Dataset Information

High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat (Dipodomys spectabilis).

ABSTRACT: Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semiarid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered in the United States. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (Dipodomys spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (Dipodomys ordii and Dipodomys stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (Ne) and linking these patterns to the species' current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

SUBMITTER: Harder AM

PROVIDER: S-EPMC8800484 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:White-tailed deer are a culturally and economically important game species in North America, especially in South Texas. The recent discovery of chronic wasting disease (CWD) in captive deer facilities in Texas has increased concern about the potential emergence of CWD in free-ranging deer. The concern is exacerbated because much of the South Texas region is a semi-arid environment with variable rainfall, where precipitation is strongly correlated with fawn recruitment. Further, the marginally productive rangelands, in combination with erratic fawn recruitment, results in populations that are frequently density-independent, and thus sensitive to additive mortality. It is unknown how a deer population in semi-arid regions would respond to the presence of CWD. We used long-term empirical datasets from a lightly harvested (2% annual harvest) population in conjunction with 3 prevalence growth rates from CWD afflicted areas (0.26%, 0.83%, and 2.3% increases per year) via a multi-stage partially deterministic model to simulate a deer population for 25 years under four scenarios: 1) without CWD and without harvest, 2) with CWD and without harvest, 3) with CWD and male harvest only, and 4) with CWD and harvest of both sexes. The modeled populations without CWD and without harvest averaged a 1.43% annual increase over 25 years; incorporation of 2% annual harvest of both sexes resulted in a stable population. The model with slowest CWD prevalence rate growth (0.26% annually) without harvest resulted in stable populations but the addition of 1% harvest resulted in population declines. Further, the male age structure in CWD models became skewed to younger age classes. We incorporated fawn:doe ratios from three CWD afflicted areas in Wisconsin and Wyoming into the model with 0.26% annual increase in prevalence and populations did not begin to decline until ~10%, ~16%, and ~26% of deer were harvested annually. Deer populations in variable environments rely on high adult survivorship to buffer the low and erratic fawn recruitment rates. The increase in additive mortality rates for adults via CWD negatively impacted simulated population trends to the extent that hunter opportunity would be greatly reduced. Our results improve understanding of the potential influences of CWD on deer populations in semi-arid environments with implications for deer managers, disease ecologists, and policy makers.

Project description:BackgroundProviding high-quality kangaroo mother care (KMC) is a strategy proven to improve outcomes in premature babies. However, whether KMC is consistently and appropriately provided in Ethiopia is unclear. This study assesses the quality of KMC services in Ethiopia and the factors associated with its appropriate initiation among low birth weight neonates.MethodsWe used data from the 2016 national Emergency Obstetric and Newborn Care (EmONC) assessment which contains data on all health facilities providing delivery care services in Ethiopia (N = 3,804). We described the quality of KMC services provided to low-birth weight (LBW) babies in terms of infrastructure, processes and outcomes (survival status at discharge). We also explored the factors associated with appropriate KMC initiation using multivariable logistic regression models.ResultsThe quality of KMC services in Ethiopia was poor. The facilities included scored only 59.0% on average on a basic index of service readiness. KMC was initiated for only 46.4% of all LBW babies included in the sample. Among those who received KMC, 66.7% survived, 13.3% died and 20.4% had no data on survival status at discharge. LBW babies born in health centers were twice more likely to receive KMC compared to those born in hospitals (AOR = 2.0, 95% CI: 1.3-3.0). Public facilities, those with a staff rotation policy in place for newborn care, and those with separate newborn corners were also more likely to initiate KMC for LBW babies.ConclusionsWe found low levels of appropriate KMC initiation, inadequate infrastructure and staffing, and poor survival among LBW babies in Ethiopia. Efforts must be made to improve the adoption of this life saving technique, particularly in hospitals and in the private sector where KMC remains underutilized. Facilities should also dedicate specific spaces for newborn care that enables mothers to provide KMC. In addition, improving record keeping and data quality for routine health data is a priority.

Dataset Information

High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat (Dipodomys spectabilis).

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