Journal of Heredity - recent issues

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Wed, 11 Nov 2009 04:10:27 PST

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Wed, 11 Nov 2009 04:10:27 PST

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Wed, 11 Nov 2009 04:10:27 PST

Wed, 11 Nov 2009 04:10:28 PST

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Genome 10K Community of Scientists — Wed, 11 Nov 2009 04:10:28 PST

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10 000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16 203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60 000 living species). In this proposal, we present precise counts for these 16 203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Detection of Cytonuclear Genomic Dissociation in the North American Captive African Elephant Collection

Lei, R., Brenneman, R. A., Schmitt, D. L., Louis, E. E. — Wed, 11 Nov 2009 04:10:28 PST

A total of 114 captive elephants (6 Asian; 108 African) from 43 private institutions or North American zoos accredited by the Association of Zoos and Aquariums were sampled and evaluated to investigate genetic status. Because previous analyses of the captive collection indicated potential cytonuclear dissociation between mitochondrial DNA (mtDNA) sequence and microsatellite nuclear DNA genotype data, we investigated this phenomenon within the captive collection with 2 X-linked genes (BGN and PHKA2) and 1 Y-linked gene (AMELY). These data reveal that individuals with forest-derived elephant mtDNA lineages carried only savannah elephant nuclear gene haplotypes. These results are concordant with a previous study of wild populations sampled across Africa, indicating that cytonuclear genomic dissociation was captured in the founders of the North American African elephant collection. These results are important for resolving questions that can potentially impact future management and breeding programs related to the collection.

Genetic Variation, Relatedness, and Effective Population Size of Polar Bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

Cronin, M. A., Amstrup, S. C., Talbot, S. L., Sage, G. K., Amstrup, K. S. — Wed, 11 Nov 2009 04:10:28 PST

Polar bears (Ursus maritimus) are unique among bears in that they are adapted to the Arctic sea ice environment. Genetic data are useful for understanding their evolution and can contribute to management. We assessed parentage and relatedness of polar bears in the southern Beaufort Sea, Alaska, with genetic data and field observations of age, sex, and mother–offspring and sibling relationships. Genotypes at 14 microsatellite DNA loci for 226 bears indicate that genetic variation is comparable to other populations of polar bears with mean number of alleles per locus of 7.9 and observed and expected heterozygosity of 0.71. The genetic data verified 60 field-identified mother–offspring pairs and identified 10 additional mother–cub pairs and 48 father–offspring pairs. The entire sample of related and unrelated bears had a mean pairwise relatedness index (r_xy) of approximately zero, parent–offspring and siblings had r_xy of approximately 0.5, and 5.2% of the samples had r_xy values within the range expected for parent-offspring. Effective population size (N_e = 277) and the ratio of N_e to total population size (N_e/N = 0.182) were estimated from the numbers of reproducing males and females. N_e estimates with genetic methods gave variable results. Our results verify and expand field data on reproduction by females and provide new data on reproduction by males and estimates of relatedness and N_e in a polar bear population.

The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp.

Wed, 11 Nov 2009 04:10:28 PST

The chamois is a useful species with which to investigate the combined genetic impact of habitat fragmentation, over hunting, and translocations. Genetic variation within and between chamois (genus Rupicapra) populations was analyzed in 259 individuals from 16 sampling sites located in Italy, Spain, Slovakia, and the Czech Republic. Two mitochondrial DNA markers (control region and cytochrome b) and 11 nuclear microsatellites were typed. The principal results of this study can be summarized as follows: 1) high and significant differentiation between almost all chamois populations is observed even on a microgeographical scale, probably caused by the patchy distribution of this species, sharp geographical barriers to gene flow, and drift effects related to recent bottlenecks; 2) historical translocation events have left a clear genetic signature, including interspecific hybridization in some Alpine localities; 3) the Apennine subspecies of chamois, Rupicapra pyrenaica ornata, shows a high and similar level of divergence (about 1.5 My) from the Pyrenean (Rupicapra pyrenaica pyrenaica) and the Alpine (Rupicapra rupicapra) chamois; therefore, the specific status of these taxa should be revised. These results confirm the potential of population genetic analyses to dissect and interpret complex patterns of diversity in order to define factors important to conservation and management.

The Genetic Basis of Melanism in the Gray Squirrel (Sciurus carolinensis)

McRobie, H., Thomas, A., Kelly, J. — Wed, 11 Nov 2009 04:10:28 PST

The black squirrel is a melanic variant of the gray squirrel (Sciurus carolinensis). We found 3 coat color variants in the gray squirrel: the wild-type gray, a jet-black, and a brown–black phenotype. These 3 morphs are due to varying distributions of eumelanin and phaeomelanin pigment in hairs. The melanocortin 1 receptor (MC1R) plays a central role in regulating eumelanin and phaeomelanin production. We sequenced the MC1R gene for all 3 coat color phenotypes and found a 24 base-pair deletion. The gray phenotype was homozygous for the wild-type allele E⁺, the jet-black phenotype was homozygous for the MC1R-24 allele E^B, and the brown–black phenotype was heterozygous for the E⁺ and E^B alleles. We conclude that melanism in gray squirrels is associated with the MC1R-24 E^B allele at amino acid positions 87–94 and that this allele is incompletely dominant to the wild-type allele. We predict that the MC1R-24 E^B allele encodes a constitutively active or hyperactive receptor.

Genetic Diversification, Vicariance, and Selection in a Polytypic Frog

Robertson, J. M., Zamudio, K. R. — Wed, 11 Nov 2009 04:10:28 PST

Spatial patterns of heritable phenotypic diversity reflect the relative roles of gene flow and selection in determining geographic variation within a species. We quantified color differentiation and genetic divergence among 20 populations of the red-eyed tree frog (Agalychnis callidryas) in lower Central America. Phylogenetic analyses revealed 5 well-supported mitochondrial DNA clades, and we infer from our phylogeny that geographic barriers have played a large role in structuring populations. Two phenotypic characters varied independently among isolated population groups: Flank coloration distinguished Caribbean from Pacific individuals, whereas leg coloration exhibited a more complex geographic pattern. We detected 3 generalized spatial patterns of genetic and phenotypic diversity: 1) phenotypic differentiation in the presence of historical connectivity, 2) phenotypic uniformity across genetically differentiated regions, and 3) codistribution of genetic and phenotypic characters. These patterns indicate that phenotypic diversification is highly regionalized and can result from spatial variation in localized adaptations, geographic isolation, genetic drift, and/or evolutionary stasis. Although the mode of selection underlying color variation was not the focal objective of this study, we discuss the possible roles of natural and sexual selection in mediating population differentiation. Our study underscores the fact that selection gradients vary across relatively small spatial scales, even in species that occupy relatively homogeneous environments.

Genetic Differentiation among Wild Populations of Tribolium castaneum Estimated Using Microsatellite Markers

Drury, D. W., Siniard, A. L., Wade, M. J. — Wed, 11 Nov 2009 04:10:28 PST

We report our characterization of the genetic variation within and differentiation among wild-collected populations of the red flour beetle, Tribolium castaneum, using microsatellite loci identified from its genome sequence. We find that global differentiation, estimated as the average F_ST across all loci and between all population pairs, is 0.180 (95% confidence intervals of 0.142 and 0.218). A majority of our pairwise population comparisons (>70%) were significant even though this species is considered an excellent colonizer by virtue of its pest status. Regional genetic variation between Tribolium populations is 2–3 times that observed in the fruit fly, Drosophila melanogaster. There was a weak positive correlation between genetic distance [F_ST/(1 – F_ST)] and geographic distance [ln(km)]; pairs of populations with the highest degree of genetic differentiation (F_ST > 0.29) have been shown to exhibit significant postzygotic reproductive isolation when crossed in previous studies. We discuss the possibility that local extinction and kin-structured colonization have increased the level of genetic differentiation between Tribolium populations.

Evolution of the GST Omega Gene Family in 12 Drosophila Species

Walters, K. B., Grant, P., Johnson, D. L. E. — Wed, 11 Nov 2009 04:10:28 PST

Gene families provide a unique system to study the evolutionary relationships between related genes both within and between organisms. We can ascertain whether members of a gene family in different species are orthologs or paralogs. We may also search for evidence that may explain why duplicate genes are present. The availability of genome sequences for 12 Drosophila species allows us to address these questions with respect to the evolution of one gene family, the glutathione S transferase (GST) omega class. This gene family is of particular interest because of its relationship with human disease and its presence in a wide range of species.

Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants

Livingstone, K., Anderson, S. — Wed, 11 Nov 2009 04:10:28 PST

Cellular metabolic networks depend on the products of many loci for proper functioning. These interrelationships between loci at the phenotypic level raise the question of whether they evolve independently. Previous research has demonstrated that in the anthocyanin pathway, which produces important secondary metabolites in plants, the genes encoding downstream enzymes show an increased rate of change at nonsynonymous sites when compared with upstream loci due to relaxed constraint. To test whether this pattern exists more broadly, we compared a set of 4 genes encoding enzymes of the carotenoid biosynthetic pathway, which produces a set of distinct colored secondary metabolites in plants. Comparisons between copies of phytoene desaturase, -carotene desaturase, lycopene β-cyclase, and zeaxanthin epoxidase from 6 taxa indicate that the 3 upstream enzymes (phytoene desaturase, -carotene desaturase, and lycopene β-cyclase) have similar proportions of codons under selective constraint, whereas the most downstream enzyme (zeaxanthin epoxidase) has more codons evolving under relaxed constraint. Overall, nonsynonymous substitution rates appear to be highest for zeaxanthin epoxidase, whereas synonymous substitution rates were highest for the intermediate enzyme lycopene β-cyclase. Analysis of codon bias shows that only lycopene β-cyclase may be under slight selection pressure for codon usage. Taken together, these results show that the enzymes of the carotenoid biosynthetic pathway are under strong selective constraint but that the most downstream enzyme is under the least constraint.

Patterns of Nucleotide Diversity at the Methionine Synthase Locus in Fragmented and Continuous Populations of a Wind-Pollinated Tree, Quercus mongolica var. crispula

Quang, N. D., Ikeda, S., Harada, K. — Wed, 11 Nov 2009 04:10:28 PST

Genetic variation is usually high within populations, and differentiation is usually low among populations of wind-pollinated outcrossing trees. As a result, population contraction causes little change in the degree of genetic diversity and differentiation among populations. The aim of this work was to determine whether or not a recent population decline has influenced the allele frequency spectrum and association among variants of different sites on the nuclear housekeeping locus methionine synthase (1376–1418 bp in length) in the oak species Quercus mongolica var. crispula. A total of 122 sequences from 18 populations were randomly sampled and analyzed in this study. Results showed that nucleotide variation was generally high within populations, and differentiation was very low among populations. Genetic diversity was slightly reduced in samples taken from the area with a recent strong reduction in population size. Nevertheless, the allele frequency spectrum was skewed toward rare variants, and the association among variants of different sites was significantly more nonrandom within these samples compared with those from the area without such a population size reduction. This pattern was robustly supported by coalescent simulations.

Mapping of Quantitative Trait Loci for Grain Iron and Zinc Concentration in Diploid A Genome Wheat

Wed, 11 Nov 2009 04:10:28 PST

Micronutrients, especially iron (Fe) and zinc (Zn), are deficient in the diets of people in underdeveloped countries. Biofortification of food crops is the best approach for alleviating the micronutrient deficiencies. Identification of germplasm with high grain Fe and Zn and understanding the genetic basis of their accumulation are the prerequisites for manipulation of these micronutrients. Some wild relatives of wheat were found to have higher grain Fe and Zn concentrations compared with the cultivated bread wheat germplasm. One accession of Triticum boeoticum (pau5088) that had relatively higher grain Fe and Zn was crossed with Triticum monococcum (pau14087), and a recombinant inbred line (RIL) population generated from this cross was grown at 2 locations over 2 years. The grains of the RIL population were evaluated for Fe and Zn concentration using atomic absorption spectrophotometer. The grain Fe and Zn concentrations in the RIL population ranged from 17.8 to 69.7 and 19.9 to 64.2 mg/kg, respectively. A linkage map available for the population was used for mapping quantitative trait loci (QTL) for grain Fe and Zn accumulation. The QTL analysis led to identification of 2 QTL for grain Fe on chromosomes 2A and 7A and 1 QTL for grain Zn on chromosome 7A. The grain Fe QTL were mapped in marker interval Xwmc382-Xbarc124 and Xgwm473-Xbarc29, respectively, each explaining 12.6% and 11.7% of the total phenotypic variation and were designated as QFe.pau-2A and QFe.pau-7A. The QTL for grain Zn, which mapped in marker interval Xcfd31-Xcfa2049, was designated as QZn.pau-7A and explained 18.8% of the total phenotypic variation.

Genetic Mapping of Resistance to Phomopsis Seed Decay in the Soybean Breeding Line MO/PSD-0259 (PI562694) and Plant Introduction 80837

Jackson, E. W., Feng, C., Fenn, P., Chen, P. — Wed, 11 Nov 2009 04:10:28 PST

Resistance to Phomopsis seed decay (PSD) in soybean (Glycine max [L.] Merr.) could provide dependable control of this important disease that affects seed quality. Studies have shown that single dominant genes that are allelomorphically different confer low levels of PSD in MO/PSD-0259 and PI 80837. The objectives of this research were to identify simple sequence repeat (SSR) markers linked to genes for PSD resistance in PI 80837 and MO/PSD-0259 and to associate the resistance genes to known linkage groups. Crosses were made between the PSD-susceptible cultivar Agripro 350 and each of the resistant lines MO/PSD-0259 and PI 80837. F₂ populations from each cross were grown and inoculated in the field. Individual plant reactions were characterized by determining the levels of seed infection, and DNA of F₂ plants was extracted for SSR analysis and mapping. F₂ segregation data showed that different single dominant genes condition PSD resistance in MO/PSD-0259 and PI 80837. Resistance in PI 80837 was linked to Sat_177 (4.3 cM) and Sat_342 (15.8 cM) on molecular linkage group (MLG) B2. In MO/PSD-0259, resistance was linked to Sat_317 (5.9 cM) and Sat_120 (12.7 cM) on MLG F. These data support work by Berger and Minor (Berger RD, Minor HC. 1999. An restriction fragment length polymorphism (RFLP) marker associated with resistance to Phomopsis seed decay in soybean PI 417479. Crop Sci 39:800–805.) in which PSD resistance in PI 417479, the resistant parent used to develop MO/PSD-0259, was associated with RFLP marker A708 on MLG F. These SSR markers should be useful in selection for resistant genotypes in breeding programs.

New Primers for the Avian SWS1 Pigment Opsin Gene Reveal New Amino Acid Configurations in Spectral Sensitivity Tuning Sites

Odeen, A., Hastad, O. — Wed, 11 Nov 2009 04:10:28 PST

Recently, polymerase chain reaction–based estimates of visual pigment spectral tuning from genomic DNA have offered an alternative to the authoritative but rather slow and complicated retinal microspectrophotometry method. The genomic DNA method involves sequencing a fragment of the short-wavelength sensitive pigment, type 1 (SWS1) opsin gene covering amino acid positions 86, 90, and 93 and has been utilized in a wide range of avian species. Other key tuning sites have been proposed but not sequenced in the genomic DNA–based spectral sensitivity studies. We have designed 5 new primers for sequencing gene fragments of the ultraviolet-/violet-tuned SWS1 opsin gene containing the first, second and third, and sixth and seventh -helical transmembrane regions and the spectral tuning sites 49, 86, 90, 93, 116, 118 and 298. Testing these primers on various bird species reveals some novel combinations of amino acid residues at the tuning sites. The potential significance of these on spectral tuning is discussed.

Localization and Characterization of 170 BAC-Derived Clones and Mapping of 94 Microsatellites in the Hessian Fly

Schemerhorn, B. J., Crane, Y. M., Morton, P. K., Aggarwal, R., Benatti, T. — Wed, 11 Nov 2009 04:10:28 PST

Ninety-four microsatellites from enriched genomic libraries of Hessian fly (Hf, Mayetiola destructor [Say]) were localized to 170 cognate clones in an Hf bacterial artificial chromosome (BAC) library. These microsatellite-positive BAC clones were physically mapped to polytene chromosomes by fluorescent in situ hybridization. The mapped microsatellite loci can be used to study the genetic diversity and population structure of Hf.

Inheritance of Salt Tolerance in Wild Soybean (Glycine soja Sieb. and Zucc.) Accession PI483463

Lee, J.-D., Shannon, J. G., Vuong, T. D., Nguyen, H. T. — Wed, 11 Nov 2009 04:10:28 PST

Tolerant soybean (Glycine max [L.] Merr.) cultivars aid in reducing salt damage in problem fields. New genes are important to reduce losses from salt injury. Objectives of this study were to determine inheritance of salt tolerance in wild soybean (Glycine soja Sieb. and Zucc.) PI483463 and to test allelism of tolerance genes from genotypes PI483463 and S-100, a common ancestor of southern in US cultivars. Tolerant (T) PI483463 was crossed to sensitive (S) cultivar Hutcheson to study inheritance. PI483463 (T) was crossed with S-100 (T) to test for allelism. Parents, F₁ plants, F₂ populations, and F_2:3 lines were assayed in a 100 mM salt solution to determine tolerance. F₂ from T x S cross segregated 3(T):1 (S) and the F_2:3 lines responded 1 (T): 2 (segregating):1 (S). F₂ plants from PI483463 (T) x S-100 (T) segregated 15 (T):1 (S) indicating different genes from the 2 sources. Results showed that G. soja line PI483463 had a single dominant gene for salt tolerance, which was different than the gene in G. max line S-100. The symbol, Ncl2, was designated for this new salt tolerance allele.

Genetic Mapping of Cgdef Gene Controlling Accumulation of 7S Globulin ({beta}-Conglycinin) Subunits in Soybean Seeds

Hayashi, M., Kitamura, K., Harada, K. — Wed, 11 Nov 2009 04:10:28 PST

Soy protein consists of mainly 7S globulin (β-conglycinin) and 11S globulin (glycinin). The 7S globulin exerts favorable and unfavorable effects on human nutrition, food processing, and human health. Therefore, it is important for the improvement of the soy protein to control the content of 7S globulin. A mutant line lacking the 7S globulin was induced by -ray irradiation, and the deficiency is controlled by a single recessive gene, cgdef. The Cgdef gene, despite its potential for improvement of the soy protein, has not been assigned to a linkage group of a soybean genetic map. We crossed "Mo-shi-dou Gong 503" with plants homozygous or heterozygous for the Cgdef allele and screened an F2 mapping population that segregated with the cgdef allele to locate the Cgdef gene on a soybean genetic map. By linkage analysis, we assigned the Cgdef gene to chromosome 19 at the position between the Satt523 and Sat_388 simple sequence repeat (SSR) markers. Six SSR markers (Sat_134, Sat_405, Satt143, Satt398, Sat_195, and Satt694) and 2 amplified fragment length polymorphism markers identified previously were mapped at the same position of the Cgdef gene. These markers should enable to conduct map-based cloning of the Cgdef gene.

Next Generation Sequencing in Nonmodel Organisms: Has the Future Arrived?

Johansson, M. L. — Wed, 11 Nov 2009 04:10:28 PST

In Pursuit of the Gene: From Darwin to DNA

Smocovitis, V. B. — Wed, 11 Nov 2009 04:10:28 PST

Announcements

Wed, 11 Nov 2009 04:10:28 PST

Architecture and Organization of Chicken Microchromosome 16: Order of the NOR, MHC-Y, and MHC-B Subregions

Delany, M. E., Robinson, C. M., Goto, R. M., Miller, M. M. — Mon, 17 Aug 2009 18:27:15 PDT

Here we present a high-resolution cytogenomic analysis of chicken microchromosome 16. We established the location of the major histocompatibility complex (MHC)-B and -Y subregions relative to each other and to the nucleolus organizer region (NOR) encoding the 18S–5.8S–28S ribosomal DNA. To do so, we employed multicolor fluorescence in situ hybridization using large-insert bacterial artificial chromosome clones with fully sequenced inserts or repetitive sequence probes specific for the subregion of interest. We show that the MHC-Y and -B regions are located on the same side of the NOR, rather than opposite ends, as previously proposed. On the q arm, the MHC-Y is closely adjacent to the NOR, whereas the MHC-B is distal near the q-terminus. A relatively large GC-rich region separates the 2 MHC subregions and includes a specialized structure, a secondary constriction. We propose that the GC-rich large physical distance is the basis for the lack of genetic linkage between the NOR and MHC-B and between the MHC-Y and -B. An integrated model for GGA 16 is presented that incorporates gene complex order in the context of key architectural features including p and q arms, primary (centromere) and secondary constrictions, telomeres, as well as AT- and GC-rich regions.

Over the Falls? Rapid Evolution of Ecotypic Differentiation in Steelhead/Rainbow Trout (Oncorhynchus mykiss)

Mon, 17 Aug 2009 18:27:15 PDT

Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history of steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce in freshwater river systems and small coastal streams but grow and mature in the ocean. Resident rainbow trout, either sympatric with steelhead or isolated above barrier dams or waterfalls, represent an alternative life-history form that lives entirely in freshwater. We analyzed population genetic data from 1486 anadromous and resident O. mykiss from a small stream in coastal California with multiple barrier waterfalls. Based on data from 18 highly variable microsatellite loci (He = 0.68), we conclude that the resident population above one barrier, Big Creek Falls, is the result of a recent anthropogenic introduction from the anadromous population of O. mykiss below the falls. Furthermore, fish from this above-barrier population occasionally descend over the falls and have established a genetically differentiated below-barrier subpopulation at the base of the falls, which appears to remain reproductively isolated from their now-sympatric anadromous ancestors. These results support a hypothesis of rapid evolution of a purely resident life history in the above-barrier population in response to strong selection against downstream movement.

Cytonuclear Patterns of Genetic Diversity and the Intricate Evolutionary History of the Inland Silverside (Menidia beryllina)

Oswald, K. J., Grady, J. M., Quattro, J. M. — Mon, 17 Aug 2009 18:27:15 PDT

DNA sequence variation at a mitochondrial and a nuclear intron locus was surveyed within and among multiple populations of the inland silverside (Menidia beryllina) from the southeastern United States and revealed discordant phylogenetic patterns but similar patterns of population genetic variation across nuclear and mitochondrial loci. Mitochondrial variation was geographically structured, with strongly supported monophyletic assemblages among Gulf of Mexico population samples and a close association of the St John's River (SJ) population with these same samples. Nuclear alleles were not strongly structured geographically, with little support for monophyly within or across basins. Conversely, population genetic parameters indicate that the bulk of genetic diversity for both genomes resides within and among Gulf of Mexico populations and that diversity within the Atlantic is largely restricted to the SJ population. The contrast in genetic variation and population phylogenies appears to be a function of historical demographic processes, most likely directed by fluctuating geomorphology of the Florida peninsula in response to North American glaciation cycles.

Population Structure of a Cave-Dwelling Bat, Miniopterus schreibersii: Does It Reflect History and Social Organization?

Mon, 17 Aug 2009 18:27:15 PDT

Many colonial bat species make regional migrations, and the consequent gene flow may eliminate geographic genetic structure resulting from history of colonization. In this study, we verified that history and social organization have detectable impacts on the genetic structure of Miniopterus schreibersii, a cave-dwelling bat with high female philopatry. After studying all known nursing colonies in Portugal, we concluded that there is a significant geographic structure and that the overall pattern is similar for mitochondrial and nuclear DNA. Both pairwise _ST and F_ST were significantly correlated with geographical distance, suggesting that isolation by distance is relevant for both mitochondrial and nuclear markers. However, structuring of mitochondrial DNA was much more marked than that of nuclear DNA, a consequence of the strong female philopatry and a bias for male-mediated gene flow. Wintering colonies were more genetically diverse than nursing colonies because the former receive individuals from distinct breeding populations. Haplotype diversity of the northern colonies, the more recent according to population expansion analyses, is only about half of that of the central and southern colonies. This is most likely a consequence of the colonization history of M. schreibersii, which presumably expanded northward from the south of the Iberian Peninsula or North Africa after the last glacial age.

A Comparative Cytogenetic Analysis of 2 Bothriuridae Species and Overview of the Chromosome Data of Scorpiones

Mon, 17 Aug 2009 18:27:15 PDT

The order Scorpiones is one of the most cytogenetically interesting groups within Arachnida by virtue of the combination of chromosome singularities found in the 59 species analyzed so far. In this work, mitotic and meiotic chromosomes of 2 species of the family Bothriuridae were detailed. This family occupies a basal position within the superfamily Scorpionoidea. Furthermore, review of the cytogenetic data of all previously studied scorpions is presented. Light microscopy chromosome analysis showed that Bothriurus araguayae and Bothriurus rochensis possess low diploid numbers compared with those of species belonging to closely related families. Gonadal cells examined under light and in transmission electron microscopy revealed, for the first time, that the Bothriuridae species possess typical monocentric chromosomes, and male meiosis presented chromosomes with synaptic and achiasmatic behavior. Moreover, in the sample of B. araguayae studied, heterozygous translocations were verified. The use of techniques to highlight specific chromosomal regions also revealed additional differences between the 2 Bothriurus species. The results herein recorded and the overview elaborated using the available cytogenetic information of Scorpiones elucidated current understanding regarding the processes of chromosome evolution that have occurred in Bothriuridae and in Scorpiones as a whole.

Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis

Mon, 17 Aug 2009 18:27:15 PDT

Microsatellite loci are standard genetic markers for population genetic analysis, whereas single nucleotide polymorphisms (SNPs) are more recent tools that require assessment of neutrality and appropriate use in population genetics. Twelve SNP markers were used to describe the genetic structure of Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae) in the United States of America and revealed a high mean observed heterozygosity (0.40 ± 0.059) and low global F_ST (0.029). Pairwise F_ST estimates ranged from 0.007 to 0.045, and all but 2 populations showed significant levels of genetic differentiation (P ≤ 0.008). Population parameters and conclusions based on SNP markers were analogous to that obtained by use of microsatellite markers from the identical population samples. SNP-based F_ST estimates were 3-fold higher than corresponding estimates from microsatellites, wherein lower microsatellite F_ST estimates likely resulted from an overestimate of migration rates between subpopulations due to convergence of allele size (homoplasy). No significant difference was observed in the proportion of SNP or microsatellite markers loci that were nonneutral within populations. SNP markers provided estimates of population genetic parameters consistent with those from microsatellite data, and their low back mutation rates may result in reduced propensity for error in estimation of population parameters.

The Male Sterility Locus ms3 Is Present in a Fertility Controlling Gene Cluster in Soybean

Mon, 17 Aug 2009 18:27:15 PDT

Soybean [Glycine max (L.) Merr.] is self-pollinated. To produce large quantities of hybrid seed, insect-mediated cross-pollination is necessary. An efficient nuclear male-sterile system for hybrid seed production would benefit from molecular and/or phenotypic markers linked to male fertility/sterility loci to facilitate early identification of phenotypes. Nuclear male-sterile, female-fertile ms3 mutant is a single recessive gene and displays high outcrossed seed set with pollinators. Our objective was to map the ms3 locus. A segregating population of 150 F₂ plants from Minsoy (PI 27890) x T284H, Ms3ms3 (A00-68), was screened with 231 simple sequence repeat markers. The ms3 locus mapped to molecular linkage group (MLG) D1b (Gm02) and is flanked by markers Satt157 and Satt542, with a distance of 3.7 and 12.3 cM, respectively. Female-partial sterile-1 (Fsp1) and the Midwest Oilseed male-sterile (msMOS) mutants previously were located on MLG D1b. msMOS and Fsp1 are independent genes located very close to each other. All 3 genes are located in close proximity of Satt157. We believe that this is the first report of clustering of fertility-related genes in plants. Characterization of these closely linked genes may help in understanding the evolutionary relationship among them.

Ploidy and the Causes of Genomic Evolution

Gerstein, A. C., Otto, S. P. — Mon, 17 Aug 2009 18:27:15 PDT

Genomes vary dramatically in size and in content. This variation is driven in part by numerous polyploidization events that have happened over the course of eukaryotic evolution. Experimental evolution studies, primarily using the yeast Saccharomyces cerevisiae, provide insights into the immediate fitness effects of ploidy mutations, the ability of organisms of different ploidy levels to mask deleterious mutations, the impact of ploidy on rates of adaptation, and the relative roles of selection versus drift in shaping ploidy evolution. We review these experimental evolution studies and present new data on differences in maximal growth rate for cells of different ploidy levels.

Going, Going, Not Quite Gone: Nucleomorphs as a Case Study in Nuclear Genome Reduction

Archibald, J. M., Lane, C. E. — Mon, 17 Aug 2009 18:27:15 PDT

Nucleomorphs are the relic nuclei of algal endosymbionts that became permanent fixtures inside nonphotosynthetic eukaryotic host cells. These unusual organelles exist in only 2 lineages, the cryptophytes, which possess nucleomorphs and plastids (chloroplasts) derived from the uptake of a red algal endosymbiont, and the chlorarachniophytes, which harbor green algal derived nucleomorphs and plastids. Despite having evolved independently of one another, the nucleomorph genomes of cryptophytes and chlorarachniophytes are strikingly similar in size and basic structure. Both are <1 Mbp in size—the smallest nuclear genomes known—and are composed of only 3 chromosomes, each with its own subtelomeric rDNA repeats. Nucleomorph-containing algae thus represent an interesting system in which to study genome and chromosome evolution in eukaryotes. Here, we provide an overview of nucleomorph genome biology and focus on new information gleaned from comparisons of complete nucleomorph genome sequences, both within and between cryptophytes and chlorarachniophytes. Such comparisons provide fascinating insight into the evolution of these highly derived organelles and, more generally, the potential causes and consequences of genome reduction in eukaryotes.

Endogenous Mechanisms for the Origins of Spliceosomal Introns

Catania, F., Gao, X., Scofield, D. G. — Mon, 17 Aug 2009 18:27:15 PDT

Over 30 years since their discovery, the origin of spliceosomal introns remains uncertain. One nearly universally accepted hypothesis maintains that spliceosomal introns originated from self-splicing group-II introns that invaded the uninterrupted genes of the last eukaryotic common ancestor (LECA) and proliferated by "insertion" events. Although this is a possible explanation for the original presence of introns and splicing machinery, the emphasis on a high number of insertion events in the genome of the LECA neglects a considerable body of empirical evidence showing that spliceosomal introns can simply arise from coding or, more generally, nonintronic sequences within genes. After presenting a concise overview of some of the most common hypotheses and mechanisms for intron origin, we propose two further hypotheses that are broadly based on central cellular processes: 1) internal gene duplication and 2) the response to aberrant and fortuitously spliced transcripts. These two nonmutually exclusive hypotheses provide a powerful way to explain the establishment of spliceosomal introns in eukaryotes without invoking an exogenous source.

The Modern RNP World of Eukaryotes

Collins, L. J., Kurland, C. G., Biggs, P., Penny, D. — Mon, 17 Aug 2009 18:27:15 PDT

Eukaryote gene expression is mediated by a cascade of RNA functions that regulate, process, store, transport, and translate RNA transcripts. The RNA network that promotes this cascade depends on a large cohort of proteins that partner RNAs; thus, the modern RNA world of eukaryotes is really a ribonucleoprotein (RNP) world. Features of this "RNP infrastructure" can be related to the high cytosolic density of macromolecules and the large size of eukaryote cells. Because of the densely packed cytosol or nucleoplasm (with its severe restriction on diffusion of macromolecules), partitioning of the eukaryote cell into functionally specialized compartments is essential for efficiency. This necessitates the association of RNA and protein into large RNP complexes including ribosomes and spliceosomes. This is well illustrated by the ubiquitous spliceosome for which most components are conserved throughout eukaryotes and which interacts with other RNP-based machineries. The complexes involved in gene processing in modern eukaryotes have broad phylogenetic distributions suggesting that the common ancestor of extant eukaryotes had a fully evolved RNP network. Thus, the eukaryote genome may be uniquely informative about the transition from an earlier RNA genome world to the modern DNA genome world.

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

Hahn, M. W. — Mon, 17 Aug 2009 18:27:15 PDT

Determining the evolutionary forces responsible for the maintenance of gene duplicates is key to understanding the processes leading to evolutionary adaptation and novelty. In his highly prescient book, Susumu Ohno recognized that duplicate genes are fixed and maintained within a population with 3 distinct outcomes: neofunctionalization, subfunctionalization, and conservation of function. Subsequent researchers have proposed a multitude of population genetic models that lead to these outcomes, each differing largely in the role played by adaptive natural selection. In this paper, I present a nonmathematical review of these models, their predictions, and the evidence collected in support of each of them. Though the various outcomes of gene duplication are often strictly associated with the presence or absence of adaptive natural selection, I argue that determining the outcome of duplication is orthogonal to determining whether natural selection has acted. Despite an ever-growing field of research into the fate of gene duplicates, there is not yet clear evidence for the preponderance of one outcome over the others, much less evidence for the importance of adaptive or nonadaptive forces in maintaining these duplicates.

Intron-Dominated Genomes of Early Ancestors of Eukaryotes

Koonin, E. V. — Mon, 17 Aug 2009 18:27:15 PDT

Evolutionary reconstructions using maximum likelihood methods point to unexpectedly high densities of introns in protein-coding genes of ancestral eukaryotic forms including the last common ancestor of all extant eukaryotes. Combined with the evidence of the origin of spliceosomal introns from invading Group II self-splicing introns, these results suggest that early ancestral eukaryotic genomes consisted of up to 80% sequences derived from Group II introns, a much greater contribution of introns than that seen in any extant genome. An organism with such an unusual genome architecture could survive only under conditions of a severe population bottleneck.

A Surrogate Approach to Study the Evolution of Noncoding DNA Elements That Organize Eukaryotic Genomes

Vermaak, D., Bayes, J. J., Malik, H. S. — Mon, 17 Aug 2009 18:27:15 PDT

Comparative genomics provides a facile way to address issues of evolutionary constraint acting on different elements of the genome. However, several important DNA elements have not reaped the benefits of this new approach. Some have proved intractable to current day sequencing technology. These include centromeric and heterochromatic DNA, which are essential for chromosome segregation as well as gene regulation, but the highly repetitive nature of the DNA sequences in these regions make them difficult to assemble into longer contigs. Other sequences, like dosage compensation X chromosomal sites, origins of DNA replication, or heterochromatic sequences that encode piwi-associated RNAs, have proved difficult to study because they do not have recognizable DNA features that allow them to be described functionally or computationally. We have employed an alternate approach to the direct study of these DNA elements. By using proteins that specifically bind these noncoding DNAs as surrogates, we can indirectly assay the evolutionary constraints acting on these important DNA elements. We review the impact that such "surrogate strategies" have had on our understanding of the evolutionary constraints shaping centromeres, origins of DNA replication, and dosage compensation X chromosomal sites. These have begun to reveal that in contrast to the view that such structural DNA elements are either highly constrained (under purifying selection) or free to drift (under neutral evolution), some of them may instead be shaped by adaptive evolution and genetic conflicts (these are not mutually exclusive). These insights also help to explain why the same elements (e.g., centromeres and replication origins), which are so complex in some eukaryotic genomes, can be simple and well defined in other where similar conflicts do not exist.

Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution

Stoltzfus, A., Yampolsky, L. Y. — Mon, 17 Aug 2009 18:27:15 PDT

The classic view of evolution as "shifting gene frequencies" in the Modern Synthesis literally means that evolution is the modulation of existing variation ("standing variation"), as opposed to a "new mutations" view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human–chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects.

Transposable Elements and Factors Influencing their Success in Eukaryotes

Pritham, E. J. — Mon, 17 Aug 2009 18:27:15 PDT

Recent advances in genome sequencing have led to a vast accumulation of transposable element data. Consideration of the genome sequencing projects in a phylogenetic context reveals that despite the hundreds of eukaryotic genomes that have been sequenced, a strong bias in sampling exists. There is a general under-representation of unicellular eukaryotes and a dearth of genome projects in many branches of the eukaryotic phylogeny. Among sequenced genomes, great variation in genome size exists, however, little difference in the total number of cellular genes is observed. For many eukaryotes, the remaining genomic space is extremely dynamic and predominantly composed of a menagerie of populations of transposable elements. Given the dynamic nature of the genomic niche filled by transposable elements, it is evident that these elements have played an important role in genome evolution. The contribution of transposable elements to genome architecture and to the advent of genetic novelty is likely to be dependent, at least in part, on the transposition mechanism, diversity, number, and rate of turnover of transposable elements in the genome at any given time. The focus of this review is the discussion of some of the forces that act to shape transposable element diversity within and between genomes.

Announcements

Mon, 17 Aug 2009 18:27:15 PDT

Galibert, F. — Mon, 29 Jun 2009 21:46:53 PDT

Primary Hyperoxaluria in Cats Is Caused by a Mutation in the Feline GRHPR Gene

Goldstein, R. E., Narala, S., Sabet, N., Goldstein, O., McDonough, S. P. — Mon, 29 Jun 2009 21:46:54 PDT

Primary hyperoxaluria (PH) is a rare, inherited disease in humans resulting from mutations in the alanine:glyoxylate aminotransferase gene (PH1) or in the glyoxylate reductase (GRHPR) gene (PH2). A disease in cats, mimicking PH2, was described with an autosomal recessive mode of inheritance. Recently, we recognized lesions consistent with PH in kidneys from 3 kittens. Genomic DNA was extracted from 1 blood and 2 formalin-fixed kidney samples from the 3 affected kittens, from blood from the affected cats’ sire, and from blood from 2 healthy unrelated cats. The 9 feline GRHPR exons and intronic donor–acceptor sites were amplified and sequenced. A point mutation G to A was identified at the acceptor site of intron 4. Affected cats were AA, normal cats GG, and the sire was heterozygous A/G. RNA from healthy, carrier, and affected cats was extracted and the GRHPR transcript sequenced revealing an exon 5 deletion in the affected transcript. The 89-bp deletion causes a frameshift and a premature stop codon 44 amino acids downstream, resulting in an anticipated 119 amino acids missing from the C-terminus of the affected cat protein. The unaffected cat expresses the normal transcript, whereas the carrier expressed both.

Mapping of the Domestic Cat "SILVER" Coat Color Locus Identifies a Unique Genomic Location for Silver in Mammals

Mon, 29 Jun 2009 21:46:54 PDT

The SILVER locus has been mapped in the domestic cat, identifying a unique genomic location distinct from that of any known reported gene associated with silver or hypopigmentation in mammals. A demonstrated lack of linkage to SILV, the strong candidate gene for silver, led to the initiation of a genome scan utilizing 2 pedigrees segregating for silver coat color. Linkage mapping defined a genomic region for SILVER as a 3.3-Mb region, (95.87–99.21 Mb) on chromosome D2, (peak logarithm of the odds = 10.5, = 0), which displays conserved synteny to a genomic interval between 118.58 and 121.85 Mb on chromosome 10 in the human genome. In the domestic cat, mutations at the SILVER locus suppress the development of pigment in the hair, but in contrast to other mammalian silver variants, there is an apparently greater influence on the production of pheomelanin than eumelanin pigment. The mapping of a novel locus for SILVER offers much promise in identifying a gene that may help elucidate aspects of pheomelanogenesis, a pathway that has been very elusive, and illustrates the promise of the cat genome project in increasing our understanding of basic biological processes of general relevance for mammals.

Artifacts of the 1.9x Feline Genome Assembly Derived from the Feline-Specific Satellite Sequence

Pontius, J. U., O'Brien, S. J. — Mon, 29 Jun 2009 21:46:54 PDT

Two percentage of the cat genome is a repetitive, feline-specific satellite sequence (FA-SAT) of 483 bp and 65% guanine-cytosine content. Previous chromosomal localization of the satellite has demonstrated the satellite’s presence on several discrete regions of the telomeres of chromosomes, predominately on the D, E, and F chromosome groups. The recent assembly of the 1.9x whole-genome shotgun (WGS) sequence of cat illustrates the challenge of the assembly of these large numbers of relatively short, similar sequences. Clones with paired end reads that include FA-SAT sequence have a high level of assembly discrepancies compared with clones with other types of repetitive elements, such as short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINEs). The influence of the presence of FA-SAT but not SINEs and LINEs on genome assembly may likely reflect the evolutionary emergence of FA-SAT, which has lead to an excess of FA-SAT copies with identical sequence, which is less an issue with older, more diverse SINE and LINE sequences. The FA-SATs are restricted to a few hundred discrete regions of the cat genome, and associated errors in the assembly seem to be restricted to these loci. The findings regarding the feline-specific sequence should be considered in the pending 8x assembly of the cat genome.

Epidemiology, Pathology, and Genetics of Histiocytic Sarcoma in the Bernese Mountain Dog Breed

Mon, 29 Jun 2009 21:46:54 PDT

Histiocytic sarcoma (HS) refers to a highly aggressive and frequently disseminated neoplastic disease belonging to the class of canine histiocytic proliferative disorders. Disseminated HS (previously called malignant histiocytosis) is highly breed specific, with Bernese mountain dogs (BMDs), rottweilers, and retrievers having a high prevalence with a frequency of approximately 25% in the BMD breed. We collected DNA samples and clinical information from 800 BMDs, of which 200 are affected by HS. To better characterize the physiopathology and epidemiology, an in-depth analysis of 89 BMD cases has been performed. The mean age of onset was 6.5 years, males and females being equally affected. The clinical features, biochemical parameters, and pathological features have been determined. The life span after diagnosis has been estimated to be 49 days. A large BMD pedigree of 327 dogs, 121 of which are affected, was assembled. Using a subset of 160 BMDs, encompassing 21 complete sibships, we now propose an oligogenic transmission mode of the disease. Whole-genome linkage scans as well as association studies using a case/control analysis, in parallel with expression profiling of neoplastic versus normal histiocytes, are all underway. Altogether, these complementary approaches are expected to localize the genes for HS in the BMD, leading to advances in our knowledge of histiocyte diseases in dogs and humans.

Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

Mon, 29 Jun 2009 21:46:54 PDT

Until recently, canine genetic research has not focused on population structure within breeds, which may confound the results of case–control studies by introducing spurious correlations between phenotype and genotype that reflect population history. Intrabreed structure may exist when geographical origin or divergent selection regimes influence the choices of potential mates for breeding dogs. We present evidence for intrabreed stratification from a genome-wide marker survey in a sample of unrelated dogs. We genotyped 76 Border Collies, 49 Australian Shepherds, 17 German Shepherd Dogs, and 17 Portuguese Water Dogs for our primary analyses using Affymetrix Canine v2.0 single-nucleotide polymorphism (SNP) arrays. Subsets of autosomal markers were examined using clustering algorithms to facilitate assignment of individuals to populations and estimation of the number of populations represented in the sample. SNPs passing stringent quality control filters were employed for explicitly phylogenetic analyses reconstructing relationships between individuals using maximum parsimony and Bayesian methods. We used simulation studies to explore the possible effects of intrabreed stratification on genome-wide association studies. These analyses demonstrate significant stratification in at least one of our primary breeds of interest, the Border Collie. Demographic and pedigree data suggest that this population substructure may result from geographic isolation or divergent selection regimes practiced by breeders with different breeding program goals. Simulation studies indicate that such stratification could result in false discovery rates significant enough to confound genome-wide association analyses. Intrabreed stratification should be accounted for when designing and interpreting the results of case–control association studies using purebred dogs.

Genetic Mapping of Fixed Phenotypes: Disease Frequency as a Breed Characteristic

Chase, K., Jones, P., Martin, A., Ostrander, E. A., Lark, K. G. — Mon, 29 Jun 2009 21:46:54 PDT

Traits that have been stringently selected to conform to specific criteria in a closed population are phenotypic stereotypes. In dogs, Canis familiaris, such stereotypes have been produced by breeding for conformation, performance (behaviors), etc. We measured phenotypes on a representative sample to establish breed stereotypes. DNA samples from 147 dog breeds were used to characterize single nucleotide polymorphism allele frequencies for association mapping of breed stereotypes. We identified significant size loci (quantitative trait loci [QTLs]), implicating candidate genes appropriate to regulation of size (e.g., IGF1, IGF2BP2 SMAD2, etc.). Analysis of other morphological stereotypes, also under extreme selection, identified many additional significant loci. Behavioral loci for herding, pointing, and boldness implicated candidate genes appropriate to behavior (e.g., MC2R, DRD1, and PCDH9). Significant loci for longevity, a breed characteristic inversely correlated with breed size, were identified. The power of this approach to identify loci regulating the incidence of specific polygenic diseases is demonstrated by the association of a specific IGF1 haplotype with hip dysplasia, patella luxation, and pacreatitis.

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

Mon, 29 Jun 2009 21:46:54 PDT

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene–containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

Highly Endangered African Wild Dogs (Lycaon pictus) Lack Variation at the Major Histocompatibility Complex

Mon, 29 Jun 2009 21:46:54 PDT

The major histocompatibility complex (MHC) is a set of highly polymorphic genes involved in the immune response. Extensive research on the canid MHC has found moderate-to-high levels of diversity at the DLA-DRB1, DLA-DRA, DLA-DQA1, and DLA-DQB1 class II loci with frequent transspecific polymorphism among Canis species. In this study, we assessed MHC variation in the more distantly related and highly endangered African wild dog (Lycaon pictus). We screened 168 African wild dogs from Eastern and Southern Africa as well as 200 samples from the European captive population for variation at MHC class II loci. As for all other canids screened to date, we found a single allele at DLA-DRA, which was the same as that found in Canis species. In contrast, we found 17 DLA-DRB1 alleles, one DLA-DQA1 allele, and two DLA-DQB1 alleles, all of which were unique to African wild dogs. At DLA-DRB1, African wild dogs were found to have comparable numbers of alleles but less overall amino acid variation than other canids. However, the low numbers of alleles at DLA-DQA1 and DLA-DQB1 are surprising, given that in other canids, these loci are also highly variable. Overall, our data suggest that African wild dogs are genetically depauperate at the MHC relative to other canids. These data are indicative of a loss of genetic variation, possibly as a result of population bottlenecks and declines experienced by this species.

MITF and White Spotting in Dogs: A Population Study

Schmutz, S. M., Berryere, T. G., Dreger, D. L. — Mon, 29 Jun 2009 21:46:54 PDT

This study was designed to determine if one of the variants found in our laboratory, or previously reported in microphthalmia-associated transcription factor (MITF), was associated with one or more spotting patterns in dogs. None of the rare variants found in the coding sequence consistently occurred in dogs of any particular spotting pattern. However, an insertion of a short interspersed nucleotide element (SINE) over 3000 bp 5' of the MITF-M start codon (Karlsson et al. 2007) did fit with random spotting in many dog breeds. Most (319/324) dogs of 45 breeds fit 1 of 2 inheritance patterns. All dogs that were homozygous for the SINE had white markings that either covered at least the ventral surface (mantle pattern) or most of the body (piebald or extreme white spotting). In most breeds, dogs heterozygous for the SINE insertion were solid colored or had minimal white, such as on the toes, but in some others, heterozygotes had white undersides, often with a white collar in the pattern called pseudo-Irish by Little (1957). However, none of the 15 dogs of 5 breeds in which all individuals have markings known as Irish spotting had the SINE insertion. Finally, we studied RNA expression in skin. The 2 MITF-M forms, M+ that contains an extra 18 bp that adds 6 amino acids between exons 5 and 6 and the M– form, were present. MITF-M is considered to be specific to melanocytes but was found in skin from a white Samoyed. A putative pseudogene containing exon 1M was also identified.

MLPH Genotype--Melanin Phenotype Correlation in Dilute Dogs

Mon, 29 Jun 2009 21:46:54 PDT

Coat color dilution in dogs is a specific pigmentation phenotype caused by a defective transport of melanosomes leading to large clumps of pigment. It is inherited as a Mendelian autosomal recessive trait and may be accompanied by hair loss, the so-called color dilution alopecia (CDA), or black hair follicular dysplasia (BHFD). We previously identified the noncoding c.-22G>A transition in the melanophilin gene (MLPH) as a candidate causative mutation for the dilute phenotype. We have now extended our study and genotyped 935 dogs from 20 breeds segregating for dilute coat color. The dilute-associated A allele segregates in many different breeds suggesting an old mutation event. We also investigated skin biopsies of dogs suspected of having either CDA or BHFD, and our data clearly indicate that the dilute mutation is required but not sufficient to develop clinical signs of the disease. The risk to develop CDA/BHFD seems to be breed specific. Interestingly, 22 out of 29 dogs with clinical signs of CDA/BHFD have clumped melanin in the epidermis, the follicular epithelium, and the hair shafts, whereas in dilute dogs without clinical disease, clumped melanin is only found in the follicular epithelium and the hair shafts but not in the epidermis.

Genetic Characterization of Hybrid Wolves across Ontario

Wilson, P. J., Grewal, S. K., Mallory, F. F., White, B. N. — Mon, 29 Jun 2009 21:46:54 PDT

Four "races" of wolves have been described in Ontario as follows: 1) Canis lupus hudsonicus inhabiting the subarctic tundra, 2) A race (Ontario type) of the eastern timber wolf (Canis lupus lycaon) that inhabits the boreal forests, 3) A second race (Algonquin type) of C. l. lycaon that inhabit the deciduous forests of the upper Great Lakes, and 4) A small wolf (Tweed type) in central Ontario that has been proposed to be a hybrid between the Algonquin type wolf and expanding coyotes, Canis latrans. Using mitochondrial DNA (mtDNA) control region sequences and 8 microsatellite loci, we developed DNA profiles for 269 wolves from across Ontario. The distribution of mtDNA was predominantly coyote and the eastern wolf, Canis lycaon, in Algonquin Park and the southern Frontenac Axis with a combination of these mtDNA and gray wolf mtDNA in northern Ontario. Bayesian clustering grouped northern Ontario wolves independent of mtDNA with a second grouping of eastern and Tweed wolves from Algonquin. Individual clustering identified 3 groups represented by 1) northern Ontario wolves, 2) eastern wolves, and 3) Tweed wolves from the Frontenac Axis. Genomic representation analyses indicate that the Tweed wolves are hybrids between the coyote and the eastern wolf and represent the Ontario distribution of the eastern coyote, whereas the wolves in the upper Great Lakes region represent products of historic and/or continuing hybridization between C. lycaon and C. lupus. There was low structuring among wolves in these regions, and Algonquin suggesting a larger northern connected metapopulation with gene flow between the Ontario and Algonquin types.

Analyses of Sweet Receptor Gene (Tas1r2) and Preference for Sweet Stimuli in Species of Carnivora

Mon, 29 Jun 2009 21:46:54 PDT

The extent to which taste receptor specificity correlates with, or even predicts, diet choice is not known. We recently reported that the insensitivity to sweeteners shown by species of Felidae can be explained by their lacking of a functional Tas1r2 gene. To broaden our understanding of the relationship between the structure of the sweet receptors and preference for sugars and artificial sweeteners, we measured responses to 12 sweeteners in 6 species of Carnivora and sequenced the coding regions of Tas1r2 in these same or closely related species. The lion showed no preference for any of the 12 sweet compounds tested, and it possesses the pseudogenized Tas1r2. All other species preferred some of the natural sugars, and their Tas1r2 sequences, having complete open reading frames, predict functional sweet receptors. In addition to preferring natural sugars, the lesser panda also preferred 3 (neotame, sucralose, and aspartame) of the 6 artificial sweeteners. Heretofore, it had been reported that among vertebrates, only Old World simians could taste aspartame. The observation that the lesser panda highly preferred aspartame could be an example of evolutionary convergence in the identification of sweet stimuli.

Journal of Heredity - recent issues

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Table of Contents

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

Detection of Cytonuclear Genomic Dissociation in the North American Captive African Elephant Collection

Genetic Variation, Relatedness, and Effective Population Size of Polar Bears (Ursus maritimus) in the southern Beaufort Sea, Alaska

The Genetic Impact of Translocations and Habitat Fragmentation in Chamois (Rupicapra) spp.

The Genetic Basis of Melanism in the Gray Squirrel (Sciurus carolinensis)

Genetic Diversification, Vicariance, and Selection in a Polytypic Frog

Genetic Differentiation among Wild Populations of Tribolium castaneum Estimated Using Microsatellite Markers

Evolution of the GST Omega Gene Family in 12 Drosophila Species

Patterns of Variation in the Evolution of Carotenoid Biosynthetic Pathway Enzymes of Higher Plants

Patterns of Nucleotide Diversity at the Methionine Synthase Locus in Fragmented and Continuous Populations of a Wind-Pollinated Tree, Quercus mongolica var. crispula

Mapping of Quantitative Trait Loci for Grain Iron and Zinc Concentration in Diploid A Genome Wheat

Genetic Mapping of Resistance to Phomopsis Seed Decay in the Soybean Breeding Line MO/PSD-0259 (PI562694) and Plant Introduction 80837

New Primers for the Avian SWS1 Pigment Opsin Gene Reveal New Amino Acid Configurations in Spectral Sensitivity Tuning Sites

Localization and Characterization of 170 BAC-Derived Clones and Mapping of 94 Microsatellites in the Hessian Fly

Inheritance of Salt Tolerance in Wild Soybean (Glycine soja Sieb. and Zucc.) Accession PI483463

Genetic Mapping of Cgdef Gene Controlling Accumulation of 7S Globulin ({beta}-Conglycinin) Subunits in Soybean Seeds

Next Generation Sequencing in Nonmodel Organisms: Has the Future Arrived?

In Pursuit of the Gene: From Darwin to DNA

Announcements

Architecture and Organization of Chicken Microchromosome 16: Order of the NOR, MHC-Y, and MHC-B Subregions

Over the Falls? Rapid Evolution of Ecotypic Differentiation in Steelhead/Rainbow Trout (Oncorhynchus mykiss)

Cytonuclear Patterns of Genetic Diversity and the Intricate Evolutionary History of the Inland Silverside (Menidia beryllina)

Population Structure of a Cave-Dwelling Bat, Miniopterus schreibersii: Does It Reflect History and Social Organization?

A Comparative Cytogenetic Analysis of 2 Bothriuridae Species and Overview of the Chromosome Data of Scorpiones

Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis

The Male Sterility Locus ms3 Is Present in a Fertility Controlling Gene Cluster in Soybean

Ploidy and the Causes of Genomic Evolution

Going, Going, Not Quite Gone: Nucleomorphs as a Case Study in Nuclear Genome Reduction

Endogenous Mechanisms for the Origins of Spliceosomal Introns

The Modern RNP World of Eukaryotes

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

Intron-Dominated Genomes of Early Ancestors of Eukaryotes

A Surrogate Approach to Study the Evolution of Noncoding DNA Elements That Organize Eukaryotic Genomes

Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution

Transposable Elements and Factors Influencing their Success in Eukaryotes

Announcements

Primary Hyperoxaluria in Cats Is Caused by a Mutation in the Feline GRHPR Gene

Mapping of the Domestic Cat "SILVER" Coat Color Locus Identifies a Unique Genomic Location for Silver in Mammals

Artifacts of the 1.9x Feline Genome Assembly Derived from the Feline-Specific Satellite Sequence

Epidemiology, Pathology, and Genetics of Histiocytic Sarcoma in the Bernese Mountain Dog Breed

Intrabreed Stratification Related to Divergent Selection Regimes in Purebred Dogs May Affect the Interpretation of Genetic Association Studies

Genetic Mapping of Fixed Phenotypes: Disease Frequency as a Breed Characteristic

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

Highly Endangered African Wild Dogs (Lycaon pictus) Lack Variation at the Major Histocompatibility Complex

MITF and White Spotting in Dogs: A Population Study

MLPH Genotype--Melanin Phenotype Correlation in Dilute Dogs

Genetic Characterization of Hybrid Wolves across Ontario

Analyses of Sweet Receptor Gene (Tas1r2) and Preference for Sweet Stimuli in Species of Carnivora