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

Nature Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

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

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 20, 2024

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

Language: Английский

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Pygmy Right Whale Caperea marginata (Gray, 1846)

Published: Jan. 1, 2024

Language: Английский

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Most “flight” baleen whale species are acoustically cryptic to killer whales, unlike “fight” species

Marine Mammal Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 31, 2025

Abstract Killer whales regularly attack and kill baleen whales, especially their calves. In response, slow‐moving maneuverable “fight” species defend calves in winter aggregations predictable shallow coastal locations; while fast‐swimming “flight” flee on contact typically disperse across deep open waters. Male singing also differs between fight flight groups, with producing more intricate songs to win group competitions, produce loud, monotonous attract distant females. Fight rely defense have less need hide acoustically, but loud‐singing might draw predatory killer whales. Since cannot detect sounds <100 Hz can only loud tones below 1500 Hz, at low frequencies would result acoustic crypsis. A review of whale calling source levels reveals that although all are capable crypsis, most populations calls >1500 (24 27, 89%), unlike (12 49, 24%). Furthermore, higher frequency produced lower level calls, greatly reducing detection distances. Thus, may call not for long‐distance communication avoid by

Language: Английский

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In search of the origin of crown Mysticeti

Journal of the Royal Society of New Zealand, Journal Year: 2023, Volume and Issue: 54(5), P. 682 - 695

Published: Aug. 24, 2023

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

Language: Английский

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The first genetically confirmed live sighting of the Deraniyagala's beaked whale (Mesoplodon hotaula), with insights into the diversity, phylogeny, and past demographic history

Marine Mammal Science, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 5, 2024

Abstract Beaked whales have recently been reported in the South China Sea but with taxonomic uncertainty due to their ambiguous morphological features. Here, we sequenced three genetic markers, control region (CR) and cytochrome b ( cytb ) of mitochondrial genome first intron nuclear muscle actin gene ACTA2 , two biopsy samples collected 2021, revealed unambiguous clustering sequences previously attributed Deraniyagala's beaked whale Mesoplodon hotaula ). Phylogenetic analysis complete mitogenomes strongly supported close relationship between ginkgo‐toothed M. ginkgodens Whole‐genome sequencing suggested a high degree heterozygosity whale. Ancient inbreeding may had greater impact than recent on whales, more are needed draw firm conclusion. The approximate effective population size was found lowest among seven examined ziphiids, which has experiencing steady decline since ~300,000 ya. Therefore, suggest that conservation status should be assessed when essential information is available. results our study provide evidence live sighting fundamental understanding morphological, behavioral, ecological perspectives this cetacean species.

Language: Английский

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

Molecular Ecology, Journal Year: 2024, Volume and Issue: 34(2)

Published: Dec. 17, 2024

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

Language: Английский

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

Journal of Heredity, Journal Year: 2023, Volume and Issue: 115(1), P. 112 - 119

Published: Nov. 21, 2023

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

Language: Английский

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Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 19, 2024

Abstract Identification of the taxonomic origin bone tools is an important, but often complicated, component studying past societies. The species used for tool production provide insight into what were exploited, potentially how, and purpose. Additionally, choice may have important implications place within larger toolkit. However, identification unsuccessful based on morphology. Here we apply three palaeoproteomic techniques, ZooMS, SPIN-like data analysis a targeted database search to narrow down unusually large Bronze Age from Heiloo, Netherlands, North Atlantic right whale ( Eubalaena glacialis ). was investigated use-wear, which showed that it likely processing plant fibres. assignment as adds support exploitation whales by coastal populations, not just meat, previously suggested, also resource production. We know no other parallel such this in terms size, use, hafting, identity.

Language: Английский

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Convergent evolution of skim feeding in baleen whales

Marine Mammal Science, Journal Year: 2023, Volume and Issue: 39(4), P. 1337 - 1343

Published: July 6, 2023

The evolutionary relationships of the pygmy right whale Caperea marginata, smallest and most enigmatic living baleen whales (mysticetes), remain contentious. For 150 years, morphological analyses have allied with based on their similar skim filter feeding strategies shared cranial features like a tall braincase, highly arched rostrum, elongate plates (Beddard, 1901; Bisconti, 2012; Gray, 1871; McLeod et al., 1993). By contrast, molecular some anatomical evidence—e.g., presence squamosal cleft, tympanic recess, four-fingered flipper—suggest closer relationship rorquals gray whales, Eschrichtius robustus (Dornburg Fordyce & Marx, 2013; Lloyd Slater, 2021; 2011; McGowen 2009, 2020; Park 2017; Steeman 2009). Reconciling these divergent interpretations has proved challenging, nontraditional character that are consistent data (e.g., Gol'din Steeman, 2015; Marx Fordyce, 2016) reputedly "gloss[ing] over substantial issue convergence posed by many balaenid Caperea" (Berta Deméré, 2018, p. 73). As result, continue to recover—or regard—Caperea as sister taxa (Bisconti, Bisconti Carnevale, 2022; 2017, Boessenecker El Adli 2014; Peredo 2018), which in turn shaped debates around phylogeny, placement fossils, prevalence role convergent evolution. Two knowledge gaps prevented emergence consensus: (1) an extremely limited fossil record currently comprises just six specimens worldwide, all already resemble (Marx 2018); (2) lack full genomic revealing true level support for either hypothesis. Recent advances sequencing generated broad comparative set includes (Árnason but not yet included beyond subset individual protein-coding genes (McGowen 2020). Here, we present first genome form high-coverage whole-genome shotgun data. We extracted DNA from kidney tissue obtained juvenile female (South Australian Museum, Adelaide, specimen M27462) stranded near Port Vincent, South Australia, September 2017. carcass was retrieved morning day after animal had perished, immediately frozen until postmortem collection. extraction performed using Kingfisher robot (Thermo Fisher Scientific), following manufacturer's Blood Tissue Extraction protocol. Around 10 μg were provided library preparation. quality assessed TapeStation ensure suitability Double-stranded libraries built Illumina TruSeq PCR-free preparation protocol then sequenced HiSeqX high output mode 2 × bp paired-end chemistry at SciLifeLab (Uppsala University, Sweden). After sequencing, mapped both our published genomes two five ~2.4 gigabase (Gb) sperm reference assembly (Physeter macrocephalus, GCF_002837175.2; Table S1). mapping genome, controlled bias driven phylogenetic distance between target organism Brandt 2015): outgroup, is equally distant focal species 2018). To infer created genome-wide tree, allowing us quantify overcome gene tree discordance caused processes such incomplete lineage sorting hybridization. split into nonoverlapping 20 kilobase (kb) windows (following Árnason 2018; Appendix Next, computed maximum likelihood (ML) trees each window RAxML v8.2.12 (Stamatakis, 2014), summarized results ML multispecies coalescent (MSC) ASTRAL v5.7.5 (Zhang Finally, alternative topology (per internal branch) visualized via quartet scores. estimate age recent common ancestor its nearest relatives, concatenated exons (n = 20,196 genes) coordinates annotated genome. used framework implemented 2014) create nucleotide sequence filtered out whose showed mean bootstrap ≤80%, indicating low information content; excessively deviated majority (Robinson-Foulds ≤4); (3) coefficient variation root-to-tip <0.1, "nonclock" behavior (i.e., excessive rate heterogeneity). 344 passed filters analyzed mcmctree function PAML v4.8a (Yang, 2007) while constraining three nodes pairwise sequentially Markovian (PSMC) v0.6.5 (Li Durbin, 2011) past fluctuations effective population size whale. Full methodological details available electronic supplementary material. Sequencing C. marginata resulted ~812 million read-pairs, nuclear 47× average depth coverage (89.33% covered ≥10×). filtering, retained 1.15 Gb per (range 1.10–1.20 Gb; 1.18 Caperea), divided 89,115 kb each. Our MSC confirms (88% trees), topologies—likely resulting sorting—receiving only 4%–8% (Figures 1a Considering this increase evidence, draws half surpasses previously more than orders magnitude, earlier studies 2009), propose traditional taxonomic grouping (superfamily Balaenoidea) be abandoned. superficially skull anatomy balaenids stem archaic crown mysticetes 2016; Werth 2018) and, thus, likely arose convergently. suggest strategies, require large cross-flow filtration surface (Werth Potvin, 2016). This achieved notably plates, functional requirements shape remainder skull. A trend, albeit much less pronounced, evident sei (Brodie Vikingsson, 2009; In rack accommodated requires braincase anteriorly positioned neck muscles support. position supraoccipital bone, tip extends eyes (Figure 1b). Further knock-on effects vertex, forcing blowhole surrounding rostral bones relatively anterior position; mandible, where comparatively small degree alpha (longitudinal) rotation—enough gutter lateral (Lambertsen 2005; 2016)—has allowed coronoid process become almost indistinct 2013). traits interrelated ultimately enlargement apparatus feeding, frequently been treated independent characters apparently uniting balaenids. call reevaluation morphology-based cladistic sets control nonindependence uncover origin record. Depending choice clock model calibration points, estimates divergence range 16.2 19.4 Ma, minima maxima 95% highest posterior densities 14.8 Ma or 23.3 respectively 1a; S2; These somewhat younger 29–19 proposed previous (Gatesy McGowen, because differences filtering temporal calibration. Regardless, even young long pre-date oldest no older 8–7 or, perhaps, 10–9 (Tsai 2017). ghost may reflect genuine undersampling earliest members misidentified, suggested regard cetotheriids (Fordyce cannot evaluate hypotheses directly, note estimated time cetotheriid origin, family dating Middle Miocene (ca. 14.8–12.5 Ma) (Collareta Gol'din, addition resolving affinities Caperea, new allow insight demographic history. trajectory (Ne) last those fin (Balaenoptera physalus), minke (B. Acutorostrata), borealis) 2018)—a gradual decline Ne since Late plateaus 800 ka, followed lasting 200 ka 1c). changes census climate change and/or changing rates flow different populations (Mazet While presently distributed exclusively Southern Ocean, there presumably few barriers flow, discovery Northern Hemisphere Pleistocene fossils Italy Japan 2017) hints structure. Periodic cooling during glacial cycles opportunities cold-adapted cross equator, known phylogeographic barrier (Davies, 1963; Holt 2020), complex dynamics otherwise temperate polar marginata. D. Stemmer, S. South, K. Roberts, J. Sumner helped collect samples. Three reviewers substantially improved manuscript. National Genomics Infrastructure Stockholm (funded Science Life Laboratory, Knut Alice Wallenberg Foundation Swedish Research Council) SNIC/Uppsala Multidisciplinary Center Advanced Computational assisted massively parallel access UPPMAX computational infrastructure. Ludovic Dutoit: Formal analysis; methodology; visualization; writing – original draft. Kieren J, Mitchell: Nicolas Dussex: Data curation; formal Catherine Kemper: Resources; review editing. Petter Larsson: Investigation; Love Dalén: supervision; Rawlence: Conceptualization; project administration; Felix G. Marx: recently learnt phylogenomic independently corroborated Wolf al. (2023). Their study provides further conclusive evidence differs ours focusing rorqual phylogeny selection cancer resistance, rather origins se. way complementary together represent comprehensive advancement understanding evolution Caperea. Raw reads (Caperea marginata) can found European Nucleotide Archive PRJEB46892. reproducibility, scripts https://doi.org/10.5281/zenodo.7588332 S1: Supporting Information Please note: publisher responsible content functionality any supporting supplied authors. Any queries (other missing content) should directed corresponding author article.

Language: Английский

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