On transition bias in mitochondrial genes of pocket gophers

The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (μ _s P _s)/(μ _v P _v), where μ _s and μ _v denote mutation rate of transitions and transversions, respectively, andP _s andP _v denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions,P _s/P_v ≈ 1 at fourfold degenerate sites, so that thes/v ratio at fourfold degenerate sites is approximately μ _s /μ _v , which is a measure of mutational contribution to transition bias. Similarly, thes/v ratio at nondegenerate sites is also an estimate of μ _s /μ _v if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochromeb (cyt-b) in pocket gophers, thes/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, thes/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the μ _s /μ _v ratio is about 2, theP _s/P_v ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content ons/v ratio of protein-coding genes. Correspondence to: X. Xia     

Genome evolution in pocket gophers (genus Thomomys)

Heterochromatin is a dominant component of the genome in the bottae group of the pocket gopher genus Thomomys, having had a major role in the karyotypic evolution of member species. Heterochromatin characteristics of two subspecies of T. bottae and one of T. umbrinus were examined with fluorochrome dyes identifying presumptive GC- and AT-rich regions. In two karyotypic forms of T. b. fulvus and in T. umbrinus, chromatin that fluoresces brightly with chromomycin A₃ is also C-band positive, although not all heterochromatin fluoresces. However, in T. b. bottae, only euchromatic regions fluoresce brightly with chromomycin. Fluorescence patterns produced with DAPI are the reverse of the chromomycin banding in all karyotypic forms. Heterochromatin in these taxa is thus highly differentiated, exhibiting heterogeneity in staining characteristics, and presumably in underlying DNA sequences, both across the genome within a given chromosomal complement as well as among the different karyotypic races and species of the bottae group of pocket gophers.     

Genome evolution in pocket gophers (genus Thomomys)

Cellular DNA content (2 C-value) was measured by fluorescence flow cytometry of chromomycin-A₃ stained spleen cells in 2 subgenera, 5 species, and 21 subspecies of pocket gophers (genus Thomomys). The data indicate that, in Thomomys: (1) interspecific variation is extensive but, while some congeneric species differ by as much as 230%, others are identical in C-value; (2) intraspecific differentiation can be extensive with C-values differing by as much as 35%; and (3) populations of the same subspecies with apparently similar karyotypes can differ significantly in C-value. The implications of these results for hypotheses of the adaptive significance of C-value variation and genome evolution are discussed.     

Soil translocation by pocket gophers in a Mima moundfield

Summary We measured soil translocation due to the tunneling of valley pocket gophers (Thomomys bottae) in a Mima moundfield at Miramar Mounds National Landmark, San Diego, California, from December, 1984 through December, 1985. We placed 1-l soil plugs containing 20 11-g iron pellets into pocket gopher tunnels at locations between mound tops and points about one mound radius beyond mound edges. After about 4–10 d, sites to which the marker-containing soil had been translocated were located with a metal detector and the horizontal and vertical displacements measured. Between 1 October and 15 May (the cooler, wetter portion of the year), pocket gophers removed an average of 63% of the experimental plugs and moved an average of 38% of the markers that we recovered. From 15 May through 1 October (the hotter, drier portion of the year), only 32% of plugs were cleared and 12% of the recovered markers were moved. On average, markers that were moved were displaced 41 cm moundward and 4.9 cm upward in elevation. The intensity of moundward translocation increased with distance from the mound center. At a distance of 0.5–1.0 mound radius beyond the edge of the mound, the moundward translocation tendency averaged 71 cm. The intensity of moundward translocation was also inversely related to maximum mound height. These observations provide strong support for the fossorial rodent hypothesis of Mima mound origin, and constitute a first step in development of a mathematical model of mound formation.     

Morphological constraints in the digging apparatus of pocket gophers (Mammalia: Geomyidae)

The digging apparatus of pocket gophers offers a unique opportunity to examine morphological constraints within a historical context because relationships among extant taxa are well resolved and the features enhancing digging performance are relatively well understood. Structural and functional considerations suggest that the muscles associated with tooth- and claw-digging in pocket gophers are subjected to contrasting levels of morphological constraints. To assess this hypothesis, we analysed the bones and muscles of the jaws and forelimbs in four genera comprising five species of pocket gophers. Morphometric analyses were performed on 12 osteological measurements selected to reflect overall skull size, variation in rostral shape and procumbency, differences in overall length of the forelimbs and processes relating to the function of lever systems used in claw-digging. In addition, dissections were made of the jaw, hyoid, neck and all of the forelimb muscles excluding the intrinsic muscles of the manus. Results of our morphometric analyses corroborate the recent suggestion that pocket gophers encompass a wide range of morphological variation extending from claw-diggers to tooth-diggers. Myologically, however, we found structural variation only in the forelimb muscles, some of which may be advantageous for digging. No changes in jaw, neck and hyoid muscles, other than differences in muscle mass or those concordant with differences in rostral shape, were noted. These results support our hypothesis that constrasting levels of morphological constraint exist between the jaw and forelimb muscles of pocket gophers. We present a discussion of the structural and functional constraints on jaws and forelimbs in gophers as well as an analysis of historical constraints acting on this group, and perhaps on mammals in general.     

Comparative body size relationships in pocket gophers and their chewing lice

In this paper, we use the method of independent contrasts to study body size relationships between pocket gophers and their chewing lice, a host-parasite system in which both host and parasite phylogcnies are well studied. The evolution of body size of chewing lice appears to be dependent only on the body size of their hosts, which confirms the 1991 findings of Harvey and Keymer. We show that there is a positive relationship between body size and hair-shaft diameter in pocket gophers, and that there is also a positive relationship between body size and head-groove width in chewing lice. Finally, we show a positive relationship between gopher hair-shaft diameter and louse head-groove width. We postulate that changes in body size of chewing lice are driven by a mechanical relationship between the parasite's head-groove dimension and the diameter of the hairs of its host. Louse species living"on larger host species may be larger simply because their hosts have thicker hairs, which requires that the lice have a wider head groove. Our study of gopher hair-shaft diameter and louse head-groove dimensions suggest that there is a 'lock-and-key' relationship between these two anatomical features.     

Seasonal patterns of nitrogen utilization by pocket gophers, Thomomys bottae

Adult pocket gophers, fed diets of natural vegetation in the laboratory during summer and winter, remained in positive N balance in all feeding trials. Nitrogen budgets for free-ranging pocket gophers were calculated and revealed that total N influx exceeded 2400 mg N . kg-1 day-1 in summer and 2300 mg N . kg-1 day-1 in winter. Apparent N assimilation was 50 and 53% in summer and winter, respectively, and truly digestible N requirements were congruent to 680 mg N . kg-1 day-1. These budgets indicate that, in spite of seasonally-changing quality of available forage, pocket gophers remain in positive N balance, due largely to shifts in forage preference with season.     

Electrophoretic characterization of the hemoglobins in pocket gophers of the genus Thomomys.

1. Hemoglobin phenotypes have been determined for closely related pocket gopher subspecies in the genus Thomomys from sea level and high altitude. 2. A single hemoglobin band was demonstrated for each gopher population with cellulose acetate membrane electrophoresis, with a mobility of 73% relative to human Hb-A. 3. Using polyacrylamide gel electrophoresis, a major Hb component (94% of the total Hb) showed a relative mobility of 68-69%; the minor Hb component showed a relative mobility of 74-75%. 4. The electrophoretic and physiological similarities of the gopher hemoglobins have persisted despite extreme differences in ambient PO2 in the habitats of each subspecies.     

Responses of pocket gophers (Thomomys bottae) to changes in diet quality

Summary We examined digestibility of dry matter, nutrients, and fiber, and food intake, metabolic fecal losses, weight change, and gut size of pocket gophers (Thomomys bottae) in relation to diet quality in the laboratory. Pocket gophers were maintained for 15–20 days on one of seven diets which contained from 18% to 56% neutral detergent fiber (NDF). NDF content of the diet was an excellent predictor of diet quality. Digestibility of dry matter, NDF, and nitrogen all decreased with increasing NDF content of the diet. In general, pocket gophers compensated for low diet quality by increasing dry matter intake, but those given high quality forage before the lowest quality diet reduced their intake. Thus, the response of pocket gophers to low quality diets may depend on their body condition. Because increased food intake resulted in increased total metabolic fecal losses and metabolic fecal nitrogen losses, decreasing food intake on low-quality diets may be advantageous. A further response of pocket gophers to decreased food quality was an increase in size of cecum and large intestine, suggesting that fermentation of cell walls became increasingly important as diet quality decreased.     

Systematics and phylogeography of pocket gophers in the genera Cratogeomys and Pappogeomys.

Mitochondrial-DNA sequence data were analyzed from individuals sampled from 38 localities across the complete geographic range of the closely related pocket gopher genera Pappogeomys and Cratogeomys. Results of phylogenetic analysis of 1133 base pairs from the cytochrome b gene are consistent with past hypotheses of relationships among members of the castanops species group within the genus Cratogeomys. However, phylogeographic variation within the gymnurus species group of the genus Cratogeomys differs significantly from relationships reflected by current taxonomy. The data indicate that there are five geographically distinct clades within the gymnurus species group. Members of the two nominal species C. gymnurus and C. tylorhinus are scattered among these clades. The three peripherally isolated species, C. fumosus, C. neglectus, and C. zinseri, do not appear to be genetically distinct from other gymnurus species group taxa. An historical biogeographic hypothesis is proposed that will be tested using nuclear DNA data.     

Respiratory adaptations in burrowing pocket gophers from sea level and high altitude.

To examine the adaptations to low O2 and high CO2 among fossorial and nonfossorial rodents, hematological parameters were determined for laboratory rats, the valley pocket gopher (Thomomys bottae) from 250 m, and the mountain pocket gopher (T. umbrinus melanotis) from 3150 m. Hematocrit, hemoglobin concentration, and O2 capacity were higher in pocket gophers than in rats. Blood PO2 at 50% saturation and pH 7.4 was 33 mmHg for both gophers and 39 mmHg for rats. Bohr factors for all three rodents were similar (-0.55 to -0.61) but buffer value, delta log PCO2/delta pH, was -2.54 for T. umbrinus, -1.97 for T. bottae, and -0.98 for Rattus. Concentrations of total acid-soluble phosphates were 50-75% higher in gophers than in rats, while bicarbonate values were within the normal mammalian range. All three rodents had similar myoglobin concentrations in cardiac muscle. Myoglobin concentrations were significantly higher in skeletal muscles (diaphragm, gastrocnemius) of T. umbrinus when compared to T. bottae, and significantly higher in both gophers when compared to rats. These differences may constitute important adaptations to the hypoxia and hypercapnia in burrows; certain of these factors in pocket gophers respond to the additional stress of high altitude hypoxia.     

Survivorship of penstemon grandiflorus in an oak woodland: combined effects of fire and pocket gophers

Summary The effects of fire and pocket gophers, Geomys bursarius, on the survivorship of Penstemon grandiflorus growing in an oak woodland in Minnesota were studied from 1986 to 1990. Plants growing in sparse vegetation experienced mortality rates twice that of plants growing in dense vegetation. This difference was due partly to pocket gophers whose earth moving activities reduce the density of vegetation and bury and kill individual Penstemon plants. Laboratory feeding trials showed that gophers readily eat Penstemon, particularly the fleshy roots. An experiment involving the removal of 25–75% of the root tissue in 90 plants showed that root loss significantly reduced survivorship, suggesting that gopher herbivory might also kill plants. When gophers were experimentally excluded, plants growing in sparse vegetation exhibited significantly lower mortality rates than those growing in dense vegetation. Plants in the smallest size class exhibited reduced survivorship following a late spring burn; however, overall patterns of survivorship of plants in burned areas did not differ markedly from those in the unburned areas. A longitudenal analysis of plants with different reproductive histories revealed no survivorship cost to reproduction. Mortality rates decreased with increasing plant size. Small plants were more likely to be killed by fire and by being buried under gopher mounds. Differences in underground energy reserves of small and large plants can account for most of the survivorship patterns observed in this study. The study shows that within openings of the oak woodland, fire and gophers reduce the survival of individual Penstemon plants. Nevertheless, since both gophers and fire also serve to perpetuate suitable habitat in the woodland, Penstemon is ultimately dependent on both for its long term persistence in the landscape.     

Reproductive cycle of the pocket gophers Orthogeomys cherriei (Rodentia: Geomyidae) in Costa Rica]

Pocket gophers (Orthogemys cherriei) is a pest in agriculture in Limón, Costa Rica; 232 animals were trapped in several farms. They reproduce continuously throughout the year. Adults of both sexes are found in reproductive condition at any time. The females produce at least 2 litters per year (1-4 newborns each). There is no correlation between position of testes and production of sperm. The position of the testes is not a reliable factor to establish the reproductive condition in males. There is a correlation between length of os penis (baculum) and length of the testes, irrespectively of its reproductive condition. These pocket gophers disperse above-ground.     

Cophylogeny and disparate rates of evolution in sympatric lineages of chewing lice on pocket gophers

Although molecular-based phylogenetic studies of hosts and parasites are increasingly common in the literature, no study to date has examined two congeneric lineages of parasites that live in sympatry on the same lineage of hosts. This study examines phylogenetic relationships among chewing lice (Phthiraptera: Trichodectidae) of the Geomydoecus coronadoi and Geomydoecus mexicanus species complexes and compares these to phylogenetic patterns in their hosts (pocket gophers of the rodent family Geomyidae). Sympatry of congeneric lice provides a natural experiment to test the hypothesis that closely related lineages of parasites will respond similarly to the same host. Sequence data from the mitochondrial COI and the nuclear EF-1alpha genes confirm that the two louse complexes are reciprocally monophyletic and that individual clades within each species complex parasitize a different species of pocket gopher. Phylogenetic comparisons reveal that both louse complexes show a significant pattern of cophylogeny with their hosts. Comparisons of rates of nucleotide substitution at 4-fold degenerate sites in the COI gene indicate that both groups of lice have significantly higher basal mutation rates than their hosts. The two groups of lice have similar basal rates of mutation, but lice of the G. coronadoi complex show significantly elevated rates of nucleotide substitution at all sites. These rate differences are hypothesized to result from population-level phenomena, such as effective population size, founder effects, and drift, that influence rates of nucleotide substitution.     

Habitat associations of California ground squirrels and Botta's pocket gophers on levees in California

Vegetation management on levees, especially removal of trees and shrubs, might affect burrowing mammals that are considered threats to levee integrity. We evaluated habitat associations of California ground squirrels (Otospermophilus beecheyi) and Botta's pocket gophers (Thomomys bottae) on levees in the Sacramento Valley to assess the effects of levee vegetation management on these species. Using burrows as an indirect measure of mammal presence, we found that the presence of trees had a negative effect on the occurrence and abundance of ground squirrels on levees, and on the location of their burrowing activities on the levee slope, potentially because visual occlusion caused by tall woody vegetation impedes detection of predators. Similarly, trees had a negative effect on the abundance of pocket gophers on levees and on the location of their burrowing activities on the levee slope, probably because of the effect of tree cover on food availability. The conversion of woodland habitats to grasslands on levees most likely will result in increased occurrence, abundance, or both of ground squirrels and pocket gophers, and thereby increase the potential threat that their burrowing activities pose to levee integrity. © 2012 The Wildlife Society.     

Predation by three owl species on northern pocket gophers of different body mass

Summary We examined the estimated sizes of Thomomys talpoides in the diets of Bubo virginianus (1,505 g), Tyto alba (437 g), and Asio otus (245 g) in north-central Oregon between 1973 and 1982. The three owl species tended to consume T. talpoides of different size and responded differently to predicted seasonal body mass changes in the T. talpoides population. On an annual basis B. virginianus preyed upon the largest individuals (x = 67.9 g), whereas A. otus preyed upon the smallest (x = 41.0 g). When compared with the predicted values for the size composition of the T. talpoides population, B. virginianus appeared to prey upon T. talpoides randomly with respect to size, whereas A. out demonstrated a high degree of selectivity, consistently preying upon relatively small individuals. However, the absence of significant seasonal changes in prey size electivities suggests that active choice is not a major factor in predation on gophers by A. otus. Instead, evidence suggests that A. otus attacks T. talpoides randomly with respect to size but captures them in accordance with size-related capture probabilities. Tyto alba preyed most commonly upon intermediate sized T. talpoides (x = 63.3 g), and the presence of T. alba coincided with the seasonal occurrence of T. talpoides of this general size.     

Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys

Using the strictly neutral model as a null hypothesis, we tested for deviations from expected levels of nucleotide polymorphism at the alcohol dehydrogenase locus (Adh-1) within and among four species of pocket gophers (Geomys bursarius major, G. knoxjonesi, G. texensis llanensis, and G. attwateri). The complete protein-encoding region was examined, and 10 unique alleles, representing both electromorphic and cryptic alleles, were used to test hypotheses (e.g., the neutral model) concerning the maintenance of genetic variation. Nineteen variable sites were identified among the 10 alleles examined, including 9 segregating sites occurring in synonymous positions and 10 that were nonsynonymous. Several statistical methods, including those that test for within-species variation as well as those that examine variation within and among species, failed to reject the null hypothesis that variation (both within and between species of Geomys) at the Adh locus is consistent with the neutral theory. However, there was significant heterogeneity in the ratio of polymorphism to divergence across the gene, with polymorphisms clustered in the first half of the coding region and fixed differences clustered in the second half of the gene. Two alternative hypotheses are discussed as possible explanations for this heterogeneity: an old balanced polymorphism in the first half of the gene or a recent selective sweep in the second half of the gene.