A new Gammarus species from Xinjiang Uygur Autonomous Region (China) with a key to Xinjiang freshwater gammarids (Crustacea, Amphipoda, Gammaridae)

The Gammarus zhouqiongi sp. nov. are described and illustrated from Xinjiang Uygur Autonomous Region, China. The new species is characterized by pereopods III-IV with long straight setae on posterior margins and inner ramus of uropod III 0.7 times as long as outer ramus. Detailed morphological comparisons with related species are discussed. The mitochondrial cytochrome c oxidase 1 (COI) sequence differs from the other Gammarus species in Xinjiang by 16.6%-32.4% in K2P distance. The mitochondrial (COI, 16S) and nuclear markers (28S, EF1α) show that the new species is an independent branch in the phylogenetic tree. A key to identify Gammarus species in the Xinjiang are also provided.

Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish

Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.

Species Phylogeny versus Gene Trees: A Case Study of an Incongruent Data Matrix Based on Paphiopedilum Pfitz. (Orchidaceae)

The phylogeny of the genus Paphiopedilum based on the plastome is consistent with morphological analysis. However, to date, none of the analyzed nuclear markers has confirmed this. Topology incongruence among the trees of different nuclear markers concerns entire sections of the subgenus Paphiopedilum. The low-copy nuclear protein-coding gene PHYC was obtained for 22 species representing all sections and subgenera of Paphiopedilum. The nuclear-based phylogeny is supported by morphological characteristics and plastid data analysis. We assumed that an incongruence in nuclear gene trees is caused by ancestral homoploid hybridization. We present a model for inferring the phylogeny of the species despite the incongruence of the different tree topologies. Our analysis, based on six low-copy nuclear genes, is congruent with plastome phylogeny and has been confirmed by phylogenetic network analysis.

An Integrative Study on Asphondylia spp. (Diptera: Cecidomyiidae), Causing Flower Galls on Lamiaceae, with Description, Phenology, and Associated Fungi of Two New Species

An integrative study on some species of Asphondylia was carried out. Two species of gall midges from Italy, Asphondylia rivelloi sp. nov. and Asphondylia micromeriae sp. nov. (Diptera: Cecidomyiidae), causing flower galls respectively on Clinopodium vulgare and Micromeria graeca (Lamiaceae), are described and illustrated. The characteristics of each developmental stage and induced galls are described, which allowed the discrimination of these new species in the complex of Asphondylia developing on Lamiaceae plants. Molecular data based on sequencing both nuclear (ITS2 and 28S-D2) and mitochondrial (COI) genes are also provided in support of this discrimination. Phylogeny based on nuclear markers is consistent with the new species, whereas COI phylogeny suggests introgression occurring between the two species. However, these species can also be easily identified using a morphological approach. Phenology of host plants and gall midges are described, and some peculiar characteristics allow the complete and confident discrimination and revision of the treated species. Gall-associated fungi were identified as Botryosphaeria dothidea,Alternaria spp., and Cladosporium spp.

Four new species of Russula subsection Roseinae from tropical montane forests in western Panama

Species of the genus Russula are key components of ectomycorrhizal ecosystems worldwide. Nevertheless, their diversity in the tropics is still poorly known. This study aims to contribute to the knowledge of the diversity of Russula species classified in subsection Roseinae based on specimens recently collected in tropical montane rainforests in western Panama. A five gene multilocus phylogeny based on the nuclear markers ITS nrDNA, MCM7, RPB1, RPB2 and TEF-1α was constructed to identify the systematic position of 22 collections from Panama. Four new species, Russula cornicolor, Russula cynorhodon, Russula oreomunneae and Russula zephyrovelutipes are formally described and illustrated. None of the four species are sister species and they are more closely related to North American or Asian species. Two of the newly described species were associated with the ectomycorrhizal tree species Oreomunnea mexicana, while the other two species were associated with Quercus species. All four species are so far only known from mountains in western Panama.

Rewinding the molecular clock in the genus Carabus (Coleoptera: Carabidae) in light of fossil evidence and the Gondwana split: A reanalysis

Molecular clocks have become powerful tools given increasing sequencing and fossil resources. However, calibration analyses outcomes depend on the choice of priors. Here, we revisited the seminal dating study published by Andújar and coworkers of the genus Carabus proposing that prior choices need re-evaluation. We hypothesized that reflecting fossil evidence and the Gondwanan split properly significantly rewinds the molecular clock. We re-used the dataset including five mitochondrial and four nuclear DNA fragments with a total length of 7888 nt. Fossil evidence for Oligocene occurrence of Calosoma was considered. Root age was set based on the fossil evidence of Harpalinae ground beetles in the Upper Cretaceous. Paleogene divergence of the outgroup taxa Ceroglossini and Pamborini is introduced as a new prior based on current paleontological and geological literature. The ultrametric time-calibrated tree of the extended nd5 dataset resulted in a median TMRCA Carabus of 53.92 Ma (HPD 95% 45.01–63.18 Ma), roughly 30 Ma older than in the Andújar study. The splits among C. rugosus and C. morbillosus (A), C. riffensis from the European Mesocarabus (B), and Eurycarabus and Nesaeocarabus (C) were dated to 17.58 (12.87–22.85), 24.14 (18.02–30.58), and 21.6 (16.44–27.43) Ma. They were decidedly older than those previously reported (7.48, 10.93, and 9.51 Ma). These changes were driven almost entirely by constraining the Carabidae time-tree root with a Harpalinae amber fossil at ~99 Ma. Utilizing the nd5 dating results of three well-supported Carabus clades as secondary calibration points for the complete MIT-NUC dataset led to a TMRCA of Carabus of 44.72 (37.54–52.22) Ma, compared with 25.16 Ma (18.41–33.04 Ma) in the previous study. Considering fossil evidence for Oligocene Calosoma and Late Cretaceous Harpalini together with the Gondwanan split as a new prior, our new approach supports the origin of genus Carabus in the Eocene. Our results are preliminary because of the heavy reliance on the nd5 gene, and thus will have to be tested with a sufficient set of nuclear markers. Additionally, uncertainties due to dating root age of the tree based on a single fossil and outgroup taxon affect the results. Improvement of the fossil database, particularly in the supertribe Carabitae, is needed to reduce these uncertainties in dating Carabus phylogeny.

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

Cell Type–Specific Nuclei Markers: The Need for Human Brain Research to Go Nuclear

Identifying and interrogating cell type–specific populations within the heterogeneous milieu of the human brain is paramount to resolving the processes of normal brain homeostasis and the pathogenesis of neurological disorders. While brain cell type–specific markers are well established, most are localized on cellular membranes or within the cytoplasm, with limited literature describing those found in the nucleus. Due to the complex cytoarchitecture of the human brain, immunohistochemical studies require well-defined cell-specific nuclear markers for more precise and efficient quantification of the cellular populations. Furthermore, efficient nuclear markers are required for cell type–specific purification and transcriptomic interrogation of archived human brain tissue through nuclei isolation–based RNA sequencing. To sate the growing demand for robust cell type–specific nuclear markers, we thought it prudent to comprehensively review the current literature to identify and consolidate a novel series of robust cell type–specific nuclear markers that can assist researchers across a range of neuroscientific disciplines. The following review article collates and discusses several key and prospective cell type–specific nuclei markers for each of the major human brain cell types; it then concludes by discussing the potential applications of cell type–specific nuclear workflows and the power of nuclear-based neuroscientific research.

Integrative Taxonomy of Dermacentor variabilis (Ixodida: Ixodidae) with Description of a New Species, Dermacentor similis n. sp.

Dermacentor variabilis is the most widely distributed three-host tick in North America, and transmits a variety of pathogens. Within the United States, this species has a discontinuous distribution, widespread east of the Rocky Mountains and with a few populations west of the Rockies. Phylogenetic evidence based on individual markers or relatively small data sets has suggested that populations at both sides of this geographic barrier may correspond to two different species. In this study, we further explore this hypothesis using an integrative taxonomy framework. Both molecular (mitochondrial and nuclear markers) and morphological analyses of specimens collected from central-eastern and western states were performed to explore species delimitation in this taxon. Results from these analyses were consistent, and provide strong evidence that D. variabilis actually corresponds to two species. Herein, the western populations are described as a new species, Dermacentor similis n. sp. The usefulness of integrative taxonomy in the context of species delimitation is also discussed.

Enlightening the black and white: species delimitation and UNITE species hypothesis testing in the Russula albonigra species complex

ABSTRACTRussula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological range and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s. lat. represents a species complex consisting of at least five European, three North American, and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra complex is proposed and a key to the described European species of R. subgen. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta, and R. ustulata. Different thresholds of UNITE species hypotheses were tested against the taxonomic data. The distance threshold of 0.5% gives a perfect match to the phylogenetically defined species within the R. albonigra complex. Publicly available sequence data can contribute to species delimitation and increase our knowledge on ecology and distribution, but the pitfalls are short and low quality sequences.