Journal of Heredity - Advance Access

Phylogeography of a Widespread North American Migratory Songbird (Setophaga ruticilla)

Colbeck, G. J., Gibbs, H. L., Marra, P. P., Hobson, K., Webster, M. S. — 2008-05-08

Genetic analyses for many widespread North American species have revealed significant east–west differentiation, indicating that many survived through the Pleistocene in 2 glacial refugia—1 in the eastern and 1 in the western part of the continent. It remains unclear, however, whether other areas may have served as important glacial refugia. Moreover, many such species exhibit widespread genetic similarity within eastern and western regions because of recent expansion from small refugial populations, making it difficult to evaluate current-day levels of gene flow. In this study, we used mitochondrial DNA (mtDNA) control region sequence and amplified fragment length polymorphism markers to survey genetic variation in a widespread migratory bird, the American redstart (Setophaga ruticilla). mtDNA analyses revealed a pattern that contrasts with that found for most other widespread species studied to date: most redstart populations across North America appear to have spread out from a single glacial refugium, possibly located in the southeastern United States, whereas populations in far-eastern Canada may have survived in a second glacial refugium located on the now-submerged Atlantic coastal shelf off the coast of Newfoundland. A pattern of isolation by distance in mtDNA suggested some constraints on current-day gene flow among extant redstart populations. This study thus reveals a recent evolutionary history for this species that differs from that of most other widespread North American passerines and provides evidence for limited gene flow in a species with potentially large dispersal distances.

Conservation of Wildlife Populations: Demography, Genetics, and Management

Wiese, R. J. — 2008-05-02

Characterization of the Cheetah Serum Amyloid A1 Gene: Critical Role and Functional Polymorphism of a Cis-Acting Element

2008-03-28

Amyloid A (AA) amyloidosis is one of the principal causes of morbidity and mortality in captive cheetahs (Acinonyx jubatus), which are in danger of extinction. For practical conservation of this species, therefore, it is critical to elucidate the etiology of AA amyloidosis, especially to understand the mechanisms of transcriptional regulation of serum amyloid A (SAA), a precursor protein of the AA protein. In this study, the structure and nucleotide sequence of the cheetah SAA1 gene including the 5'-flanking promoter/enhancer region was determined. Putative nuclear factor kappa-B (NF-B) and CCAAT/enhancer binding protein β (C/EBPβ) cis-acting elements, which play key roles in SAA1 transcriptional induction in response to inflammation, were identified in the 5'-flanking region of the cheetah SAA1 gene. Fortuitously, a single nucleotide polymorphism was identified in the captive cheetah cohort in the putative NF-B cis-acting element and had a remarkable effect on SAA1 transcriptional induction. These results provide a foundation not only for clarifying the etiology of AA amyloidosis in the cheetah but also for contriving a strategy for conservation of this species.

Defining the Assumptions Underlying Modeling of Epistatic QTL Using Variance Component Methods

Ronnegard, L., Pong-Wong, R., Carlborg, O. — 2008-03-15

Variance component models are commonly used to detect quantitative trait loci (QTL) in general pedigrees. The variance–covariance structure of the random QTL effect is given by the identity by descent (IBD) between genotypes. Epistatic effects have previously been modeled, both for unlinked and linked loci, as a random effect with a variance–covariance structure given by the Hadamard product between the IBD matrices of the direct QTL effects. In the original papers, the model was given but not derived. Here, we identify the underlying assumptions of this previously proposed model. It assumes that either an unlinked QTL or a fully informative marker (i.e., all marker alleles are unique in the base generation) is located between the loci. We discuss the need of developing a general algorithm to estimate the variance–covariance structure of the random epistatic effect for linked loci.

Protein Polymorphism between 2 Picea abies Populations Revealed by 2-Dimensional Gel Electrophoresis and Tandem Mass Spectrometry

Valcu, C.-M., Lalanne, C., Muller-Starck, G., Plomion, C., Schlink, K. — 2008-03-15

In species with high gene flow and consequent low interpopulation differentiation over wide geographic ranges, differential gene expression along ecological gradients often reveals adaptive significance. We investigated potential differences in protein expression between Picea abies ecotypes adapted to contrasting altitude conditions. Protein expression patterns were compared between needles and roots of 2-month-old P. abies seedlings by means of 2-dimensional electrophoresis. Proteins exhibiting differential expression between the 2 ecotypes were analyzed by tandem mass spectrometry. A total of 19 proteins exhibited qualitative or quantitative polymorphism between the 2 populations. These proteins exhibited organ-specific expression, and the level of interpopulation protein polymorphism was organ dependent. Among differentially expressed proteins, we identified proteins involved in photosynthesis, photorespiration, root tracheary element differentiation, and transmitochondrial membrane transport. Our results show that P. abies seedlings from locally adapted ecotypes exhibit consistent differences in protein expression. The expression polymorphism of some of these proteins has potential adaptive significance.

Nucleotide Diversity and Linkage Disequilibrium in Wild Avocado (Persea americana Mill.)

Chen, H., Morrell, P. L., de la Cruz, M., Clegg, M. T. — 2008-03-14

Resequencing studies provide the ultimate resolution of genetic diversity because they identify all mutations in a gene that are present within the sampled individuals. We report a resequencing study of Persea americana, a subtropical tree species native to Meso- and Central America and the progenitor of cultivated avocado. The sample includes 21 wild accessions from Mexico, Costa Rica, Ecuador, and the Dominican Republic. Estimated levels of nucleotide polymorphism and linkage disequilibrium (LD) are obtained from fully resolved haplotype data from 4 nuclear loci that span 5960 nucleotide sites. Results show that, although avocado is a subtropical tree crop and a predominantly outcrossing plant, the overall level of genetic variation is not exceptionally high (nucleotide diversity at silent sites, _sil = 0.0102) compared with available estimates from temperate plant species. Intralocus LD decays rapidly to half the initial value within about 1 kb. Estimates of recombination rate (based on the sequence data) show that the rate is not exceptionally high when compared with annual plants such as wild barley or maize. Interlocus LD is significant owing to substantial population structure induced by mixing of the 3 botanical races of avocado.

Inheritance of Pollen-less Anthers and "Thrum" and "Pin" Flowers in Periwinkle

Kulkarni, R. N., Baskaran, K. — 2008-03-13

Two mutants, 1 with small, pollen-less anthers (OR-EA) and another with "pin" flowers (EMS 13-2), in contrast to "thrum" flowers found in normal periwinkle (Catharanthus roseus) plants, were isolated after induced mutagenesis in strain OR and cultivar, "Dhawal," respectively. Inheritance of these 2 traits, pollen-less anthers, and pin flowers was studied by crossing the mutants with their respective parental strains. Segregation ratios observed in F₂ and testcross generations of the cross OR-EA x OR suggested that the pollen-less anthers trait was determined by duplicate recessive genes. Data obtained from F₂ and F₃ generations of the cross involving mutant EMS 13-2 with pin flowers and its parental variety Dhawal, suggested that production of pin (mutant) and thrum (normal) flowers was under the control of inhibitory epistatic interaction between 2 independently inherited genes.

An Induced Mass Spawn of the Hermaphroditic Lion-Paw Scallop, Nodipecten subnodosus: Genetic Assignment of Maternal and Paternal Parentage

Petersen, J. L., Ibarra, A. M., Ramirez, J. L., May, B. — 2008-03-11

The Pacific lion-paw scallop is commonly propagated for aquaculture by induced mass spawns of few individuals. Parentage of a mass spawn of this species has not been evaluated nor has the maternal and paternal contribution of each of these functional hermaphrodites to the progeny. Genotypes of 6 spawners and 374 resulting progeny at 6 microsatellite loci were coupled with mitochondrial DNA sequencing to assign maternal and paternal parentage. After the identification of a high proportion of null alleles (9.7%), microsatellite data revealed that 51.7% of the progenies were full siblings, with a significant, unequal contribution of the 6 spawners to the progeny. Three progenies were the result of self-fertilization. All spawners contributed paternally (though unequally); however, 2 spawners were the maternal parents of all but 7 progenies resulting in a variance effective population size of 3.52. DNA sequencing confirmed 4 microsatellite mutations within 4476 alleles scored, all in the paternal germ line. With minor exception, the loci conformed to Mendelian rules of segregation when null alleles were accounted for, and 2 loci were found to be linked. These results lend insight to the genetic composition of induced mass spawns and provide a basis for the development of more effective spawning techniques.

Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

Schlueter, J. A., Scheffler, B. E., Jackson, S., Shoemaker, R. C. — 2008-03-02

Extended comparison of gene sequences found on homeologous soybean Bacterial Artificial Chromosomes to Medicago truncatula and Arabidopsis thaliana genomic sequences demonstrated a network of synteny within conserved regions interrupted by gene addition and/or deletions. Consolidation of gene order among all 3 species provides a picture of ancestral gene order. The observation supports a genome history of fractionation resulting from gene loss/addition and rearrangement. In all 3 species, clusters of N-hydroxycinnamoyl/benzoyltransferase genes were identified in tandemly duplicated clusters. Parsimony-based gene trees suggest that the genes within the arrays have independently undergone tandem duplication in each species.

PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution

Cai, J. J. — 2008-02-29

Assessing genetic diversity within populations is vital for understanding the nature of evolutionary processes at the molecular level. PGEToolbox is a Matlab-based open-sourced software package for data analysis in population genetics. The main features of this software are as follows: 1) capability for handling both DNA sequence polymorphisms and single nucleotide polymorphisms (SNPs), which include genotype and haplotype data; 2) exhaustive population genetic analyses and neutrality tests based on the coalescent theory; 3) extendibility and scalability for complex and large genome-wide datasets; 4) simple yet effective graphic user interfaces and sophisticated visualization of data and results. For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox.

Construction and Analysis of 2 Reciprocal Arabidopsis Introgression Line Populations

2008-02-28

Two new large reciprocal sets of introgression lines (ILs) were created between the Arabidopsis accessions Col-0 and C24. In both sets (78 ILs with Col-0 background and 62 ILs with C24 background), the donor segments cover almost the entire genome with an average substitution size of 18.3 cM. In addition to the basic sets of ILs, further subILs were developed for 2 genomic regions allowing better mapping resolution. SubILs carrying donor segments with candidate genes for flowering time and reduced fertility were used to demonstrate the usefulness of the reciprocal ILs for quantitative trait loci detection and fine mapping. For subIL development at high resolution around the reduced fertility locus, we used modified CelI-based assays in one-well format for both marker development and genotyping. This serves as a very flexible and cost-effective approach.

Expression and Nucleotide Diversity of the Maize RIK Gene

2008-02-28

The K homology (KH) domain is a conserved sequence present in a wide variety of RNA-binding proteins. The rough sheath2–interacting KH domain (RIK) protein of maize has been implicated in the maintenance of the repressed chromatin state of knox genes during leaf primordia initiation. The amino acid sequences of the publicly available plant RIK proteins contain a splicing factor 1 (SF1)–like KH domain core sequence motif that distinguishes them from all other SF1-like KH domain–containing proteins. We demonstrate that the maize RIK gene exhibits surprisingly little nucleotide sequence diversity among Zea species and subspecies. Microarray hybridization experiments demonstrate that RIK has a higher level of expression in the shoot apical meristem as compared with 14-day seedling. Reverse transcriptase–polymerase chain reaction analysis of RIK indicates that the gene is expressed in many tissues, albeit at lower levels in older leaf samples. Taken together, these data suggest that the RIK protein may be involved in the maintenance of an inactive chromatin state of knox and possibly other genes in nonmeristematic tissues.

Phenotypic Effects of the "Mini-Muscle" Allele in a Large HR x C57BL/6J Mouse Backcross

2008-02-28

From outbred Hsd:ICR mice, we selectively bred 4 replicate lines for high running (High-Runner [HR] lines) on wheels while maintaining 4 nonselected lines as controls (C lines). An apparent Mendelian recessive, the "mini-muscle" (MM) allele, whose main phenotypic effect is to reduce hindlimb muscle mass by 50%, was discovered in 2 HR lines and 1 C line. This gene of major effect has gone to fixation in one selected line, remains polymorphic in another, and is now undetectable in the one C line. Homozygotes exhibit various pleiotropic effects, including a doubling of mass-specific muscle aerobic capacity, and larger hearts, livers, and spleens. To create a population suitable for mapping the genomic location of the MM allele and to better characterize its pleiotropic effects, we crossed females fixed for the MM allele with male C57BL/6J. F₁ males were then backcrossed to the MM parent females. Backcross (BC) mice (N = 404) were dissected, and a 50:50 ratio of normal to MM phenotype was observed with no overlap in relative muscle mass. In the BC, analysis of covariance revealed that MM individuals ran significantly more on days 5 and 6 of a 6-day exposure to running wheels (as in the routine selective-breeding protocol), were smaller in body mass, and had larger ventricles and spleens.

An Intron Loss of Dfak Gene in Species of the Drosophila melanogaster Subgroup and Phylogenetic Analysis

2008-02-28

Drosophila focal adhesion kinase (Dfak) gene is a single-copy nuclear gene. Previous study revealed that Drosophila melanogaster and Drosophila simulans had lost an intron precisely within the tyrosine kinase (TyK) domain of this gene. However, this did not happen in several other Drosophila species, including Drosophila elegans, Drosophila ficusphila, Drosophila biarmipes, Drosophila jambulina, Drosophila prostipennis, Drosophila takahashii, and Drosophila pseudoobscura. In the current study, homologous sequences of Drosophila sechellia, Drosophila mauritiana, Drosophila yakuba, Drosophila teissieri, Drosophila santomea, and Drosophila erecta were amplified by polymerase chain reaction, and further sequencing analysis indicated that these species were missing a TyK domain intron, indicating they were closely related. The relationship of the D. melanogaster species group was reconstructed using TyK domain nucleotide sequences. The resulting phylogenetic tree revealed that these 8 species were the most related species in the melanogaster group. These results strongly support previously proposed classifications based on morphological and molecular data.