18 Works

Gapless genome assembly of East Asian finless porpoise, Neophocaena asiaeorientalis sunameri

Denghua Yin, Chunhai Chen, Danqing Lin, Jialun Zhang, Congping Ying, Yan Liu, Wang Liu, Zhichen Cao, Chenxi Zhao, Chenhe Wang, Liping Liang, Pao Xu, Jianbo Jian & Kai Liu
There are the genome sequence, gene set, coding sequence and protein sequence of Neophocaena asiaeorientalis sunameri.

Additional file 1 of Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics

Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin & John M. Archibald
Additional file 1: Figure S1. Physical maps of nucleomorph chromosome 1 for three Cryptomonas species (5 strains in total). Genes on the left indicate transcription from bottom to top, and genes on the right indicate transcription from top to bottom. Colors of the CDS blocks correspond to predicted functional categories, and re-arranged genes are highlighted in yellow. Gene losses between the photosynthetic species C. curvata and the non-photosynthetic species C. paramecium and Cryptomonas sp. CCAC1634B...

Distinctive, fine-scale distribution of Eastern Caribbean sperm whale vocal clans reflects island fidelity rather than environmental variables

Felicia Vachon, Ana Eguiguren, Luke Rendell, Shane Gero & Hal Whitehead
Environmental variables are often the primary drivers of species’ distributions as they define their niche. However, individuals, or groups of individuals, may sometimes adopt a limited range within this larger suitable habitat as a result of social and cultural processes. This is the case for Eastern Caribbean sperm whales. While environmental variables are reasonably successful in describing the general distribution of sperm whales in the region, individuals from different cultural groups have distinct distributions around...

Resolving higher-level phylogenetic networks with repeated hybridization in a complex of polytypic salamanders (Plethodontidae: Desmognathus)

Robert Pyron, Kyle O'Connell, Hector Banos, Edward Myers & David Beamer
Repeated hybridization between newly forming lineages is a common feature of ecological speciation and ecomorphological diversification. However, computational constraints currently limit our ability to reconstruct network radiations from gene-tree data. Available methods are limited to level-1 networks wherein reticulations do not share edges, and higher-level networks may be non-identifiable in many cases. We present a heuristic method for recovering information from higher-level networks across a range of potentially identifiable empirical scenarios, supported by a theorem...

The genomic consistency of the loss of anadromy in an Arctic fish (Salvelinus alpinus)

Sarah Salisbury, Gregory McCracken, Robert Perry, Donald Keefe, Kara Layton, Tony Kess, Cameron Nugent, Jong Leong, Ian Bradbury, Ben Koop, Moira Ferguson & Daniel Ruzzante
The potentially significant genetic consequences associated with the loss of migratory capacity of diadromous fishes which have become landlocked in freshwater are poorly understood. Consistent selective pressures associated with freshwater residency may drive repeated differentiation both between allopatric landlocked and anadromous populations and within landlocked populations (resulting in sympatric morphs). Alternatively, the strong genetic drift anticipated in isolated landlocked populations could hinder consistent adaptation, limiting genetic parallelism. Understanding the degree of genetic parallelism underlying differentiation...

The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles

Chaoyue Liu, Toby Kenney, Robert Beiko & Hong Gu
Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally...

Increases in vein length compensate for leaf area lost to lobing in grapevine

Zoë Migicovsky, Joel F. Swift, Zachary Helget, Laura L. Klein, Anh Ly, Matthew Maimaitiyiming, Karoline Woodhouse, Anne Fennell, Misha Kwasniewski, Allison J. Miller, Peter Cousins & Daniel H. Chitwood
There is considerable variation in leaf lobing and leaf size, including among grapevines, some of the most well-studied leaves. We examined the relationship between leaf lobing and leaf size across grapevine populations which varied in extent of leaf lobing. We used homologous landmarking techniques to measure 2,632 leaves across two years in 476 unique, genetically distinct grapevines from 5 biparental crosses which vary primarily in the extent of lobing. We determined to what extent leaf...

Additional file 2 of Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics

Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin & John M. Archibald
Additional file 2: Table S1. Gene content of eight cryptophyte nucleomorph genomes. Table S2. Sequence similarities of hypothetical ORFs across eight cryptophyte nucleomorph genomes. Table S3. Conserved hypothetical ORFs (nORFs) in eight cryptophyte nucleomorph genomes.

Genomic basis of deep‐water adaptation in Arctic Charr (Salvelinus alpinus) morphs

Tony Kess, J. Brian Dempson, Sarah J. Lehnert, Kara Layton, Anthony Einfeldt, Paul Bentzen, Sarah Salisbury, Amber Messmer, Steven Duffy, Daniel Ruzzante, Cameron Nugent, Moira Ferguson, Jong Leong, Ben Koop, Michael O'Connell, Ian Bradbury, Kara K. S. Layton, Sarah J. Salisbury, Amber M. Messmer, Daniel E. Ruzzante, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop, Michael F. O’Connell … & Ian R. Bradbury
Colonization of extreme habitats requires extensive adaptation to novel environmental challenges. Deep-water environments (>50 m) have high hydrostatic pressure, low temperature, and low light, requiring physiological and visual system adaptation, but genomic mechanisms underlying evolution in these environments are rarely known. Post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Here, we compare genomic and morphometric divergence...

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

Halvor Knutsen, Diana Catarino, Lauren Rogers, Marte Sodeland, Morten Mattingsdal, Marlene Jahnke, Jeffrey Hutchings, Ida Mellerud, Sigurd Espeland, Kerstin Johanneson, Olivia Roth, Michael Hansen, Sissel Jentoft, Carl Andre & Per Erik Jorde
Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to...

Atlantic salmon survival at sea: temporal changes that lack regional synchrony

Maria Tirronen, Jeffrey A. Hutchings, Sebastián A. Pardo & Anna Kuparinen
Spatial and temporal synchrony in abundance or survival trends can be indicative of whether populations are affected by common environmental drivers. In Atlantic salmon (Salmo salar L.), return rates to natal rivers have generally been assumed to be affected primarily by shared oceanic conditions, leading to spatially synchronous trends in mortality. Here, we investigate the existence of parallel trends in salmon sea survival, using data on migrating smolts and returning adults from seven Canadian populations...

Additional file 2 of Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics

Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin & John M. Archibald
Additional file 2: Table S1. Gene content of eight cryptophyte nucleomorph genomes. Table S2. Sequence similarities of hypothetical ORFs across eight cryptophyte nucleomorph genomes. Table S3. Conserved hypothetical ORFs (nORFs) in eight cryptophyte nucleomorph genomes.

Gapless genome assembly of East Asian finless porpoise, Neophocaena asiaeorientalis sunameri

Denghua Yin, Chunhai Chen, Danqing Lin, Jialun Zhang, Congping Ying, Yan Liu, Wang Liu, Zhichen Cao, Chenxi Zhao, Chenhe Wang, Liping Liang, Pao Xu, Jianbo Jian & Kai Liu
There are the genome sequence, gene set, coding sequence and protein sequence of Neophocaena asiaeorientalis sunameri.

TCCON data from Eureka (CA), Release GGG2020.R0

K. Strong, S. Roche, J. E. Franklin, J. Mendonca, E. Lutsch, D. Weaver, P. F. Fogal, J. R. Drummond, R. Batchelor, R. Lindenmaier & E. McGee
The Total Carbon Column Observing Network (TCCON) is a network of ground-based Fourier Transform Spectrometers that record direct solar absorption spectra of the atmosphere in the near-infrared. From these spectra, accurate and precise column-averaged abundances of atmospheric constituents including CO2, CH4, N2O, HF, CO, H2O, and HDO, are retrieved. This is the GGG2020 data release of observations from the TCCON station at Eureka, Canada

Genotyping-by-sequencing of Canada’s Apple Biodiversity Collection

Zoë Migicovsky, Gavin M. Douglas & Sean Myles
Canada’s Apple Biodiversity Collection (ABC) is one of the most diverse collections of apples in the world, which was designed to enable genetic mapping. The ABC is located at the Agriculture and Agri-Food Canada (AAFC) Kentville Research and Development Centre in Nova Scotia, Canada. In addition to phenotypic descriptions of the ABC, sequencing the accessions in the collection provides a valuable resource not only for researchers working on the collection, but for those studying apples...

Additional file 1 of Gene loss, pseudogenization, and independent genome reduction in non-photosynthetic species of Cryptomonas (Cryptophyceae) revealed by comparative nucleomorph genomics

Jong Im Kim, Goro Tanifuji, Minseok Jeong, Woongghi Shin & John M. Archibald
Additional file 1: Figure S1. Physical maps of nucleomorph chromosome 1 for three Cryptomonas species (5 strains in total). Genes on the left indicate transcription from bottom to top, and genes on the right indicate transcription from top to bottom. Colors of the CDS blocks correspond to predicted functional categories, and re-arranged genes are highlighted in yellow. Gene losses between the photosynthetic species C. curvata and the non-photosynthetic species C. paramecium and Cryptomonas sp. CCAC1634B...

Differential reproductive plasticity under thermal variability in a freshwater fish (Danio rerio)

Melanie D. Massey, M. Kate Fredericks, David Malloy, Suchinta Arif & Jeffrey Hutchings
Human-driven increases in global mean temperatures are associated with concomitant increases in thermal variability. Yet, few studies have explored the impacts of thermal variability on fitness-related traits, limiting our ability to predict how organisms will respond to dynamic thermal changes. Among the myriad organismal responses to thermal variability, one of the most proximate to fitness – and, thus, a population’s ability to persist - is reproduction. Here, we examine how a model freshwater fish (Danio...

A climate risk index for marine life

Daniel Boyce, Derek Tittensor, Cristina Garilao, Stephanie Henson, Kristen Kaschner, Kathleen Kesner-Reyes, Alex Pigot, Rodolfo Reyes, Gabriel Reygondeau, Kathryn Schleit, Nancy Shackell, Patricia Sorongon-Yap & Boris Worm
Climate change is impacting virtually all marine life. Adaptation strategies will require a robust understanding of the risk to species and ecosystems and how those propagate to human societies. We develop a unified and spatially explicit index to comprehensively evaluate the climate risks to marine life. Under high emissions (SSP5-8.5), almost 90% of ~25,000 species are at high or critical risk, with species at risk across 85% of their native distributions. One-tenth of the ocean...

Registration Year

  • 2022
    18

Resource Types

  • Dataset
    18

Affiliations

  • Dalhousie University
    17
  • Guilin Medical University
    2
  • Tianjin Medical University General Hospital
    2
  • Henan University
    2
  • Sun Yat-sen University
    2
  • Agricultural University of Hebei
    2
  • Zhejiang University
    2
  • National Institute of Diabetes and Digestive and Kidney Diseases
    2
  • Wuhan University of Science and Technology
    2
  • Guangxi Institute of Botany
    2