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  • Oxford University Press (OUP)  (50)
  • Biodiversity Research  (50)
  • 1
    Online Resource
    Online Resource
    Reference genome of the California glossy snake, Arizona elegans occidentalis : A declining California Species of Special Concern
    Oxford University Press (OUP) ; 2022
    In:  Journal of Heredity Vol. 113, No. 6 ( 2022-11-30), p. 632-640
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 113, No. 6 ( 2022-11-30), p. 632-640
    Abstract: The glossy snake (Arizona elegans) is a polytypic species broadly distributed across southwestern North America. The species occupies habitats ranging from California’s coastal chaparral to the shortgrass prairies of Texas and southeastern Nebraska, to the extensive arid scrublands of central México. Three subspecies are currently recognized in California, one of which is afforded state-level protection based on the extensive loss and modification of its preferred alluvial coastal scrub and inland desert habitat. We report the first genome assembly of A. elegans occidentalis as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technologies to produce a de novo assembled genome. The assembly comprises a total of 140 scaffolds spanning 1,842,602,218 base pairs, has a contig NG50 of 61 Mb, a scaffold NG50 of 136 Mb, and a BUSCO complete score of 95.9%, and is one of the most complete snake genome assemblies. The A. e. occidentalis genome will be a key tool for understanding the genomic diversity and the basis of adaptations within this species and close relatives within the hyperdiverse snake family Colubridae.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esac040
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Reference genome of the black rail, Laterallus jamaicensis
    Oxford University Press (OUP) ; 2023
    In:  Journal of Heredity Vol. 114, No. 4 ( 2023-06-22), p. 436-443
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 114, No. 4 ( 2023-06-22), p. 436-443
    Abstract: The black rail, Laterallus jamaicensis, is one of the most secretive and poorly understood birds in the Americas. Two of its five subspecies breed in North America: the Eastern black rail (L. j. jamaicensis), found primarily in the southern and mid-Atlantic states, and the California black rail (L. j. coturniculus), inhabiting California and Arizona, are recognized across the highly disjunct distribution. Population declines, due primarily to wetland loss and degradation, have resulted in conservation status listings for both subspecies. To help advance understanding of the phylogeography, biology, and ecology of this elusive species, we report the first reference genome assembly for the black rail, produced as part of the California Conservation Genomics Project (CCGP). We produced a de novo genome assembly using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology with an estimated sequencing error rate of 0.182%. The assembly consists of 964 scaffolds spanning 1.39 Gb, with a contig N50 of 7.4 Mb, scaffold N50 of 21.4 Mb, largest contig of 44.8 Mb, and largest scaffold of 101.2 Mb. The assembly has a high BUSCO completeness score of 96.8% and represents the first genome assembly available for the genus Laterallus. This genome assembly can help resolve questions about the complex evolutionary history of rails, assess black rail vagility and population connectivity, estimate effective population sizes, and evaluate the potential of rails for adaptive evolution in the face of growing threats from climate change, habitat loss and fragmentation, and disease.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad025
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
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  • 3
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    Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages
    Oxford University Press (OUP) ; 2024
    In:  Journal of Heredity Vol. 115, No. 4 ( 2024-07-10), p. 339-348
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 115, No. 4 ( 2024-07-10), p. 339-348
    Abstract: Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India’s Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan’s wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad066
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
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  • 4
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    Online Resource
    Reference genome for the Mojave poppy bee ( Perdita meconis ), a specialist pollinator of conservation concern
    Oxford University Press (OUP) ; 2024
    In:  Journal of Heredity Vol. 115, No. 4 ( 2024-07-10), p. 470-479
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 115, No. 4 ( 2024-07-10), p. 470-479
    Abstract: The Mojave poppy bee, Perdita meconis Griswold (Hymenoptera: Anthophila: Andrenidae), is a species of conservation concern that is restricted to the eastern Mojave Desert of North America. It is a specialist pollinator of two poppy genera, Arctomecon and Argemone (Papaveraceae), and is being considered for listing under the US Endangered Species Act along with one of its pollinator hosts, the Las Vegas bearpoppy (Arctomecon californica). Here, we present a near chromosome-level genome of the Mojave poppy bee to provide a genomic resource that will aid conservation efforts and future research. We isolated DNA from a single, small ( & lt;7 mm), male specimen collected using non-ideal preservation methods and then performed whole-genome sequencing using PacBio HiFi technology. After quality and contaminant filtering, the final draft genome assembly is 327 Mb, with an N50 length of 17.5 Mb. Annotated repetitive elements compose 37.3% of the genome, although a large proportion (24.87%) of those are unclassified repeats. Additionally, we annotated 18,245 protein-coding genes and 19,433 transcripts. This genome represents one of only a few genomes from the large bee family Andrenidae and one of only a few genomes for pollinator specialists. We highlight both the potential of this genome as a resource for future research, and how high-quality genomes generated from small, non-ideal (in terms of preservation) specimens could facilitate biodiversity genomics.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esad076
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
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  • 5
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    The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies
    Oxford University Press (OUP) ; 2024
    In:  Journal of Heredity Vol. 115, No. 4 ( 2024-07-10), p. 480-486
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 115, No. 4 ( 2024-07-10), p. 480-486
    Abstract: Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esae013
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
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  • 6
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    A genome assembly of the American black bear, Ursus americanus , from California
    Oxford University Press (OUP) ; 2024
    In:  Journal of Heredity ( 2024-07-15)
    Details
    In: Journal of Heredity, Oxford University Press (OUP), ( 2024-07-15)
    Abstract: The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esae037
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2024
    detail.hit.zdb_id: 3044-2
    detail.hit.zdb_id: 1466720-4
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  • 7
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    Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
    Oxford University Press (OUP) ; 2019
    In:  Molecular Biology and Evolution Vol. 36, No. 8 ( 2019-08-01), p. 1746-1763
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 36, No. 8 ( 2019-08-01), p. 1746-1763
    Abstract: Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans—an observation known as Peto’s Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msz099
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 998579-7
    detail.hit.zdb_id: 2024221-9
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  • 8
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    Ancient Hybridization with an Unknown Population Facilitated High-Altitude Adaptation of Canids
    Oxford University Press (OUP) ; 2020
    In:  Molecular Biology and Evolution Vol. 37, No. 9 ( 2020-09-01), p. 2616-2629
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 37, No. 9 ( 2020-09-01), p. 2616-2629
    Abstract: Genetic introgression not only provides material for adaptive evolution but also confounds our understanding of evolutionary history. This is particularly true for canids, a species complex in which genome sequencing and analysis has revealed a complex history of admixture and introgression. Here, we sequence 19 new whole genomes from high-altitude Tibetan and Himalayan wolves and dogs and combine these into a larger data set of 166 whole canid genomes. Using these data, we explore the evolutionary history and adaptation of these and other canid lineages. We find that Tibetan and Himalayan wolves are closely related to each other, and that ∼39% of their nuclear genome is derived from an as-yet-unrecognized wolf-like lineage that is deeply diverged from living Holarctic wolves and dogs. The EPAS1 haplotype, which is present at high frequencies in Tibetan dog breeds and wolves and confers an adaptive advantage to animals living at high altitudes, was probably derived from this ancient lineage. Our study underscores the complexity of canid evolution and demonstrates how admixture and introgression can shape the evolutionary trajectories of species.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msaa113
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 998579-7
    detail.hit.zdb_id: 2024221-9
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  • 9
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    New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
    Oxford University Press (OUP) ; 2019
    In:  Molecular Biology and Evolution Vol. 36, No. 4 ( 2019-04-01), p. 757-765
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 36, No. 4 ( 2019-04-01), p. 757-765
    Abstract: The resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msz012
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 998579-7
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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  • 10
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    Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
    Oxford University Press (OUP) ; 2019
    In:  Molecular Biology and Evolution Vol. 36, No. 7 ( 2019-07-01), p. 1580-1595
    Details
    In: Molecular Biology and Evolution, Oxford University Press (OUP), Vol. 36, No. 7 ( 2019-07-01), p. 1580-1595
    Type of Medium: Online Resource
    ISSN: 0737-4038 , 1537-1719
    URL: Article
    DOI: 10.1093/molbev/msz053
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 998579-7
    detail.hit.zdb_id: 2024221-9
    SSG: 12
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