Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands DOI Creative Commons
Joannes Dekker, Dorothea Mylopotamitaki,

Annemieke Verbaas

et al.

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: Aug. 30, 2024

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

A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography DOI Creative Commons
Yury V. Bukhman, Phillip A. Morin,

Susanne Meyer

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(3)

Published: Feb. 20, 2024

Abstract The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance cancer. To further this other whale-related research, we report a reference-quality, long-read-based genome assembly of fascinating species. We assembled from PacBio long reads utilized Illumina/10×, optical maps, Hi-C data for scaffolding, polishing, manual curation. also provided read RNA-seq facilitate annotation by NCBI Ensembl. Additionally, annotated both haplotypes using TOGA measured size flow cytometry. then compared whale with cetaceans artiodactyls, including vaquita (Phocoena sinus), world's smallest cetacean, investigate whale's unique biological traits. found dramatic amplification several genes resulting recent burst segmental duplications, though possible connection between giant body requires study. discovered sites insulin-like growth factor-1 gene correlated cetaceans. Finally, our examine heterozygosity historical demography Pacific Atlantic populations, that genomes populations are highly heterozygous their genetic isolation dates last interglacial period. Taken together, these results indicate how high-quality, will serve as resource biology, evolution, conservation research.

Language: Английский

Citations

8
Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise DOI Creative Commons
Denghua Yin, Chunhai Chen,

Danqing Lin

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis, YFP) and the East Asian sunameri, EFP) are 2 subspecies of narrow-ridged that live in freshwater saltwater, respectively. main objective this study was to provide contiguous chromosome-level genome assemblies for YFP EFP. Results Here, we generated upgraded genomes EFP at telomere-to-telomere level through integration PacBio HiFi long reads, ultra-long ONT Hi-C sequencing data with a total size 2.48 Gb 2.50 Gb, scaffold N50 125.12 Mb (YFP) 128 (EFP) 1 contig chromosome. telomere repeat centromere position were clearly identified both genomes. In total, 5,480 newfound genes detected genome, including 56 located newly regions. Additionally, synteny blocks, structural similarities, phylogenetic relationships, gene family expansion, inference selection studied connection other related mammals. Conclusions Our research findings evidence gradual adaptation marine environment potential sensitivity genetic damage. Compared 34 cetacean sourced from public databases, new demonstrate superior continuity longest values, as well lowest number contigs. improvement gap-free reference resources supports conservation genetics population management porpoises.

Language: Английский

Citations

3
Ocean‐Wide Conservation Genomics of Blue Whales Suggest New Northern Hemisphere Subspecies DOI Creative Commons
Magnus Wolf, Menno de Jong, Axel Janke

et al.

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

Citations

2
Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale DOI Creative Commons
Richard W. Orton, Philip K. Hamilton, Timothy R. Frasier

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(12)

Published: Dec. 1, 2024

ABSTRACT The reduced genetic diversity and frequent inbreeding associated with small population size may underpin the accumulation expression of deleterious mutations (mutation load) in some declining populations. However, demographic perturbations coupled purifying selection can also purge populations mutations, leading to intriguing recoveries. To better understand links between variation status, we assess patterns diversity, inbreeding, mutation load across genomes three species Balaenidae whale different histories recoveries following end commercial whaling 1980s. Unlike bowhead (BH) Southern right whales (SRW), which show signs recent recovery, reproductive rates endangered North Atlantic (NARW) remain lower than expected. We that NARW is currently marked by low historical a high load. Still, reveal evidence purging has frequency highly alleles NARW, could increase chances future recovery. identify suite putatively linked congenital defects occur at frequencies nulliparous females but are rare success. These same nearly absent BH SRW this study, suggesting key variants shape probability As anthropogenic disturbances continue reduce sizes many nature, resolving dynamics become increasingly important.

Language: Английский

Citations

1
Chromosome level genome assembly of the Etruscan shrew Suncus etruscus DOI Creative Commons
Yury V. Bukhman,

Susanne Meyer,

Li‐Fang Chu

et al.

Scientific Data, Journal Year: 2024, Volume and Issue: 11(1)

Published: Feb. 7, 2024

Abstract Suncus etruscus is one of the world’s smallest mammals, with an average body mass about 2 grams. The Etruscan shrew’s small accompanied by a very high energy demand and numerous metabolic adaptations. Here we report chromosome-level genome assembly using PacBio long read sequencing, 10X Genomics linked short reads, optical mapping, Hi-C reads. partially phased, 2.472 Gbp primary pseudohaplotype 1.515 alternate. We manually curated identified 22 chromosomes, including X Y sex chromosomes. NCBI annotation pipeline 39,091 genes, 19,819 them protein-coding. also segmental duplications, inferred GO term annotations, computed orthologs human mouse genes. This reference-quality will be important resource for research on mammalian development, metabolism, size control.

Language: Английский

Citations

0
Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales DOI Creative Commons
Gabrielle Genty, Jonathan Sandoval‐Castillo, Luciano B. Beheregaray

et al.

Gene, Journal Year: 2024, Volume and Issue: 929, P. 148822 - 148822

Published: Aug. 3, 2024

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

Language: Английский

Citations

0
Phylogenomics and pervasive genome-wide phylogenetic discordance among fin whales (Balaenoptera physalus) DOI Creative Commons
Fabrício Furni, Eduardo R. Secchi, Camilla Speller

et al.

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(6), P. 873 - 885

Published: Aug. 15, 2024

Abstract Phylogenomics has the power to uncover complex phylogenetic scenarios across genome. In most cases, no single topology is reflected entire genome as signal differs among genomic regions due processes, such introgression and incomplete lineage sorting. Baleen whales are largest vertebrates on Earth with a high dispersal potential in relatively unrestricted habitat, oceans. The fin whale (Balaenoptera physalus) one of enigmatic baleen species, currently divided into four subspecies. It been matter debate whether phylogeographic patterns explain taxonomic variation whales. Here we present chromosome-level whole analysis relationships from multiple ocean basins. First, estimated concatenated consensus phylogenies for both mitochondrial nuclear genomes. based upon autosomal uncovered monophyletic clades associated each basin, aligning current understanding subspecies division. Nevertheless, discordances were detected Y chromosome, genome, X chromosome. Furthermore, signs pervasive discordance This scenario could be explained by puzzle introgressive events, not yet documented Similarly, sorting low lead discordances. Our study reinforces pitfalls relying or locus determine below species level illustrating underlying nuances that some approaches may fail capture. We emphasize significance accurate delineation exploring crucial information revealed through genome-wide assessments.

Language: Английский

Citations

0
Palaeoproteomic identification of a whale bone tool from Bronze Age Heiloo, the Netherlands DOI Creative Commons
Joannes Dekker, Dorothea Mylopotamitaki,

Annemieke Verbaas

et al.

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: Aug. 30, 2024

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

Citations

0