Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities

The first genetic study of the holotype of the Gansu short-tailed shrew, Blarinella griselda Thomas, 1912, is presented. The mitochondrial analysis demonstrated that the type specimen of B. griselda is close to several recently collected specimens from southern Gansu, northern Sichuan and Shaanxi, which are highly distinct from the two species of Asiatic short-tailed shrews of southern Sichuan, Yunnan, and Vietnam, >B. quadraticauda and B. wardi. Our analysis of four nuclear genes supported the placement of B. griselda as sister to B. quadraticauda / B. wardi, with the level of divergence between these two clades corresponding to that among genera of Soricinae. A new generic name, Parablarinella, is proposed for the Gansu short-tailed shrew. Karyotypes of Parablarinella griselda(2n = 49, NFa = 50) and B. quadraticauda (2n = 49, NFa = 62) from southern Gansu are described. The tribal affinities of Blarinellini and Blarinini are discussed.Copyright Anna A. Bannikova et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

The effect of climate change on avian offspring production: A global meta-analysis

Climate change affects timing of reproduction in many bird species, but few studies have investigated its influence on annual reproductive output. Here, we assess changes in the annual production of young by female breeders in 201 populations of 104 bird species (N = 745,962 clutches) covering all continents between 1970 and 2019. Overall, average offspring production has declined in recent decades, but considerable differences were found among species and populations. A total of 56.7% of populations showed a declining trend in offspring production (significant in 17.4%), whereas 43.3% exhibited an increase (significant in 10.4%). The results show that climatic changes affect offspring production through compounded effects on ecological and life history traits of species. Migratory and larger-bodied species experienced reduced offspring production with increasing temperatures during the chick-rearing period, whereas smaller-bodied, sedentary species tended to produce more offspring. Likewise, multi-brooded species showed increased breeding success with increasing temperatures, whereas rising temperatures were unrelated to repro- ductive success in single-brooded species. Our study suggests that rapid declines in size of bird populations reported by many studies from different parts of the world are driven only to a small degree by changes in the production of young

Identification of Alternative Splicing in Proteomes of Human Melanoma Cell Lines without RNA Sequencing Data

Alternative splicing is one of the main regulation pathways in living cells beyond simple changes in the level of protein expression. Most of the approaches proposed in proteomics for the identification of specific splicing isoforms require a preliminary deep transcriptomic analysis of the sample under study, which is not always available, especially in the case of the re-analysis of previously acquired data. Herein, we developed new algorithms for the identification and validation of protein splice isoforms in proteomic data in the absence of RNA sequencing of the samples under study. The bioinformatic approaches were tested on the results of proteome analysis of human melanoma cell lines, obtained earlier by high-resolution liquid chromatography and mass spectrometry (LC-MS). A search for alternative splicing events for each of the cell lines studied was performed against the database generated from all known transcripts (RefSeq) and the one composed of peptide sequences, which included all biologically possible combinations of exons. The identifications were filtered using the prediction of both retention times and relative intensities of fragment ions in the corresponding mass spectra. The fragmentation mass spectra corresponding to the discovered alternative splicing events were additionally examined for artifacts. Selected splicing events were further validated at the mRNA level by quantitative PCR

Identification of Alternative Splicing in Proteomes of Human Melanoma Cell Lines without RNA Sequencing Data

Alternative splicing is one of the main regulation pathways in living cells beyond simple changes in the level of protein expression. Most of the approaches proposed in proteomics for the identification of specific splicing isoforms require a preliminary deep transcriptomic analysis of the sample under study, which is not always available, especially in the case of the re-analysis of previously acquired data. Herein, we developed new algorithms for the identification and validation of protein splice isoforms in proteomic data in the absence of RNA sequencing of the samples under study. The bioinformatic approaches were tested on the results of proteome analysis of human melanoma cell lines, obtained earlier by high-resolution liquid chromatography and mass spectrometry (LC-MS). A search for alternative splicing events for each of the cell lines studied was performed against the database generated from all known transcripts (RefSeq) and the one composed of peptide sequences, which included all biologically possible combinations of exons. The identifications were filtered using the prediction of both retention times and relative intensities of fragment ions in the corresponding mass spectra. The fragmentation mass spectra corresponding to the discovered alternative splicing events were additionally examined for artifacts. Selected splicing events were further validated at the mRNA level by quantitative PCR

Who are you, Griselda? A replacement name for a new genus of the Asiatic short-tailed shrews (Mammalia, Eulipotyphla, Soricidae): molecular and morphological analyses with the discussion of tribal affinities

The first genetic study of the holotype of the Gansu short-tailed shrew, Blarinella griselda Thomas, 1912, is presented. The mitochondrial analysis demonstrated that the type specimen of B. griselda is close to several recently collected specimens from southern Gansu, northern Sichuan and Shaanxi, which are highly distinct from the two species of Asiatic short-tailed shrews of southern Sichuan, Yunnan, and Vietnam, B. quadraticauda and B. wardi. Our analysis of four nuclear genes supported the placement of B. griselda as sister to B. quadraticauda / B. wardi, with the level of divergence between these two clades corresponding to that among genera of Soricinae. A new generic name, Parablarinella, is proposed for the Gansu short-tailed shrew. Karyotypes of Parablarinella griselda (2n = 49, NFa = 50) and B. quadraticauda (2n = 49, NFa = 62) from southern Gansu are described. The tribal affinities of Blarinellini and Blarinini are discussed

A Molecular Phylogeny of <i>Stylodipus</i> (Dipodidae, Mammalia): A Small Genus with a Complex History

A range-wide phylogenetic/phylogeographic study of the three-toed jerboas of the genus Stylodipus is conducted using the mitochondrial cytb gene and fragments of several nuclear genes. The genus has been believed to include three species: S. telum (W Central Asia, SE Europe), S. andrewsi (E Central Asia), and S. sungorus (Dzungar basin). Our data support the dichotomy between S. andrewsi and the other taxa forming S. telum species group. Within the latter, both mtDNA and nuclear loci indicate a species-level divergence between S. telum and the S. t. birulae lineage (Zaisan depression, NE Kazakhstan), previously considered a subspecies of S. telum and here elevated to full species. S. sungorus is recovered as a close sister group to S. birulae on the basis of nuclear data but clustered with S. telum in the mitochondrial tree. The latter taxon is the most variable and includes two closely related eastern and western sublineages, separated by the Volga-Ural sands and joined by a more divergent S. t. karelini lineage (E Kazakhstan). The observed mitonuclear discordance is hypothesized to occur due to mtDNA introgression resulting from hybridization between S. sungorus and S. t. karelini, which highlights the important role of reticulations in the evolution of Dipodidae

MS/MS-Free Protein Identification in Complex Mixtures Using Multiple Enzymes with Complementary Specificity

In this work, we present the results of evaluation of a workflow that employs a multienzyme digestion strategy for MS1-based protein identification in “shotgun” proteomic applications. In the proposed strategy, several cleavage reagents of different specificity were used for parallel digestion of the protein sample followed by MS1 and retention time (RT) based search. Proof of principle for the proposed strategy was performed using experimental data obtained for the annotated 48-protein standard. By using the developed approach, up to 90% of proteins from the standard were unambiguously identified. The approach was further applied to HeLa proteome data. For the sample of this complexity, the proposed MS1-only strategy determined correctly up to 34% of all proteins identified using standard MS/MS-based database search. It was also found that the results of MS1-only search were independent of the chromatographic gradient time in a wide range of gradients from 15–120 min. Potentially, rapid MS1-only proteome characterization can be an alternative or complementary to the MS/MS-based “shotgun” analyses in the studies, in which the experimental time is more important than the depth of the proteome coverage