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.     

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.     

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.     

Fluctuating asymmetry and allozymic heterozygosity among natural populations of pocket gophers (Thomomys bottae)

Fluctuating asymmetry, or random deviations from bilateral symmetry, has been widely used as a measure of developmental stability. The relationship between fluctuating asymmetry (FA) and allozymic heterozygosity was evaluated using 18 natural populations of pocket gophers ( Thomomys bottae ). Heterozygosity in local populations of pocket gophers ranges over more than an order of magnitude (1.5—18.4%), making this burrowing rodent particularly apt for such studies. Two measures of FA in mensural skull characters were examined: absolute deviations between left and right sides and the variance of signed differences. After log transformations, levels of FA among individuals and populations were not related to size. Repeated-measures analyses of variance showed that FA was significant relative to measurement error, both across populations and within them. Asymmetries of different characters were uncorrelated, despite positive significant correlations among the characters themselves. FA levels varied only slightly among populations of gophers, and this variation was not significant for most characters. FA levels of populations were not correlated with allozymic heterozygosity, and analyses of variance in FA employing heterozygosity were not significant. Heterozygosity levels in these rodents appear more strongly related to aspects of population history (especially effective size and gene flow) than to developmental stability. Because so many genomic and environmental factors can affect morphological variation, caution is needed in interpreting correlations between genetic and phenetic variation.     

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.      

Phylogenetic relationships among middle American pocket gophers (genus Orthogeomys) based on mitochondrial DNA sequences.

Relationships among members representing each of the three subgenera of the Middle American rodent genus Orthogeomys (Rodentia: Geomyidae) were studied by comparing DNA sequence data from two regions of the mitochondrial genome. Results from 527 bp from the 16 S rDNA region and a 402-bp fragment of the cytochrome b gene indicate that the three subgenera are well differentiated genetically, with the subgenus Orthogeomys being distantly related to Macrogeomys and Heterogeomys, and Macrogeomys appearing as the most derived. Within the subgenus Macrogeomys, O. heterodus and O. cherriei form a distinct clade, as do O. dariensis and O. cavator. As with previous protein-electrophoretic studies, the placement of O. underwoodi could not be determined definitively within the subgenus Macrogeomys. We interpret our inability to determine phylogenetic relationships among these three clades as evidence for a rapid phyletic radiation within this subgenus. Sequence divergence estimates indicate that the Macrogeomys radiation took place following the time of completion of the Panamanian land bridge (1.9-2.9 mya). Additionally, the near identity of sequences of a newly described species, O. thaeleri, with those of O. dariensis (percentage sequence divergence = 0.3%) suggests that the two may be conspecific.     

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     

Morphology, genetics, and ecology of pocket gophers (genus Geomys) in a narrow hybrid zone

A population of hybrid pocket gophers ( Geomys bursarius × G. lutescens ) exists 1–2 km west of Oakdale, Antelope County, Nebraska, U.S.A. The hybrids occur in soil that has characteristics intermediate between that occupied by G. lutescens (sand) and by G. bursarius (silt loam); the vegetation associations on the different soils are Sandhills Prairie and Tall-grass Prairie, respectively, with mixed prairie on the intermediate soils. Hybrids are identifiable on the basis of both qualitative and quantitative morphological characteristics, allozymes and karyology. Concordance between morphological, allozymic, karyotypic and ecological data sets is very high. Hybrids appear to reproduce normally and survive well; i.e. they suffer no obvious loss of fitness. Backcrossing to either parental type is apparently rare. The parental species each support obligate parasitic lice ( Geomydoecus : Trichodectidae) of different species; these species are not sister species. We suggest that hybrid zones resulting from primary and secondary contact may be distinguished by (1) concordance of clines in different character sets, (2) fossil and biogeographic data, and (3) parasite data. We conclude that this zone resulted from secondary contact, and that the zone is maintained either by selection against hybrids (less likely) or by hybrid superiority (more likely).     

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.     

Infrared spectra of carbonyl hemoglobins: characterization of dynamic heme pocket conformers

The infrared spectra for carbon monoxide complexed to hemoglobins were examined in the C-O stretch region. Deconvolution of the spectra requires four bands and supports the presence of four distinct conformers at the ligand binding site. Most typical hemoglobins exhibit only one predominant conformer for each subunit represented by a band at 1951 cm-1 in contrast to myoglobins, which typically exist in two major conformations. Several hemoglobins with an enlarged heme pocket are shown to shift the C-O frequency into the higher frequency conformer regions. Many factors, including pH, temperature, solvents, and divalent metals, are also shown to be capable of expanding the heme pocket. Only very specific structural changes that can reduce the size of the heme pocket will result in the lower frequency conformers. The weighted averages of the multiple CO vibrational frequencies are linearly related to the single 13CO NMR chemical shift values and to the exponential of fast CO on-rates. Conformer interconversion occurs at a rate greater than 10(4) s-1. The infrared C-O stretch spectra provide qualitative and quantitative information on the structural dynamics, stability, and ligand binding properties of hemoglobins.     

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.     

Adaptive nature of chromosomal rearrangement: differential fitness in pocket gophers

A chromosomal centric fusion polymorphism in populations of the plains pocket gopher, Geomys bursarius, was studied to determine the relative fitness associated with the karyotypic phenotypes. There was a greater number of heterozygous individuals than expected χ₁ ²=8.58, P=0.001. Calculations indicate that the viabilities of the two chromosomal homozygotes were only 35 and 76 percent or that of the heterozygote. Differences in fitness values for the chromosomal morphs for Geomys strongly emphasize the possible adaptive nature of the karyotype and provides a primary mechanism for chromosomal evolution, even in species composed of demes of relatively large size. This is the first case of positive chromosomal heterosis in vertebrates. The plains pocket gopher can now be added to the few empirically documented samples of balanced polymorphism.     

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 livingon 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.