested the optimized SSCP procedure with 73 Thai isolates of dictyostelid that had the SSU rDNA gene sequences published. The SSCP fingerprint patterns were related to the genus-level taxonomy of dictyostelids, but the fingerprint dendrogram did not reflect the deep phylogeny. This method is rapid, cost-effective, and suitable for large-scale sample screening as compared with the phylogenetic analysis of the SSU rDNA gene sequences.

Model deep learning untuk klasifikasi fragmen metagenom dengan spaced k-mers sebagai ekstraksi fitur

An open challenge in bioinformatics is the analysis of the sequenced metagenomes from the various environments. Several studies demonstrated bacteria classification at the genus level using k-mers as feature extraction where the highest value of k gives better accuracy but it is costly in terms of computational resources and computational time. Spaced k-mers method was used to extract the feature of the sequence using 111 1111 10001 where 1 was a match and 0 was the condition that could be a match or did not match. Currently, deep learning provides the best solutions to many problems in image recognition, speech recognition, and natural language processing. In this research, two different deep learning architectures, namely Deep Neural Network (DNN) and Convolutional Neural Network (CNN), trained to approach the taxonomic classification of metagenome data and spaced k-mers method for feature extraction. The result showed the DNN classifier reached 90.89 % and the CNN classifier reached 88.89 % accuracy at the genus level taxonomy.

Re-examination of the genus-level taxonomy of the pollen beetle subfamily Meligethinae – Part 1. Sagittogethes Audisio and Cline 2009 and allied genera; with description of a new genus (Coleoptera: Nitidulidae)

Recent molecular and morphological data derived from members of the pollen-beetle subfamily Meligethinae suggest the need to separate the genus Sagittogethes Audisio and Cline, 2009, including species mostly distributed in Western Palaearctic areas, into two distinct (although related) genera, Sagittogethes and Teucriogethes gen. n. This new genus, comprising the Western European Meligethes obscurus Erichson, 1845 as its type species, includes less than ten species distributed between the Iberian Peninsula and North Africa westward, and China and Japan eastward. All inclusive species utilize members of the genus Teucrium L. (Lamiacaeae: Ajugoideae) as larval host-plants. Morphological and bionomical information, and molecular data clearly demonstrate the necessity for updating the taxonomic position of the two clades. Based on molecular evidence, the new genus represents the sister-group of Thymogethes Audisio and Cline, 2009, while the sister-group relationships of the remaining Sagittogethes taxa with other Lamiaceae-associated genera of Meligethinae remain uncertain. Within the new genus, the relictual and rare Western Mediterranean species T. minutus (C.N.F. Brisout de Barneville, 1863) seems to occupy an isolated position.

Re-examination of the genus-level taxonomy of the pollen beetle subfamily Meligethinae – Part 1. &lt;em&gt;Sagittogethes&lt;/em&gt; Audisio and Cline 2009 and allied genera; with description of a new genus (Coleoptera: Nitidulidae)

Recent molecular and morphological data derived from members of the pollen-beetle subfamily Meligethinae suggest the need to separate the genus Sagittogethes Audisio and Cline, 2009, including species mostly distributed in Western Palaearctic areas, into two distinct (although related) genera, Sagittogethes and Teucriogethes gen. n. This new genus, comprising the Western European Meligethes obscurus Erichson, 1845 as its type species, includes less than ten species distributed between the Iberian Peninsula and North Africa westward, and China and Japan eastward. All inclusive species utilize members of the genus Teucrium L. (Lamiacaeae: Ajugoideae) as larval host-plants. Morphological and bionomical information, and molecular data clearly demonstrate the necessity for updating the taxonomic position of the two clades. Based on molecular evidence, the new genus represents the sister-group of Thymogethes Audisio and Cline, 2009, while the sister-group relationships of the remaining Sagittogethes taxa with other Lamiaceae-associated genera of Meligethinae remain uncertain. Within the new genus, the relictual and rare Western Mediterranean species T. minutus (C.N.F. Brisout de Barneville, 1863) seems to occupy an isolated position.

Within and Among Fish Species Differences in Simulated Turbine Blade Strike Mortality: Limits on the Use of Surrogacy for Untested Species

Use of surrogacy remains a useful method for prioritizing research on representatives of at-risk groups of fishes, yet quantifiable evidence in support of its use is generally not available. Blade strike impact represents one of the most traumatic stressors experienced by fish during non-volitional movements through hydropower turbines. Here, we use data generated from laboratory trials on blade strike impact experiments to directly test use of surrogacy for salmonid and clupeid fishes. Results of logistic regression indicated that a -taxonomic (genus) variable was not a significant predictor of mortality among large rainbow trout and brook trout. Similar results were found for young-of-the-year shad species, but genus-level taxonomy was a significant predictor of mortality while species was not. Multivariate analysis of morphometric data showed that shad clustered together based on similarities in fish shape which was also closely associated with genus. Logistic regression including size as a major covariate suggested total fish length was not a significant predictor of mortality, yet dose–response data suggest differential susceptibility to lower strike velocities. We suggest that use of surrogacy among species is justifiable but should be avoided within a species since the effects of size remain unclear.

A LITTLE LEARNING IS A DANGEROUS THING – ON THE USEFULNESS OF BARCODE DATA FOR GENUS-LEVEL TAXONOMY

The paper comments the usefulness of barcode data for genus-level taxonomy.

Taxonomy-based differences in feeding guilds of fish.

It has been taken for granted that feeding guilds and behavior in animals are linked to the taxonomic relatedness of species, but empirical evidence supporting such relationship is virtually missing. To examine the importance of taxonomy on trophic ecology, I here present the first well-resolved dietary taxonomy analysis based on feeding guilds (predation, herbivory, and filtering) among families and genera within the fish order Perciformes. Taxonomic relatedness in feeding did not vary with ecosystem dimension (marine vs. freshwater). Although predation dominates among Perciformes fishes, this study shows that in most cases taxonomic units (family or genus) are composed by species with several feeding guilds. Related species are more similar in feeding compared with species that are taxonomically more distant, demonstrating that there is a greater variation of feeding guilds within families than genera. Thus, there is no consistency in feeding guilds between family- and genus-level taxonomy. This study provides empirical support for the notion that genera are more informative than families, underlining that family-level taxonomy should be avoided to infer feeding habits of fish species at finer taxonomic resolution. Thus, the choice of taxonomic resolution (family or genus level) in ecological studies is key to avoid information loss and misleading results. I conclude that high-rank taxonomic units (i.e., above the generic level) are not appropriate to test research hypotheses about the feeding of fish.

A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution

Kangaroos and wallabies of the Macropus complex include the largest extant marsupials and hopping mammals. They have traditionally been divided among the genus Macropus (with three subgenera: Macropus, Osphranter and Notamacropus) and the monotypic swamp wallaby, Wallabia bicolor. Recent retrotransposon and genome-scale phylogenetic analyses clarify the placement of Wallabia as sister to Notamacropus, with Osphranter and Macropus branching successively deeper. In view of the traditional Macropus concept being paraphyletic, we undertake to resolve the species-level phylogeny and genus-level taxonomy of the Macropus complex. For the first time, we include nuclear and mitochondrial DNA covering all extant species, and the first DNA sequences from the extinct Toolache wallaby (Notamacropus greyi), which we find groups with the black-gloved wallaby (Notamacropus irma). Morphological variation was examined using geometric morphometric methods on three-dimensional surface-scanned skulls. Wallabia skull shape fell close to Notamacropus (or Thylogale when controlling for allometry). We recommend the subgenera Macropus, Osphranter and Notamacropus be elevated to genera, alongside Wallabia, based on comparisons with other established macropodine genera for cranial disparity, ecology and molecular divergence. Our time tree estimates that all four ‘Macropus’ genera diverged close to the Miocene–Pliocene boundary (~6–5 Mya), then diversified coincident with Pliocene expansion of grasslands in Australia.

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

BackgroundPan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family- or genus-level taxonomy. Moreover, sequencing errors often inflate the number of taxa present. Pacific Biosciences’ (PacBio’s) long-read technology in particular suffers from high error rates per base. Herein, we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome data.ResultsAnalysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity with regard to taxonomic classification. Examination of a 250-plus species mock community demonstrated correct species-level classification of > 90% of taxa, and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed. Propiniobacterium acnes (recently renamed Cutibacterium acnes) was the predominant species throughout, but was found at distinct relative abundances by site.ConclusionsOur microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene-based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution. Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.

Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification

The widespread Old World avian family Locustellidae (‘grassbirds and allies’) comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.

Taxonomic notes on the ground beetles in the genus Trephionus Bates, 1883 from central Honshu, Japan (Coleoptera, Carabidae, Sphodrini, Synuchina).

Trephionus Bates, 1883, a Japanese endemic genus in the subtribe Synuchina (Coleoptera, Carabidae, Sphodrini), is revised taxonomically based mainly on the shape of the endophallus, a membranous inner sac everted from the aedeagus of the male genitalia. Three known species from central Honshu, T. kinoshitai Habu, 1954; T. shibataianus Habu, 1978; and T. babai Habu, 1978, are re-defined based on this genital character, and five new species are described from the region: T. cylindriphallus Sasakawa, sp. n., T. niumontanus Sasakawa, sp. n., T. inexpectatus Sasakawa & Itô, sp. n., T. abiba Sasakawa & Itô, sp. n., and T. bifidilobatus Sasakawa & Itô, sp. n. The observed interspecies differences in endophallus morphology are discussed in terms of the species-level phylogeny and genus-level taxonomy of Trephionus.

Coalescent Species Tree Inference ofColuberandMasticophis

The genus-level taxonomy of the New World racers and whipsnakes (Coluber and Masticophis) has long been contentious regarding whether the two genera are mutually exclusive clades. This argument is based on morphological characters and largely single-locus analyses. Herein we examine the phylogenetic history of this group using multi-locus data in a coalescent framework, where paraphyly of Masticophis would result in support for the recognition of only a single genus (Coluber) for these species. We sample all currently recognized species and incorporate broad geographic sampling for the more widespread species groups to explore biogeographic patterns across North America. Our analyses suggest that Masticophis is monophyletic with respect to Coluber constrictor, albeit with low support. These results also demonstrate that there is undescribed cryptic diversity in this group, and we underscore additional avenues of study to further delimit unrecognized species in this clade. The biogeography of the island en...

Characterization of the complete chloroplast genomes of seven Manglietia and one Michelia species (Magnoliales: Magnoliaceae)

Complete chloroplast (cp) genomes were reconstructed for seven Manglietia (Ma. aromatica, Ma. calcarea, Ma. conifera, Ma. duclouxii, Ma. glaucifolia, Ma. insignis and Ma. megaphylla) and one Michelia (Mi. alba) species using Illumina sequencing technology, with their genome sizes ranging from 159,973 to 160,106 bp. They all comprise a pair of inverted repeat (IR) regions, which were separated by a large single-copy (LSC) region and a small single-copy (SSC) region, and encode the same set of 132 genes, including 87 protein-coding genes (79 PCG species), 37 tRNA genes (30 tRNA species) and eight rRNA genes (four rRNA species). Sixteen gene species contain one or two introns. These cp genomes have almost identical A + T-biased nucleotide compositions. Phylogenetic analysis supported the current subfamily-level taxonomy of the family Magnoliaceae, but challenged the genus-level taxonomy of the subfamily Magnolioideae.

Phenotypic evolution in marmoset and tamarin monkeys (Cebidae, Callitrichinae) and a revised genus-level classification

Marmosets and tamarins (Cebidae, Callitrichinae) constitute the most species-rich subfamily of New World monkeys and one of the most diverse phenotypically. Despite the profusion of molecular phylogenies of the group, the evolution of phenotypic characters under the rapidly-emerging consensual phylogeny of the subfamily has been little studied, resulting in taxonomic proposals that have limited support from other datasets. We examined the evolution of 18 phenotypic traits (5 continuous and 13 discrete), including pelage, skull, dentition, postcrania, life-history and vocalization variables in a robust molecular phylogeny of marmoset and tamarin monkeys, quantifying their phylogenetic signal and correlations among some of the traits. At the family level, our resulting topology supports owl monkeys (Aotinae) as sister group of Callitrichinae. The topology of the callitrichine tree was congruent with previous studies except for the position of the midas group of Saguinus tamarins, which placement as sister of the bicolor group did not receive significant statistical support in both Maximum Parsimony and Bayesian Inference analyses. Our results showed that the highest value of phylogenetic signal among continuous traits was displayed by the long call character and the lowest was exhibited in the home range, intermediate values were found in characters related to osteology and skull size. Among discrete traits, pelage and osteology had similar phylogenetic signal. Based on genetic, osteological, pelage and vocalization data, we present an updated genus-level taxonomy of Callitrichinae, which recognizes six genera in the subfamily: Callimico, Callithrix, Cebuella, Mico, Leontopithecus and Saguinus. To reflect their phenotypic distinctiveness and to avoid the use of the informal “species group”, we subdivided Saguinus in the subgenera Leontocebus, Saguinus and Tamarinus (revalidated here).

Historical insights on nearly 130 years of research on Paleozoic radiolarians

ABSTRACT This paper summarizes and highlights the history of descriptive genus-level taxonomy on Paleozoic radiolarians grouped in five major phases: 1) initial discoveries in the 1890s; 2) ignored during the first half of the 1900s; 3) renewed interest during the 1950s to 1970s; 4) the “fast” years of the late 1970s to 1990s; and 5) the early 21st century quest for the oldest and significant progress in the late Permian. In the 1890s, radiolarians were identified with certainty by Hinde in Ordovician radiolarian cherts. Following Hinde's great discovery, and after a 50-year dormant period, Deflandre revived the study of Paleozoic radiolarians through his groundbreaking study of Albaillella from Carboniferous phosphatic nodules, combined with his genius for understanding evolutionary implications. Additional important work was conducted in this third phase by Foreman, particularly with respect to the description of the radiolarian internal structures based on material extracted from Devonian carbonate nod...