scholarly journals De novo chromosome-length assembly of the mule deer (Odocoileus hemionus) genome

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Sydney Lamb ◽  
Adam M. Taylor ◽  
Tabitha A. Hughes ◽  
Brock R. McMillan ◽  
Randy T. Larsen ◽  
...  
Keyword(s):  
De Novo ◽  
Mule Deer ◽  
Odocoileus Hemionus ◽  
Chromosome Length

scholarly journals De novo chromosome level assembly of the mule deer (Odocoileus hemionus) genome

2021 ◽  
Author(s):  
Sydney Lamb ◽  
Adam M. Taylor ◽  
Tabitha A. Hughes ◽  
Brock R. McMillan ◽  
Randy T. Larsen ◽  
...  
Keyword(s):  
De Novo ◽  
Demographic History ◽  
Large Population ◽  
Mule Deer ◽  
Continuous Distribution ◽  
Odocoileus Hemionus ◽  
Chromosome Length ◽  
Future Research ◽  
A Genome ◽  
Genomic Studies

The mule deer (Odocoileus hemionus) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.

Tolazoline-Induced Apnea in Mule Deer (Odocoileus hemionus)

2011 ◽  
Vol 42 (1) ◽  
pp. 105-107 ◽  
Author(s):  
Jack Alan Mortenson ◽  
Jason Andrew Robison
Keyword(s):  
Mule Deer ◽  
Odocoileus Hemionus

Growth and seasonal weight changes as they relate to spring and autumn set points in mule deer

1991 ◽  
Vol 69 (3) ◽  
pp. 744-747 ◽  
Author(s):  
Lyle A. Renecker ◽  
W. M. Samuel
Keyword(s):  
Growth Rate ◽  
Weight Loss ◽  
Weight Gain ◽  
Mule Deer ◽  
Odocoileus Hemionus ◽  
Weight Changes ◽  
Annual Cycles ◽  
Body Weights ◽  
Compensatory Gain ◽  
Highly Correlated

Growth rate and potential, 25 hand-reared mule deer (Odocoileus hemionus hemionus) were examined. When possible, body weights of all animals were recorded weekly. Female deer matured faster than males, but males attained a larger body size. Regressions of winter weight loss of both sexes on peak autumn weight were highly correlated. Similarly, spring and summer compensatory gain in females could be predicted from the minimum spring weight. Annual cycles of intake and weight gain may have adaptations that improve reproductive success and winter survival.

EVALUATION OP STRESS AND ITS EFFECTS ON THE IMMUNE SYSTEM OF HAND-REARED MULE DEER FAWNS (Odocoileus hemionus)

1978 ◽  
Vol 14 (4) ◽  
pp. 523-537 ◽  
Author(s):  
BRUCE D. TRINDLE ◽  
LON D. LEWIS ◽  
LLOYD H. LAUERMAN
Keyword(s):  
Immune System ◽  
Mule Deer ◽  
Odocoileus Hemionus

Impacts of recolonizing gray wolves (Canis lupus) on survival and mortality in two sympatric ungulates

2018 ◽  
Vol 96 (7) ◽  
pp. 760-768 ◽  
Author(s):  
J.A. Dellinger ◽  
C.R. Shores ◽  
M. Marsh ◽  
M.R. Heithaus ◽  
W.J. Ripple ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Mule Deer ◽  
Survival Rates ◽  
Odocoileus Hemionus ◽  
Mortality Rates ◽  
Adult Survival ◽  
Mortality Data ◽  
Gray Wolf ◽  
Gray Wolves ◽  
Large Predators

There is growing recognition that humans may mediate the strength and nature of the ecological effects of large predators. We took advantage of ongoing gray wolf (Canis lupus Linnaeus, 1758) recolonization in Washington, USA, to contrast adult survival rates and sources of mortality for mule deer (Odocoileus hemionus (Rafinesque, 1817)) and white-tailed deer (Odocoileus virginianus (Zimmermann, 1780)) in areas with and without wolf packs in a managed landscape dominated by multiple human uses. We tested the hypothesis that the addition of wolves to the existing predator guild would augment predator-induced mortality rates for both ungulates. Source of mortality data from adult mule deer and white-tailed deer, respectively, revealed that wolf-related mortality was low compared with that inflicted by other predators or humans. Predator-caused mortality was largely confined to winter. There was little effect of wolf presence on adult deer mortality rates, and there was no difference in mortality between the two deer species relative to wolf-free or wolf-occupied sites. Although this study occurred early in wolf recovery in Washington, our results differ from those demonstrated for gray wolves in protected areas. Thus, we encourage further investigation of effects of direct predation by recolonizing large carnivores on prey in human-dominated landscapes.

scholarly journals HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C

2020 ◽  
Vol 36 (13) ◽  
pp. 3966-3974
Author(s):  
Ryo Nakabayashi ◽  
Shinichi Morishita
Keyword(s):  
Viterbi Algorithm ◽  
De Novo ◽  
Gene Prediction ◽  
Effective Means ◽  
Cost Effective ◽  
Synteny Block ◽  
Chromosome Length ◽  
Model Organisms ◽  
Contact Frequency ◽  
Reference Quality

Abstract Motivation De novo assembly of reference-quality genomes used to require enormously laborious tasks. In particular, it is extremely time-consuming to build genome markers for ordering assembled contigs along chromosomes; thus, they are only available for well-established model organisms. To resolve this issue, recent studies demonstrated that Hi-C could be a powerful and cost-effective means to output chromosome-length scaffolds for non-model species with no genome marker resources, because the Hi-C contact frequency between a pair of two loci can be a good estimator of their genomic distance, even if there is a large gap between them. Indeed, state-of-the-art methods such as 3D-DNA are now widely used for locating contigs in chromosomes. However, it remains challenging to reduce errors in contig orientation because shorter contigs have fewer contacts with their neighboring contigs. These orientation errors lower the accuracy of gene prediction, read alignment, and synteny block estimation in comparative genomics. Results To reduce these contig orientation errors, we propose a new algorithm, named HiC-Hiker, which has a firm grounding in probabilistic theory, rigorously models Hi-C contacts across contigs, and effectively infers the most probable orientations via the Viterbi algorithm. We compared HiC-Hiker and 3D-DNA using human and worm genome contigs generated from short reads, evaluated their performances, and observed a remarkable reduction in the contig orientation error rate from 4.3% (3D-DNA) to 1.7% (HiC-Hiker). Our algorithm can consider long-range information between distal contigs and precisely estimates Hi-C read contact probabilities among contigs, which may also be useful for determining the ordering of contigs. Availability and implementation HiC-Hiker is freely available at: https://github.com/ryought/hic_hiker.

Hybrid swarm between divergent lineages of mule deer (Odocoileus hemionus)

2011 ◽  
Vol 20 (24) ◽  
pp. 5265-5279 ◽  
Author(s):  
EMILY K. LATCH ◽  
ELIZABETH M. KIEREPKA ◽  
JAMES R. HEFFELFINGER ◽  
OLIN E. RHODES
Keyword(s):  
Mule Deer ◽  
Odocoileus Hemionus ◽  
Hybrid Swarm
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