Genetic variation at pig plasma protein locus PLP1 and its assignment to chromosome 5

A new genetic polymorphism of an unidentified plasma protein (PLP1) in pigs was described by using a method of two-dimensional gel electrophoresis and protein staining. Two codominant alleles, with frequencies of 0.83 and 0.17, were found in the Swedish Yorkshire breed. The PLP1 marker was typed in a three-generation pedigree and tested for linkage against a set of 128 markers. The PLP1 locus showed significant LOD score values with three different microsatellite markers (S0092, DAGK and S005), previously assigned to chromosome 5.     

Conservation genetics: beyond the maintenance of marker diversity

One of the major problems faced by conservation biologists is the allocation of scarce resources to an overwhelmingly large number of species in need of preservation efforts. Both demographic and genetic information have been brought to bear on this problem; however, the role of information obtained from genetic markers has largely been limited to the characterization of gene frequencies and patterns of diversity. While the genetic consequences of rarity may be a contributing factor to endangerment, it is widely recognized that demographic factors often may be more important. Because patterns of genetic marker variation are influenced by the same demographic factors of interest to the conservation biologist, it is possible to extract useful demographic information from genetic marker data. Such an approach may be productive for determining plant mating systems, inbreeding depression, effective population size, and metapopulation structure. In many cases, however, data consisting only of marker frequencies are inadequate for these purposes. Development of genealogical based analytical methods coupled with studies of DNA sequence variation within and among populations is likely to yield the most information on demographic processes from genetic marker data. Indeed, in some cases it may be the only means of obtaining information on the long-term demographic properties that may be most useful for determining the future prospects of a species of interest.     

Some new variants of serum protease inhibitors in Meishan pigs

Serum samples of Meishan (13 animals) and Meishan x Wild Boar crosses (361 animals) were analysed by means of two-dimensional electrophoresis. Some new variants in protease inhibitor systems PO1A, PO1B and PI2 are reported.     

Migration timing and distance from shore of southbound eastern Pacific gray whales (Eschrichtius robustus) off Ensenada,Baja California,Mexico

Eastern Pacific gray whales were monitored off Ensenada, Mexico, during the southbound migration. The objectives were to determine southbound migration timing and width of the migration corridor during three seasons (2003–2006). Migration timing was determined by fitting a generalized additive model to the shore counts for each season and estimating the 10, 50, and 90 percentiles of the fitted curves. To estimate abundance from shore‐based counts, a probability density function for the shore based distances was estimated by a product of a gamma distribution fit to the boat survey distance data for 2006/2007 and a half‐normal detection function using combined data of the three seasons. The parameters of the gamma distribution were corrected to account for less boat survey effort carried out 20–40 km than 0–20 km from shore. The onset of the migration off Ensenada was in late December/early January and ended around 13 February. The median date was 23–26 January for the first and third season and a week early for the second season. Boat surveys indicated a wide (20 km) migration corridor but most gray whales traveled within 9.9 km from shore. The estimated total number of whales during watch hours was 2,298 (95% CI = 1,536–4,447).     

Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north–south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long‐lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.     

Allozyme polymorphisms, outerossing rates, and hybridization of South AmericanNothofagus

Electrophoretically detectable genetic variation was used to describe the genetic structure of three South American species ofNothofagus: the widespreadN. betuloides andN. dombeyi, and the geographically restrictedN. nitida. Although the widespread species possess higher levels of genetic variation, the three species have more genetic variation within than among populations. These results are consistent with the theoretical expectations for woody, presumably highly outerossed species with wind-borne seeds.Estimates of outcrossing rates from progeny arrays yielded slightly higher average t-values forN. nitida (1.158) andN. dombeyi (range 0.873–1.045) than forN. betuloide (0.878). Hierarchical analysis of population structure revealed values of F_IS and FIT that were positive and significantly different from zero at most loci and for each species. The levels of inbreeding detected by F-statistics indicate some degree of self-fertilization and/or population substructuring into discrete family groups. Reduced seed vagility and regeneration of natural stands after disturbance by a few remnant individuals would probably generate the recruitment of related seedlings underneath parent trees.The analysis of a putative hybrid population betweenN. nitida andN. betuloides indicated that individuals clearly segregated intonitida-like orbetuloides- like individuals. The reduced outcrossing rate ofbetuloides-like individuals from the hybrid site (t=0.585) is interpreted in concert with low pollen availability and the increased probability of selfing and/or hybridization inNothofagus.     

RUNAWAY COEVOLUTION: ADAPTATION TO HERITABLE AND NONHERITABLE ENVIRONMENTS

Populations evolve in response to the external environment, whether abiotic (e.g., climate) or biotic (e.g., other conspecifics). We investigated how adaptation to biotic, heritable environments differs from adaptation to abiotic, nonheritable environments. We found that, for the same selection coefficients, the coadaptive process between genes and heritable environments is much faster than genetic adaptation to an abiotic nonheritable environment. The increased rate of adaptation results from the positive association generated by reciprocal selection between the heritable environment and the genes responding to it. These associations result in a runaway process of adaptive coevolution, even when the genes creating the heritable environment and genes responding to the heritable environment are unlinked. Although tightening the degree of linkage accelerates the coadaptive process, the acceleration caused by a comparable amount of inbreeding is greater, because inbreeding has a cumulative effect on reducing functional recombination over generations. Our results suggest that that adaptation to local abiotic environmental variation may result in the rapid diversification of populations and subsequent reproductive isolation not directly but rather via its effects on heritable environments and the genes responding to them.     

Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry)

A method for estimating and comparing population genetic variation using random amplified polymorphic DNA (RAPD) profiling is presented. An analysis of molecular variance (AMOVA) is extended to accomodate phenotypic molecular data in diploid populations in Hardy-Weinberg equilibrium or with an assumed degree of selfing. We present a two step strategy: 1) Estimate RAPD site frequencies without preliminary assumptions on the unknown population structure, then perform significance testing for population substructuring. 2) If population structure is evident from the first step, use this data to calculate better estimates for RAPD site frequencies and sub-population variance components. A nonparametric test for the homogeneity of molecular variance (HOMOVA) is also presented. This test was designed to statistically test for differences in intrapopulational molecular variances (heteroscedasticity among populations). These theoretical developments are applied to a RAPD data set in Vaccinium macrocarpon (American cranberry) using small sample sizes, where a gradient of molecular diversity is found between central and marginal populations. The AMOVA and HOMOVA methods provide flexible population analysis tools when using data from RAPD or other DNA methods that provide many polymorphic markers with or without direct allelic data.     

The impact of hybrids between genetically modified crop plants and their related species: general considerations

Factors influencing the fate and impact of hybrids between crop plants and their related species operate from the early zygote, through to plant establishment in different habitats, to their ability to form self-sustaining populations. Many of the classes of genes being introduced by modern methods of genetic modification are similar to those manipulated by conventional plant breeding. In assessing the impact of transgenes in hybrids between crops and related species, therefore, it is important to be informed about the consequences of hybridization between conventionally bred varieties and their relatives. Some transgenes will have novel effects (e.g. production of pharmaceutical substances or certain fatty acids) on plants, and are likely to need specific assessment studies to determine their impact on hybrids. This will be particularly important if there is the possibility of these transgenes becoming established in wild populations. Some recommendations for further research are outlined.