High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (<i>Phocoena phocoena</i>)

Autenrieth, Marijke; Hartmann, Stefanie; Lah, Ljerka; Roos, Anna; Dennis, Alice B.; Tiedemann, Ralph

doi:10.1111/1755-0998.12932

Cited by 13 publications

(12 citation statements)

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“…Sequencing of reference genomes is increasingly recognized as an important contribution to identify, characterize and conserve biodiversity (Garner et al., 2016; Harrisson et al., 2014; He et al., 2016; Morin et al., 2020; Supple & Shapiro, 2018), especially for species that are naturally rare and difficult to study. Reference genomes provide primary data to understand evolutionary relationships (Arnason et al., 2018; Zhou et al., 2018), historical demography (Armstrong et al., 2019; Foote et al., 2016; Morin, Foote, Baker, et al., 2018; Robinson et al., 2016; Westbury et al., 2019), evolution of genes and traits (Autenrieth et al., 2018; Fan et al., 2019; Foote et al., 2015; Morin et al., 2020; Springer, Emerling, et al., 2016; Springer, Starrett, et al., 2016; Yim et al., 2014) and susceptibility to inbreeding and outbreeding depression (Chattopadhyay et al., 2019; Hedrick et al., 2019; Robinson et al., 2018; Tunstall et al., 2018). Genomic resources also provide the tools for broader studies of population structure, relatedness and potential for recovery (e.g., Garner et al., 2016; Morin, Foote, Hill, et al., 2018; Tunstall et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

Reference genome and demographic history of the most endangered marine mammal, the vaquita

Morin

Archer

Avila

et al. 2020

Molecular Ecology Resources

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The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding methods with long‐ and short‐read RNA sequencing to generate a near error‐free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome‐length autosome scaffolds and the X‐chromosome scaffold, with a scaffold N50 of 115 Mb. Genome‐wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long‐term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long‐term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

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Section: Introductionmentioning

confidence: 99%

Reference genome and demographic history of the most endangered marine mammal, the vaquita

Morin

Archer

Avila

et al. 2020

Molecular Ecology Resources

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“…Freshwater and seawater environments differ in many ways, with the higher salinity of seawater promoting oxidative stress (Bal et al., 2021). Such adaptations may be mirrored by the harbour porpoise ( Phocoena phocoena ), a species sequenced in 2018 (Autenrieth et al., 2018). Harbour porpoises are found in low‐ and high‐salinity habitats; however, population genomics studies are not available.…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of the superoxide dismutase gene family in Cetartiodactyla

Tian

Geng

Guo

et al. 2021

J of Evolutionary Biology

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Cetacea, whales, dolphins and porpoises form an order of mammals adapted to aquatic life. Their transition to an aquatic habitat resulted in exceptional protection against cellular insults, including oxidative and osmotic stress. Here, we considered the structure and molecular evolution of the superoxide dismutase (SOD) gene family, which encodes essential enzymes in the mammalian antioxidant system, in the superorder Cetartiodactyla. To this end, we juxtaposed cetaceans and their closest extant relatives (order Artiodactyla). We identified 94 genes in 23 species, of which 70 are bona fide intact genes. Although the SOD gene family is conserved in Cetartiodactyla, lineage‐specific gene duplications and deletions were observed. Phylogenetic analyses show that the SOD2 subfamily diverged from a clade containing SOD1 and SOD3, suggesting that cytoplasmic, extracellular and mitochondrial SODs have started down independent evolutionary paths. Specific‐amino acid changes (e.g. K130N in SOD2) that may enhance ROS elimination were identified in cetaceans. In silico analysis suggests that the core transcription factor repertoire of cetartiodactyl SOD genes may include Sp1, NF‐κB, Nrf2 and AHR. Putative transcription factors binding sites responding to hypoxia were (e.g. Suppressor of Hairless; Su(H)) found in the cetacean SOD1 gene. We found significant evidence for positive selection in cetaceans using codon models. Cetaceans with different diving abilities also show divergent evolution of SOD1 and SOD2. Our genome‐wide analysis of SOD genes helps clarify their relationship and evolutionary trajectory and identify putative functional changes in cetaceans.

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“…We downloaded the assembled genomes and raw sequencing reads from nine toothed whales from the superfamily Delphinoidea. The data included five Delphinidae: Pacific white‐sided dolphin (NCBI Biosample: SAMN09386610), Indo‐Pacific bottlenose dolphin (NCBI Biosample: SAMN06289676), bottlenose dolphin (NCBI Biosample: SAMN09426418), killer whale (NCBI Biosample: SAMN01180276) and long‐finned pilot whale (NCBI Biosample: SAMN11083132); two Phocoenidae: harbour porpoise (Autenrieth et al, 2018) and finless porpoise (NCBI Biosample: SAMN02192673); and two Monodontidae: beluga (NCBI Biosample: SAMN06216270) and narwhal (NCBI Biosample: SAMN10519625). To avoid reference biases, where reads more similar to the reference map more successfully than more divergent reads, artificially inflating signals of genetic similarities between a highly divergent outgroup and an ingroup species used as mapping reference (Liu et al, 2021), we downloaded the assembled outgroup baiji genome (Genbank accession code: GCF_000442215.1) as mapping reference in the gene flow analyses.…”

Section: Methodsmentioning

confidence: 99%

A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea

et al. 2023

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The impact of post‐divergence gene flow in speciation has been documented across a range of taxa in recent years, and may have been especially widespread in highly mobile, wide‐ranging marine species, such as cetaceans. Here, we studied individual genomes from nine species across the three families of the toothed whale superfamily Delphinoidea (Delphinidae, Phocoenidae and Monodontidae). To investigate the role of post‐divergence gene flow in the speciation process, we used a multifaceted approach, including (i) phylogenomics, (ii) the distribution of shared derived alleles and (iii) demographic inference. We found the divergence of lineages within Delphinoidea did not follow a process of pure bifurcation, but was much more complex. Sliding‐window phylogenomics reveal a high prevalence of discordant topologies within the superfamily, with further analyses indicating these discordances arose due to both incomplete lineage sorting and gene flow. D‐statistics and f‐branch analyses supported gene flow between members of Delphinoidea, with the vast majority of gene flow occurring as ancient interfamilial events. Demographic analyses provided evidence that introgressive gene flow has likely ceased between all species pairs tested, despite reports of contemporary interspecific hybrids. Our study provides the first steps towards resolving the large complexity of speciation within Delphinoidea; we reveal the prevalence of ancient interfamilial gene flow events prior to the diversification of each family, and suggest that contemporary hybridisation events may be disadvantageous, as hybrid individuals do not appear to contribute to the parental species' gene pools.

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High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

Cited by 13 publications

References 99 publications

Reference genome and demographic history of the most endangered marine mammal, the vaquita

Reference genome and demographic history of the most endangered marine mammal, the vaquita

Comparative analysis of the superoxide dismutase gene family in Cetartiodactyla

A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea

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