High-quality reference genome for an arid-adapted mammal, the banner-tailed kangaroo rat (Dipodomys spectabilis)

Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semi-arid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered. 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 (D. 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 (D. ordii and D. 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.

Conservation of endangered Tipton kangaroo rats (Dipodomys nitratoides nitratoides): status surveys, habitat suitability, and conservation recommendations

The Tipton kangaroo rat (Dipodomys nitratoides nitratoides; TKR) is listed as endangered both Federally and by the state of California due to profound habitat loss throughout its range in the southern San Joaquin Valley of California. Habitat loss is still occurring and critical needs for TKR include identifying occupied sites, quantifying optimal habitat conditions, and conserving habitat. Our objectives were to (1) conduct surveys to identify sites where TKR were extant, (2) assess habitat attributes on all survey sites, (3) generate a GIS-based model of TKR habitat suitability, (4) use the model to determine the quantity and quality of remaining TKR habitat, and (5) use these results to develop conservation recommendations. We surveyed for TKR on 44 sites by live-trapping and detected TKR on 15 sites. Sites with TKR tended to have larger alkali scalds and no obvious sign of past tilling compared to sites without TKR. Also, sites with TKR usually had relatively sparse ground cover and seepweed (Suaeda nigra) was present. The non-protected Heermann’s kangaroo rat (Dipodomys heermanni), a larger competitor, was either absent or present in relatively low numbers at sites with TKR, and when present its abundance was inversely related to that of TKR. Based on our habitat suitability modeling, an estimated 30,000 ha of moderately high or high quality TKR habitat and 60,000 ha of lower or medium quality habitat remain. However, habitat is still being lost and conversion of at least one survey site with TKR occurred during this project. Recommendations for TKR conservation are to (1) conduct additional TKR surveys on unsurveyed but suitable sites, (2) conserve suitable habitat on unprotected lands, (3) manage vegetation on occupied sites if necessary, (4) restore disturbed lands to increase suitability for TKR, and (5) research methods and conduct translocations of TKR to unoccupied sites with suitable habitat.

Modern extirpation of the Texas kangaroo rat, Dipodomys elator, in Oklahoma: changing land use and climate over a century of time as the road to eventual extinction

Surveys conducted during three years (2014-2017) provide the most extensive documentation to date for the possible presence of the Texas kangaroo rat (Dipodomys elator), a Tier II species considered to be of greatest conservation need, in seven counties in southwestern Oklahoma. The project encompassed 15 surveys on 93 nights; 266 localities were surveyed for a total of 9,094 trap nights and more than 32,428 km of paved and unpaved roads were surveyed for potential habitat and activity. No Texas kangaroo rats were captured or observed. However, 2,178 individuals of 17 mammal species were captured and individuals of 12 additional mammal species were collected and/or observed. New locality and natural history information for mammal species was obtained and six county records were recorded based on specimens and/or observations. Project results and historical information suggest that the Texas kangaroo rat (D. elator) is likely extirpated from the state of Oklahoma.

Survey for Morro Bay Kangaroo Rat: A Rare Mammal of Uncertain Status

The Morro Bay kangaroo rat Dipodomys heermanni morroensis is a small, nocturnal, burrowing rodent endemic to the vicinity of Morro Bay in San Luis Obispo County, California. It was listed as endangered pursuant to the U.S. Endangered Species Act in 1973. Despite many searches over three decades, the Morro Bay kangaroo rat has not been captured or sighted in the wild since 1986. While recognizing that the Morro Bay kangaroo rat may be extinct, Kofron and Villablanca (2016) also speculated it may be persisting at extremely low density in isolated colonies, and they recommended surveying with wildlife scent-detection dogs and baited camera traps. We searched with a wildlife scent-detection dog and baited camera traps in four historically-occupied areas and detected no Morro Bay kangaroo rats. Unfortunately our data combined with all other existing data do not allow us to conclude whether the Morro Bay kangaroo rat is extinct or extant. Essentially, the international standard has not been met to make a definitive determination of extinction. That is, a species should be considered extinct only when there is no reasonable doubt that the last individual has died (International Union for the Conservation of Nature 2012). We acknowledge that because of resource limitation we surveyed only a small sample of the numerous patches of habitat in the expansive landscape. Further, we now consider the Morro Bay sand spit (total area 4.35 km2, foredunes 3.75 km2), a peripheral area, as potentially part of the geographic range with suitable habitat, and it has never been searched. Therefore, considering all available information, we conclude that the Morro Bay kangaroo rat must be considered as possibly extant. We recommend that search efforts continue in several specific areas, including the Morro Bay sand spit. If the Morro Bay kangaroo still exists, it will be challenging and difficult to rediscover because of its likely low density and patchy distribution in the expansive landscape, combined with its small size, nocturnal nature, and secretive lifestyle.

Ultraviolet vision in Ord’s kangaroo rat (Dipodomys ordii)

Knowledge of a species’ visual system has far reaching implications that affect our understanding of a species’ ecology and evolutionary history. As a model taxon, the heteromyid rodent genus Dipodomys has been valuable in elucidating patterns and mechanisms in biomechanics, ecology, adaptive physiology, biogeography, and more. Although studied extensively, the visual system of Dipodomys has not been described beyond anecdotal mention of their large eyes. Here, the transmittance parameters of the cornea and lens of Ord’s kangaroo rat (Dipodomys ordii) were analyzed and photoreceptor proteins (opsins) expressed in the retina were identified with immunohistochemical (IHC) labeling. Retina maps were constructed to illustrate the relative densities of photoreceptor cells expressing short wavelength (SWS1) opsins, middle/long wavelength (MW/LW) opsins, and rhodopsin (RH1). The retina of D. ordii has variable densities of SWS1 opsin with the highest density being ventral to the optic nerve, high density of MW/LW opsin, and uniform distribution and high density of RH1 across the retina. Our results suggest that D. ordii has a UV-sensitive visual system. Composition and densities of MW/LW- and SWS1-expressing cells resemble that of a crepuscular/diurnal species thereby supporting previous authors who have reported such activity patterns. Uniform retinal distribution of RH1 indicates visual acuity at night, also confirming the paradigm of D. ordii as primarily a nocturnal species and suggesting visual acuity at all times of the day in the species. These results demonstrate not only that the species is capable of UV vision and has a retina characteristic of a diurnal mammal, but that many previously unknown photic niche selective advantages likely have shaped the evolution and ecology of this model taxon.