The genome of the pygmy right whale illuminates the evolution of rorquals

Ocean-Wide Conservation Genomics of Blue Whales Suggest New Northern Hemisphere Subspecies

The blue whale is an endangered and globally distributed species of baleen whale with multiple described subspecies, including the morphologically and genetically distinct pygmy blue whale. North Atlantic and North Pacific populations, however, are currently regarded as a single subspecies despite being separated by continental land masses and acoustic call differences. To determine the degree of isolation among the Northern Hemisphere populations, 14 North Pacific and 6 Western Australian blue whale nuclear and mitochondrial genomes were sequenced and analysed together with 11 publicly available North Atlantic blue whale genomes. Population genomic analyses revealed distinctly differentiated clusters and limited genetic exchange among all three populations, indicating a high degree of isolation between the Northern Hemisphere populations. Nevertheless, the genomic and mitogenomic distances between all blue whale populations, including the Western Australian pygmy blue whale, are low when compared to other inter-subspecies distances in cetaceans. Given that the Western Australian pygmy blue whale is an already recognised subspecies and further supported by previously reported acoustic differences, a proposal is made to treat the two Northern Hemisphere populations as separate subspecies, namely Balaenoptera musculus musculus (North Atlantic blue whale) and Balaenoptera musculus sulfureus (North Pacific blue whale). Furthermore, a first molecular viability assessment of all three populations not only found a generally high genomic diversity among blue whales but also a lack of alleles at low frequency, non-neutral evolution and increased effects of inbreeding. This suggests a substantial anthropogenic impact on the genotypes of blue whales and calls for careful monitoring in future conservation plans.

Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness

Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in genomic studies. Here, we report a 2.85-Gb gap-free telomere-to-telomere genome of a ram (T2T-sheep1.0), including all autosomes and the X and Y chromosomes. This genome adds 220.05 Mb of previously unresolved regions and 754 new genes to the most updated reference assembly ARS-UI_Ramb_v3.0; it contains four types of repeat units (SatI, SatII, SatIII and CenY) in centromeric regions. T2T-sheep1.0 has a base accuracy of more than 99.999%, corrects several structural errors in previous reference assemblies and improves structural variant detection in repetitive sequences. Alignment of whole-genome short-read sequences of global domestic and wild sheep against T2T-sheep1.0 identifies 2,664,979 new single-nucleotide polymorphisms in previously unresolved regions, which improves the population genetic analyses and detection of selective signals for domestication (for example, ABCC4) and wool fineness (for example, FOXQ1).

Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales

Marine ecosystems are ideal for studying evolutionary adaptations involved in lineage diversification due to few physical barriers and reduced opportunities for strict allopatry compared to terrestrial ecosystems. Cetaceans (whales, dolphins, and porpoises) are a diverse group of mammals that successfully adapted to various habitats within the aquatic environment around 50 million years ago. While the overall adaptive transition from terrestrial to fully aquatic species is relatively well understood, the radiation of modern whales is still unclear. Here high-quality genomes derived from previously published data were used to identify genomic regions that potentially underpinned the diversification of baleen whales (Balaenopteridae). A robust molecular phylogeny was reconstructed based on 10,159 single copy and complete genes for eight mysticetes, seven odontocetes and two cetacean outgroups. Analysis of positive selection across 3,150 genes revealed that balaenopterids have undergone numerous idiosyncratic and convergent genomic variations that may explain their diversification. Genes associated with aging, survival and homeostasis were enriched in all species. Additionally, positive selection on genes involved in the immune system were disclosed for the two largest species, blue and fin whales. Such genes can potentially be ascribed to their morphological evolution, allowing them to attain greater length and increased cell number. Further evidence is presented about gene regions that might have contributed to the extensive anatomical changes shown by cetaceans, including adaptation to distinct environments and diets. This study contributes to our understanding of the genomic basis of diversification in baleen whales and the molecular changes linked to their adaptive radiation, thereby enhancing our understanding of cetacean evolution.

Telomere-to-telomere genome assembly of a male goat reveals variants associated with cashmere traits

A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing insights into domestication and selection in goats and related species. Here, we assemble a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), including a Y chromosome of 20.96 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrects numerous genome-wide structural and base errors in previous assemblies and adds 288.5 Mb of previously unresolved regions and 446 newly assembled genes to the reference genome. We sequence the genomes of five representative goat breeds for PacBio reads, and use T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 (7.42%) in the previously unresolved regions. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the previously unresolved regions. Also, our analyses reveal a set of selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

The tympanoperiotic complex of the blue whale, Balaenoptera musculus

The tympanoperiotic complex of a blue whale Balaenoptera musculus is described and compared to the homologous structures in the other extant and fossil baleen whale species. The periotic and the tympanic bulla represent informative anatomical regions in both functional and phylogenetic studies and for this reason a micro-CT scan of the bones was performed in order to better characterize their external aspect and to reconstruct the inner structures. In particular, the cochlea, the semicircular canals and associated portions of the periotic are reconstructed so that these structures may be used in phylogenetic analyses. We observed that the blue whale periotic is characterized by the presence of a strong dorsal protrusion which is posteriorly bordered by a previously undescribed morphological character that we name the posterotransverse fossa. The peculiar shape of the anterior process and the en echelon organization of the posterior foramina of the pars cochlearis are also described and compared. From a phylogenetic perspective, the blue whale is confirmed to be closely related to the fin whale, Balaenoptera physalus, but it is suggested, based on ear bone characters only, that it diverged before the other balaenopterid species in the phylogeny of Balaenopteridae. This placement supports a series of morphological observations suggesting that the extant blue whale was an early-diverging member of Balaenoptera. Our results help to decipher the evolutionary origin of the blue whale, the largest living animal, by allowing new and more detailed morphological analyses of the balaenopterid fossil record.

The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils

Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.

In search of the origin of crown Mysticeti

Recent research on mysticete fossils from the Late Eocene and Oligocene has revolutionised our understanding of the diversity and evolutionary scenarios for early baleen whales. For example, aetiocetids are a possible, though controversial, lineage that bridges the gap between the toothed and baleen-bearing mysticetes, and eomysticetids show a further transitional step towards the baleen-bearing status, with the presence of non-functional dentition in adults. However, information about the origin of crown mysticetes, including the most recent common ancestor of all extant lineages and its descendants, is critical to further understanding the evolution of baleen whales. The phylogenetic positions of the Oligocene Toipahautea, Whakakai, Horopeta, and Mauicetus from New Zealand remain unresolved and problematic, but all four genera show a close relationship with crown mysticetes. The original and subsequent cladistic analyses have consistently revealed a sister relationship between the Toipahautea-to-Mauicetus grade and crown mysticetes, and Horopeta has been placed close to the cetotheriids within the crown group. This review aims to stimulate more research on this topic by elucidating the origin of crown mysticetes, which likely experienced a poorly known radiation event during the Oligocene that established the modern lineages.