DNA-based occurrence dataset on peatland fungal communities studied by metabarcoding in north-western Siberia.

Background: The paper represents the first DNA-based occurrence dataset on peatland fungal communities published for north-western Siberia, the first for Russia and complements several existing datasets on metabarcoding of peat soils globally. New information: The aim of the present publication is to describe the first DNA-based occurrence dataset on fungal communities in peat soils and other substrates studied by the eDNA approach in the Mukhrino raised bog, located in a large paludified area of north-western Siberia. A comparison of the species diversity of larger fungi identified by the conventional approach and by eDNA showed a high proportion of shared taxa. Other groups (mainly Ascomycota), described by metabarcoding, revealed high diversity compared with conventional observation. Overall, the species richness identified in one peatland locality (the Mukhrino Bog) was comparable in number of species to the global estimation of fungal diversity in peatlands, previously reported in literature.

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Phylogenomics of the world's otters.

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.

Chromosome-Level Genome Assemblies Expand Capabilities of Genomics for Conservation Biology.

Genome assemblies are in the process of becoming an increasingly important tool for understanding genetic diversity in threatened species. Unfortunately, due to limited budgets typical for the area of conservation biology, genome assemblies of threatened species, when available, tend to be highly fragmented, represented by tens of thousands of scaffolds not assigned to chromosomal locations. The recent advent of high-throughput chromosome conformation capture (Hi-C) enables more contiguous assemblies containing scaffolds spanning the length of entire chromosomes for little additional cost. These inexpensive contiguous assemblies can be generated using Hi-C scaffolding of existing short-read draft assemblies, where N50 of the draft contigs is larger than 0.1% of the estimated genome size and can greatly improve analyses and facilitate visualization of genome-wide features including distribution of genetic diversity in markers along chromosomes or chromosome-length scaffolds. We compared distribution of genetic diversity along chromosomes of eight mammalian species, including six listed as threatened by IUCN, where both draft genome assemblies and newer chromosome-level assemblies were available. The chromosome-level assemblies showed marked improvement in localization and visualization of genetic diversity, especially where the distribution of low heterozygosity across the genomes of threatened species was not uniform.

The communities of terrestrial macrofungi in different forest types in vicinities of Khanty-Mansiysk (middle taiga zone of West Siberia).

BACKGROUND: The diversity of macrofungi in the vicinities of Khanty-Mansiysk (Yugra, Russia) was surveyed using a method of permanent sampling plots. Ten plots, each consisting of a number of micro-plots, were established in several different communities ranging from old-growth mixed taiga forest to its derivatives in cutting succession and bogged areas. For more complete registration of the mycota, plots were supplemented with random walking routes directly nearby. Survey results were subjected to various quantitative analyses which allowed not only to evaluate the diversity of fungi but also to obtain valuable information on occurrence, abundance and ecology of individual species as well as community structure and its dynamics in the course of ecological succession. The paper reports the results of the first year of observations. NEW INFORMATION: 460 species of terrestrial macrofungi revealed in a poorly explored area in middle taiga of West Siberia. The plot-based study revealed differences between communities of terrestrial macrofungi of old coniferous forests, their after-cutting secondary formations and bogged stages. The survey allowed to reveal records of 3 species listed in the Red Data Book of Russia and 9 species listed in the Red Data Book of Yugra.