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J C Patton

Publications and source records attributed to J C Patton.

16 recordsLinked to original sources
PubMed2004

Conservation genetics and demographic history of the endangered Cape Fear shiner (Notropis mekistocholas).

We examined allelic variation at 22 nuclear-encoded markers (21 microsatellites and one anonymous locus) and mitochondrial (mt)DNA in two geographical samples of the endangered cyprinid fish Notropis mekistocholas (Cape Fear shiner). Genetic diversity was relatively high in comparison to other endangered vertebrates, and there was no evidence of small population effects despite the low abundance reported for the species. Significant heterogeneity (following Bonferroni correction) in allele distribution at three microsatellites and in haplotype distribution in mtDNA was detected between the two localities. This heterogeneity may be due to reduced gene flow caused by a dam built in the early 1900 s. Bayesian coalescent analysis of microsatellite variation indicated that effective population size of Cape Fear shiners has declined in recent times (11-25 435 years ago, with highest posterior probabilities between 126 and 2007 years ago) by one-two orders of magnitude, consistent with the observed decline in abundance of the species. A decline in effective size was not indicated by analysis of mtDNA, where sequence polymorphism appeared to carry the signature of an older expansion phase that dated to the Pleistocene ( approximately 12 700 > 1 million years ago). Cape Fear shiners thus appear to have undergone an expansion phase following a glacial cycle but to have declined significantly in more recent times. These results suggest that rapidly evolving markers such as microsatellites may constitute a suitable tool when inferring recent demographic dynamics of populations.

Animals↗
PubMed2003

Genetic variation in caribou and reindeer (Rangifer tarandus).

Genetic variation at seven microsatellite DNA loci was quantified in 19 herds of wild caribou and domestic reindeer (Rangifer tarandus) from North America, Scandinavia and Russia. There is an average of 2.0-6.6 alleles per locus and observed individual heterozygosity of 0.33-0.50 in most herds. A herd on Svalbard Island, Scandinavia, is an exception, with relatively few alleles and low heterozygosity. The Central Arctic, Western Arctic and Porcupine River caribou herds in Alaska have similar allele frequencies and comprise one breeding population. Domestic reindeer in Alaska originated from transplants from Siberia, Russia, more than 100 years ago. Reindeer in Alaska and Siberia have different allele frequencies at several loci, but a relatively low level of genetic differentiation. Wild caribou and domestic reindeer in Alaska have significantly different allele frequencies at the seven loci, indicating that gene flow between reindeer and caribou in Alaska has been limited.

Animals↗
PubMed1998

Cytosolic isocitrate dehydrogenase in humans, mice, and voles and phylogenetic analysis of the enzyme family.

In this study, we report cDNA sequences of the cytosolic NADP-dependent isocitrate dehydrogenase for humans, mice, and two species of voles (Microtus mexicanus and Microtus ochrogaster). Inferred amino acid sequences from these taxa display a high level of amino acid sequence conservation, comparable to that of myosin beta heavy chain, and share known structural features. A Caenorhabditis elegans enzyme that was previously identified as a protein similar to isocitrate dehydrogenase is most likely the NADP-dependent cytosolic isocitrate dehydrogenase enzyme equivalent, based on amino acid similarity to mammalian enzymes and phylogenetic analysis. We also suggest that NADP-dependent isocitrate dehydrogenases characterized from alfalfa, soybean, and eucalyptus are most likely cytosolic enzymes. The phylogenetic tree of various isocitrate dehydrogenases from eukaryotic sources revealed that independent gene duplications may have given rise to the cytosolic and mitochondrial forms of NADP-dependent isocitrate dehydrogenase in animals and fungi. There appears to be no statistical support for a hypothesis that the mitochondrial and cytosolic forms of the enzyme are orthologous in these groups. A possible scenario of the evolution of NADP-dependent isocitrate dehydrogenases is proposed.

Amino Acid Sequence↗
PubMed1996

K-casein gene phylogeny of higher ruminants (Pecora, Artiodactyla).

To assess phylogenetic relationships among the higher ruminants (infraorder Pecora, order Artiodactyla), we analyzed K-casein DNA sequences, including 434 nucleotides of the fourth exon. The higher ruminant families Bovidae, Cervidae, Giraffidae, and Antilocapridae each have monophyletic K-casein sequences. Maximum parsimony and distance analyses identify Giraffidae as a sister group to either Cervidae or a Bovidae-Cervidae clade and Antilocapridae as a sister group to a Bovidae-Cervidae-Giraffidae clade. At a higher level these four families occur as a monophyletic clade relative to Tragulidae and Suidae. Within Cervidae, the subfamily Odocoileinae is monophyletic and Cervinae and Muntiacinae occur as independent lineages within a separate clade. Within Bovidae, the subfamilies Bovinae and Caprinae are monophyletic. Genera within Cervinae (Cervus, Elaphurus) and Bovinae (Bison, Bos) are paraphyletic. There is intraspecific allelic variation in Cervus elaphus, Odocoileus hemionus, and Bison bison. The rate of K-casein fourth exon DNA sequence evolution is estimated to be about 0.004 nucleotide substitutions per million years. The K-casein phylogeny is discussed relative to other molecular and morphological data.

Animals↗
PubMed1995

Genetic variation in domestic reindeer and wild caribou in Alaska.

Reindeer (Rangifer tarandus tarandus) were introduced into Alaska 100 years ago and have been maintained as semidomestic livestock. They have had contact with wild caribou (R.t.granti) herds, including deliberate crossbreeding and mixing in the wild. Reindeer have considerable potential as a domestic animal for meat or velvet antler production, and wild caribou are important to subsistence and sport hunters. Our objective was to quantify the genetic relationships of reindeer and caribou in Alaska. We identified allelic variation among five herds of wild caribou and three herds of reindeer with DNA sequencing and restriction enzymes for three loci: a DQA locus of the major histocompatibility complex (Rata-DQA1), kappa-casein and the D-loop of mitochondrial DNA. These loci are of interest because of their potential influence on domestic animal performance and the fitness of wild populations. There is considerable genetic variation in reindeer and caribou for all three loci, including five, three and six alleles for DQA, kappa-casein and D-loop respectively. Most alleles occur in both reindeer and caribou, which may be the result of recent common ancestry or genetic introgression in either direction. However, allele frequencies differ considerably between reindeer and caribou, which suggests that gene flow has been limited.

Alaska↗
PubMed1993

Partial endonuclease digestion mapping of restriction sites using PCR-amplified DNA.

Although direct DNA sequencing is now readily available, restriction enzyme analyses are still widely used in population genetics and molecular systematics studies. These analyses provide cheaper and faster ways to assay patterns of nucleotide differentiation across a large number of individuals. In this paper, we introduce a new approach to restriction enzyme analyses in which high-resolution restriction site maps are obtained from partial digestions of PCR products. This procedure increases the level of resolution at least an order of magnitude over the double-digestion method for restriction enzyme mapping, can target specific DNA regions with the use of specific primers, and, because it uses chemiluminescent detection of DNA, can be easily implemented in laboratories that lack the necessary setups to handle radioactive substances.

Animals↗
PubMed1988

M13 repeat probe detects DNA minisatellite-like sequences in gymnosperms and angiosperms.

Several kinds of minisatellite DNA, all of which are composed of low to moderately repetitive DNA, have been identified in tetrapod genomes. While the repeating oligonucleotide elements (subrepeats) of a given minisatellite are virtually identical, subrepeat nucleotide composition differs between different minisatellites. Several minisatellites have exhibited moderate to high levels of restriction length polymorphism in a number of tetrapods. Such hypervariable markers provide powerful tools for genetic analyses in several fields of biology. Minisatellite applications have been restricted to tetrapods, but here we demonstrate that one probe, the M13 repeat probe previously used to detect minisatellites in humans and bovines, also reveals minisatellite-bearing endonuclease fragments in gymnosperms and angiosperms. While the plant minisatellites appear to be somatically stable within an individual, they often vary within species in potentially useful ways. These results demonstrate that minisatellite-like families may be distributed over a wide taxonomic range in eukaryotes, opening the possibility of a commensurately wide utility of minisatellite probes in genetic analyses.

DNA Probes↗
PubMed1983

An empirical evaluation of qualitative Hennigian analyses of protein electrophoretic data.

In an empirical evaluation of a qualitative approach to construction of phylogenetic trees from protein-electrophoretic data, we have employed Hennigian cladistic principles to generate molecular trees for water-fowl, rodents, bats, and other phylads. This procedure of tree construction is described in detail. Branching structures of molecular trees produced by three different algorithms were compared against those of "model" classifications previously proposed by other systematists. In each case, the qualitative cladistic trees provided fits to model phylogenies which were strong and as good or better than those resulting from phenetic-clustering or distance-Wagner trees based on manipulation of quantitative values in matrices of genetic distance. The qualitative Hennigian approach has several pragmatic (as well as theoretical) advantages for analyzing routine sets of electrophoretic data: (1) the analyses are simple and can be performed by hand; (2) they provide the researcher with a strong "feel" for the data; (3) additional data (from new loci or species) can readily be added to the tree without need to recalculate distance matrices; and (4) the qualitative output of the analyses explicitly defines character states along all branches of the tree, and hence affords a high degree of testability. However, these advantages are counterbalanced by a number of serious disadvantages which will likely limit the general applicability of this qualitative approach. These drawbacks are also discussed in detail. For a deeper appreciation of electrophoretic-based protein phylogenies, it is suggested that both quantitative phenetic and qualitative cladistic analyses be employed when possible, and that results of the two approaches be contrasted.

Animals↗
PubMed1982

Evolutionary genetics of birds. V. Genetic distances within Mimidae (mimic thrushes) and vireonidae (Vireos).

Genetic distances (D's) between five species within each of the families Mimidae and Vireonidae were estimated from frequencies of protein electromorphs at 23 loci. For three mimid species in the genus Toxostoma, D equals 0.084 (range, 0.069-0.104); and among three mimid genera, D equals 0.223 (0.167-0.278). These distances typify values previously reported in other birds at comparable levels of taxonomic recognition. In sharp contrast, the mean genetic distance among five congeneric species of Vireonidae is far higher, D = 0.360 (0.027-0.578). One possible explanation for these results is that Vireo species are considerably older, on the average, than are species of Toxostoma or than are members of several other avain genera assayed to date. Conventional thought about the origin and relative age of the Vireonidae appears compatible with this explanation. Although genetic distances in the Vireonidae are large by "avian standards," they remain modest or even small in comparison with distances between many nonavian vertebrate congeners. Results for the Mimidae and the Vireonidae are directly contrasted with genetic distances in well-known genera of Amphibia and Reptilia.

Animals↗
PubMed1979

Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis.

Restriction endonuclease assay of mitochondria DNA (mtDNA) and standard starch-gel electrophoresis of proteins encoded by nuclear genes have been used to analyze phylogenetic relatedness among a large number of pocket gophers (Geomys pinetis) collected throughout the range of the species. The restriction analysis clearly distinguishes two populations within the species, an eastern and a western form, which differ by at least 3% in mtDNA sequence. Qualitative comparisons of the restriction phenotypes can also be used to identify mtDNA "clones" within each form. The mtDNA clones interconnect in a phylogenetic network which represents an estimate of matriarchal phylogeny for G. pinetis. Although the protein electrophoretic data also differentiate the eastern and western forms, the data are of limited usefulness in establishing relationships among more local subpopulations. The comparison between these two data sets suggests that restriction analysis of mtDNA is probably unequalled by other techniques currently available for determining phylogenetic relationships among conspecific organisms.

Albumins↗
PubMedDate not supplied

Biogeographic implications of cytochrome b sequences and allozymes in sockeye (Oncorhynchus nerka).

Nucleotide sequence and restriction site analyses of the cytochrome b gene of mitochondrial DNA revealed three relatively common haplotypes among sockeye salmon (N = 80) from eight populations representing four major drainages from Kamchatka (Russia), Alaska, and British Columbia. Macrogeographic variation in mtDNA was compared to that of three variable allozyme loci assayed for a much larger number of fish (N = 779). Sockeye from the Fraser River drainage of British Columbia were distinct from those from the other three drainages in both analyses. The GT haplotype was found in all four populations, but the GC haplotype was absent from the Fraser River (southern) drainage and present in the three northern drainages. The AC haplotype was common in the Fraser River drainage (frequency = 0.4), rare in the Skeena River drainage of British Columbia (0.1), and absent from the Alaskan and Russian samples. Cluster analysis (UPGMA) of allozyme allele frequencies showed a similar pattern of divergence with the populations from the Fraser River drainage being most divergent and clustering at an identity value of 0.93 with the rest of the populations. Five of the remaining six populations clustered at or above an identity value of 0.99. These data, combined with allozyme data for sockeye and mitochondrial DNA data for chinook salmon and the Steller sea lion, indicate the presence of a phylogeographic break between northern and southern populations ostensibly derived from glacial refugia in Beringia and the Columbia River, respectively.

Animals↗