Using ultraconserved elements to reconstruct the termite tree of life

The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting 50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of Cryptocercus, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted in silico between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: https://github.com/oist/TER-UCE-DB/.

Virtual tour of Circassian costume exhibition created by Madina Hatsukova

This article explores the works of the famous Kabardian fashion designer Madina Alisagovna Hatsukova, whose costumes are worn by the guards of the King of Jordan, artists of Kabardino-Balkaria and Karachay-Cherkessia, prominent statesmen of the Chechen Republic, popular singers and musicians, and numerous ladies for their wedding ceremonies. The article represents a panoramic overview of the works of Madina Hatsukova, taking into account all aspects of interest of the designer. Description is given to various types of activity of the fashion designer – from hand embroidery and lace weaving to creating sewing patterns and scientific research on decoding of the ornaments in the museum samples of ancient costumes. This publication is inspired by the Madina Hatsukova’s personal exhibition “Princess of the Sun”, held in the North Caucasus branch of the State Museum of Oriental Art in Maykop in September-October 2021. The novelty of this article consists in comprehensive analysis of the works of Madina Hatsukova, which are widely known in North Caucasus and not so much to the Russians audience interested in modern ethnic costume. Although Madina’s works are intentionally limited to the traditional patterns and configuration, she experiments with different types of fabrics, their combinations and color solutions. National costume for a symbol of cultural revival, rather than a symbol of the past; it is the symbol of ethnic identification. Madina Hatsukova contributes to high symbolic load of the traditional costume, forms empathy of not only Circassians, but the entire multicultural population of the Russian Federation.

PSXII-1 Tracing the historical genetic components in turano-mongolian cattle breeds based on the microsatellite analysis of modern and museum samples

In their centuries-long history, the nomads of the south of Russia developed the local cattle breeds, which are well adapted to the harsh steppe conditions. In 20th century, the population size of such cattle breeds was dramatically decreased. At the same time, intensive cross breeding with high-producing transboundary breeds had been practiced on the small remaining part of population. The aim of our study was to trace the historical genetic components in modern populations of local cattle breeds of the turano-mongolian origin. The historical specimens of Kalmyk (n = 10), Kyrgyz (n = 11) and Kazakh (n = 3) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry and subjected to the study. The modern representatives of Kalmyk (n = 28), Kyrgyz (n = 20), Kazakh White-headed (n = 30), Hereford (n = 26), and Mongolian (n = 41) cattle were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst research Center for Animal Husbandry. The samples were genotyped for 11 microsatellite loci (BM1818, BM2113, BM1824, ETH10, ETH225, INRA023, SPS115, TGLA53, TGLA122, TGLA126, and TGLA227). For historical samples, the PCR reactions were carried out in five replicates to determine the consensus genotypes. In total, 132 alleles were identified, including 97 alleles in historical samples and 124 alleles in modern samples. The values of unbiased expected heterozygosity were 0.767–0.776 and 0.653–0.778 for the historical and modern samples, respectively. The STRUCTURE clustering showed the visible differences in genetic structure between the historical and modern populations of Kalmyk, Kyrgyz and Kazakh cattle breeds; however, the historical genetic components were still maintained in modern representatives of all of studied breeds. The research results will be useful for the sustainable breeding and conservation of valuable local genetic resources. The study was funded by the RSF No. 19-76-20012.

Using historical museum samples to examine divergent and parallel evolution in the invasive starling

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

Integrative description of new giant pill-millipedes from southern Thailand (Diplopoda, Sphaerotheriida, Zephroniidae)

Two new species of giant pill-millipedes, Zephronia viridisoma Rosenmejer & Wesener sp. nov. and Sphaerobelum aesculus Rosenmejer & Wesener sp. nov., are described based on museum samples from southern Thailand. Zephronia viridisoma sp. nov. comes from Khao Lak, while the type locality of S. aesculus sp. nov. is on Phuket Island. Both species are described integratively, combining light microscopy, scanning electron microscopy, multi-layer photography, micro-CT scans and genetic barcoding. Genetic barcoding was successfully conducted for holotypes of both new species, which could be added to a dataset of all published sequences of the family Zephroniidae, including all described species from Thailand, Laos and Cambodia up to 2020. Genetic barcoding of the COI gene revealed another female of S. aesculus sp. nov., 160 km east of the type locality. Both new species are genetically distant from all other Zephroniidae from Thailand and surrounding countries, showing uncorrected p-distances of 16.8–23.1%. A virtual cybertype of a paratype of Z. viridisoma sp. nov. was created and made publically accessible.

Comparative Study of the Genetic Diversity of Local Steppe Cattle Breeds from Russia, Kazakhstan and Kyrgyzstan by Microsatellite Analysis of Museum and Modern Samples

The comparative molecular genetic study of museum and modern representatives of cattle breeds can help to elucidate the origin and maintenance of historical genetic components in modern populations. We generated the consensus genotypes for 11 microsatellite loci for 24 museum samples of Kalmyk, Kyrgyz, and Kazakh cattle, dated from the first quarter of the 20th century, and compared them with those of modern Kalmyk, Kyrgyz, and Kazakh white-headed breeds. The level of genetic diversity of the modern Kalmyk and Kyrgyz cattle (uHe = 0.771–0.778) was similar to those observed in the museum samples (uHe = 0.772–0.776), while a visible decrease in genetic variability in the modern Kazakh white-headed breed compared to museum Kazakh cattle was detected (uHe = 0.726 and 0.767, respectively). The PCA plot, FST- and Jost’s D-based networks, and STRUCTURE clustering provided strong evidence of the maintenance of the historical genetic background in modern populations of Kalmyk and Kyrgyz cattle. In spite of the allele pool of Kazakh white-headed cattle having undergone great changes compared to the museum Kazakh cattle, several animals still carry the visible aspect of the historical genetic components. Our results can be used for the selection of individuals for the creation of gene banks and may significantly improve the efficiency of conservation programs aimed at preserving genetic diversity in the national genetic resources of cattle.

Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

Recent and Rapid Radiation of the Highly Endangered Harlequin Frogs (Atelopus) into Central America Inferred from Mitochondrial DNA Sequences

Populations of amphibians are experiencing severe declines worldwide. One group with the most catastrophic declines is the Neotropical genus Atelopus (Anura: Bufonidae). Many species of Atelopus have not been seen for decades and all eight Central American species are considered “Critically Endangered”, three of them very likely extinct. Nonetheless, the taxonomy, phylogeny, and biogeographic history of Central American Atelopus are still poorly known. In this study, the phylogenetic relationships among seven of the eight described species in Central America were inferred based on mitochondrial DNA sequences from 103 individuals, including decades-old museum samples and two likely extinct species, plus ten South American species. Among Central American samples, we discovered two candidate species that should be incorporated into conservation programs. Phylogenetic inference revealed a ladderized topology, placing species geographically furthest from South America more nested in the tree. Model-based ancestral area estimation supported either one or two colonization events from South America. Relaxed-clock analysis of divergence times indicated that Atelopus colonized Central America prior to 4 million years ago (Ma), supporting a slightly older than traditional date for the closure of the Isthmus. This study highlights the invaluable role of museum collections in documenting past biodiversity, and these results could guide future conservation efforts. An abstract in Spanish (Resumen) is available as supplementary material.

Bats Out of Africa: Disentangling the Systematic Position and Biogeography of Bats in Cabo Verde

Cabo Verde Archipelago presents one of the largest knowledge gaps in the distribution and taxonomy of bats in the world. Old works indicated that there are five species classified as European taxa. We have conducted an integrative taxonomy to revise the systematic position and distribution of Cabo Verdean bats with molecular, morphological, and ecological data, to test their native or exotic origin, and infer possible colonization patterns based on fieldwork and museum samples. Results showed that Cabo Verde Hypsugo is closely related to those from the Canary Islands, in which the taxonomic status is under debate, presenting unique mitochondrial and nuclear haplotypes. We also expanded the distribution of Taphozous nudiventris for Fogo Island through pellets and acoustic identification, showed unique haplotypes for this species, and that Miniopterus schreibersii shared a haplotype with European, North African, and Western Asian specimens. The morphological and acoustic identification of Cabo Verdean specimens was challenging because of the lack of modern morphological descriptions and similarity of echolocation calls within the same genus. More studies are definitely needed to access the systematic of bat species in the archipelago, but this work is the first step for the establishment of conservation actions of the probable only native Cabo Verdean mammals.