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One adaptation of ecological and evolutionary interest is the extraordinary ability of desert rodents to retain water during waste production. Much is known regarding the unique kidney physiology of kangaroo rats (Dipodomys spp.) and their ability to retain water during waste production, yet the genetic basis of these physiological adaptations is relatively unknown. Herein, we utilized RNA-seq data to conduct a comparative study to identify osmoregulatory genes expressed in heteromyid rodents. We sequenced kidney tissue from two temperate desert species (Dipodomys spectabilis and Chaetodipus baileyi) from two separate subfamilies of the Heteromyidae and compared these transcriptomes to a tropical mesic species (Heteromys desmarestianus) from a third subfamily. The evolutionary history of these subfamilies provided a robust phylogenetic control that allowed us to separate shared evolutionary history from convergence. Using two methods to detect differential expression (DE), we identified 1890 genes that showed consistent patterns of DE between the arid and mesic species. A three-species reciprocal BLAST analysis revealed 3511 sets of putative orthologues that, upon comparison to known Mus musculus sequences, revealed 323 annotated and full-length genic regions. Selection tests displayed evidence of positive selection (dn/ds > 1) on six genes in the two desert species and remained significant for one of these genes after correction for multiple testing. Thus, our data suggest that both the coding sequence and expression of genes have been shaped by natural selection to provide the genetic architecture for efficient osmoregulation in desert-adapted heteromyid rodents.

Seed dispersal by caching rodents is a context‐dependent mutualism in many systems. Plants benefit when seed remaining in shallow caches germinates before being eaten, often gaining protection from beetles and a favorable microsite in the process. Caching in highly unfavorable microsites, conversely, could undermine the dispersal benefit for the plant. Plant invasions could disrupt dispersal benefits of seed caching by attracting rodents to the protection of a dense invasive canopy which inhibits the establishment of native seedlings beneath it. To determine whether rodents disproportionately cache seed under the dense canopy of an invasive grass in southeastern Arizona, we used nontoxic fluorescent powder and ultraviolet light to locate caches of seed offered to rodents in the field. We fitted a general habitat‐use model, which showed that disproportionate use of plant cover by caching rodents (principally Chaetodipus spp.) increased with moonlight. Across all moon phases, when rodents cached under plants, they cached under the invasive grass disproportionately to its relative cover. A greenhouse experiment showed that proximity to the invasive grass reduced the growth and survival of seedlings of a common native tree (Parkinsonia microphylla) whose seeds are dispersed by caching rodents. Biased dispersal of native seed to the base of an invasive grass could magnify the competitive effect of this grass on native plants, further reducing their recruitment and magnifying the effect of the invasion.

29. Bailey's Pocket Mouse Chaetodipus baileyi French: Souris-a-abajoues de Bailey / German: Bailey-Rauhaartaschenmaus / Spanish: Raton de abazones de Bailey Taxonomy. Perognathus baileyi Merriam, 1894, Magdalena, Sonora, Mexico. Based on detailed sequencing of nDNA and mtDNA genes, C. baileyi is a close relative of C. rudinoris (formerly considered conspecific), and the two species make up one of the three “ancient” clades of coarse-haired pocket mice. Chaetodipus rudinoris has a chromosomal complement with a higher FN (66), lacks any supernumerary chromosomes, and is differentiated based on allozymes and mtDNA sequence. Two subspecies recognized. Subspecies and Distribution. C.b.baileysMerriam,1894—SWUSAandNWMexicoWofColoradoRiver(SArizona,SWNewMexico,Sonora,andN Sinaloa). C. b. insularis Townsend, 1912 — NW Mexico (Tiburon I, Gulf of California, Sonora). Descriptive notes. Head-body 85-99 mm, tail 103-124 mm, ear 7-11 mm, hindfoot 25-27 mm; weight 24-28 g. Male Bailey's Pocket Mice are slightly larger than females. It is large-sized for the genus; hindfoot is usually longer than 25 mm, with strongly crested and tufted tail that is longer than head-body length. Dorsal pelage is relatively smooth, lacks spines on rump, and is grayish, washed to a varying degree with yellow, and under parts are whitish. Basic chromosomal complement of Bailey’s Pocket Mouse has 2n = 46 and FN = 64, but there is extensive diploid number variation within and among populations due to supernumerary (or “B”) chromosomes and variation in FN due to fixed differences: populations from Tiburén Island (insularis) and adjacent mainland (Bahia Kino, Sonora) have FN = 62. Known from only 18 other species of rodents, the B-chromosome system in Bailey's Pocket Mouse is unique among the family. Supernumerary chromosomes are usually (but not always) entirely heterochromatic, are by definition lacking in some (usually most) individuals in a population, and while not necessary for the life of the individual, do generally have some expression and so are not usually “silent.” In Bailey's Pocket Mouse, supernumerary chromosomes increase from zero to two in the west along the Colorado River from two to twelve in south-eastern Sonora, with significant differences among populations in mean and range of supernumeraries. In populations studied more intensively, males and females do not differ in mean number of supernumeraries, and number per individual is randomly distributed around the population mean; mean numbers remained stable over a ten-year period; and young individuals tended to have higher numbers of supernumeraries. This suggests that natural selection is acting to offset the meiotic tendency to increase number of supernumeraries and that they have some expression on the phenotype. Bailey’s Pocket Mouse is parapatric with its close relative, the Peninsular Pocket Mouse (C. rudinoris), on the opposite side of the Colorado River. Bailey’s Pocket Mouse on the east side of the Colorado River has darker pelage and wider rostrum than the Peninsular Pocket Mouse on the west side of the river. In its Sonoran Desert distribution, Bailey's Pocket Mouse co-occurs with seven other species of coarse-haired pocket mice. Bailey's Pocket Mouse is larger than all others except perhaps the Hispid Pocket Mouse (C. hispidus), which has a shorter, non-crested, and non-tufted tail; browner and hispid pelage color; and a conspicuous buffy-to-ocherous lateral stripe. In addition to being larger than the othersix species with which it can be found, Bailey's Pocket Mouse favors more open areas of pebbly soils that mark transitions from sandyflats to rocky alluvial slopes or “bajadas,” apart from the sand-obligate smooth-haired species in the same vicinity (the Desert Pocket Mouse, C. penicillatus; the Sinaloan Pocket Mouse, C. pernix; and the Chihuahuan Desert Pocket Mouse, C. eremicus) and apart from the saxicolous (rock-dwelling), coarse-haired species in the vicinity (the Rock Pocket Mouse, C. intermedius; Goldman's Pocket Mouse, C. goldmani, and the Narrow-skulled Pocket Mouse, C. artus). Habitat. Areas of medium to large bushes and trees, often in ecotones between rocky hillsides and desert flats. Bailey's Pocket Mouse also occurs in low-desert flats, small sandy washes, and rocky hillsides. It occurs most frequently with the Desert Pocket Mouse, sometimes using areas with coarser, more gravelly soils. In some areas,it is associated with jojoba (Simmondsia chinensis, Simmondsiaceae), and combined distribution of Bailey's Pocket Mouse and its close relative, the Peninsular Pocket Mouse, closely matches distribution ofjojoba. Burrows are often found at the base ofjojoba bushes, and in one study, Bailey's Pocket Mouse was found on all study plots with jojoba, and the Desert Pocket Mouse on all plots without jojoba. Bailey's Pocket Mouse does occur in the absence ofjojoba (and vice versa) but reachesits highest densities in dense stands of jojoba. In long-term study plots in south-eastern Arizona, Bailey’s Pocket Mouse established new colonies following greater than average winter precipitation that increased shrub cover. In south-western New Mexico, Bailey’s Pocket Mouse might have expanded its distribution slightly to the north and east during the past 30 years. Food and Feeding. Diet of Bailey's Pocket Mouse consists largely of seeds of shrubs, annuals, and grasses, but it also includes smaller amounts of green vegetation and insects. In laboratory experiments, it selected larger seeds than other heteromyids tested. Bailey’s Pocket Mouse apparently has some detoxification mechanism that allows it to eat seeds ofjojoba, which contain toxic cyanogenic glucosides and are rejected by the Desert Pocket Mouse, the Rock Pocket Mouse, and Merriam’s Kangaroo Rat (Dipodomys merriami) in laboratory tests. Other common foods of Bailey's Pocket Mouse are cholla (Opuntia, Cactaceae) and ocotillo (Fouquieria, Fouquieriaceae); grass seeds are less frequently taken. Food items are collected in external, fur-lined cheek pouches and transported back to burrows, where they are stored in burrow caches. Volume of cheek pouches (1-6 cm?) is sufficient to carry daily energy requirements of an individual in a single seed load. Bailey’s Pocket Mouse does not need to drink water, subsisting entirely on water from its food and water produced as a byproduct of metabolism. Breeding. Male Bailey's Pocket Mice are reproductively active in all months exceptJanuary; females were not reproductively active until March or June. Reproductive peaks occur in spring following winter rains and early autumn following summer monsoons. Young-of-the-year breed in late summer. Litter size averages 3-5 young. Activity patterns. Bailey’s Pocket Mouse is nocturnal and terrestrial, and it is active throughout the year, with peak activity in autumn and reduced winter activity after December. Movements, Home range and Social organization. Density estimates of Bailey's Pocket Mouse are 2-2-86-1 ind/ha. At one site, they varied between 17-1 ind/ha and 52-4 ind/ha over several years. Status and Conservation. Classified as Least Concern on The IUCN Red List. Bibliography. Aquino & Neiswenter (2014), Ceballos & Oliva (2005), Geluso (2009), Linzey, Timm, Alvarez-Castaneda, Castro-Arellano & Lacher (2008h), Patton (1972), Patton & Rogers (1993), Patton et al. (1981), Paulson (1988a), Price (1999b), Riddle, Hafner & Alexander (2000), Williams et al. (1993)., Published as part of Don E. Wilson, Thomas E. Lacher, Jr & Russell A. Mittermeier, 2016, Heteromyidae, pp. 170-233 in Handbook of the Mammals of the World – Volume 6 Lagomorphs and Rodents I, Barcelona :Lynx Edicions on pages 211-212, DOI: 10.5281/zenodo.6611160

Phylogenetic analysis of 699 bp of the mitochondrial DNA (mtDNA) COIII and 450 bp of the cytochrome b genes among 14 species of coarse-haired pocket mice (Heteromyidae: Chaetodipus) corroborated previous indications that genetic divergence between species and species groups within the genus is generally very high, suggesting old times of divergence, and that the nominal species C. baileyi represents a highly divergent lineage within the genus, with no closely related extant sister species. Analysis of phylogeographic structure among 51 individuals from 12 localities throughout the geographic range of C. baileyi revealed three geographically separate mtDNA haplotype lineages. The oldest split separates populations east and west of the Colorado River, a pattern that is congruent with chromosomal and allozyme electrophoretic evidence. We consider the western populations to represent a distinct species, C. rudinoris. Within C. rudinoris, mtDNA haplotypes are further subdivided into northern and southern lineages along the Baja California Peninsula. Comparison of phylogeographic structure in the baileyi species group and the codistributed Peromyscus eremicus species group implies two points of codivergence and thus supports two historical vicariance hypotheses proposed for biotas distributed across the peninsular and continental warm deserts: a late Neogene (3 Ma) northern extension of the Sea of Cortez and a mid-Pleistocene (1 Ma) midpeninsular seaway across Baja California.

Chaetodipus baileyi Merriam, 1894. Proc. Acad. Nat. Sci. Philadelphia, 46:262. TYPE LOCALITY: Mexico, Sonora, Magdalena. DISTRIBUTION: S California, S Arizona, SW New Mexico (USA), south to N Sinaloa and Baja California (Mexico). SYNONYMS: domensis Goldman, extimus Nelson and Goldman, fornicatus Burt, hueyi Nelson and Goldman, insularis Townsend, knekus Elliot, mesidios Huey, rudinoris Elliot. COMMENTS: Reviewed by Paulson (1988a, Mammalian Species, 297)., Published as part of James L. Patton, 1993, Order Rodentia - Family Heteromyidae, pp. 477-486 in Mammal Species of the World (2 nd Edition), Washington and London :Smithsonian Institution Press on page 483, DOI: 10.5281/zenodo.7353079, {"references":["Paulson, D. D. 1988 a. Chaetodipus baileyi. Mammalian Species, 297: 1 - 5."]}