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PubMed2001

Invasion history and genetic population structure of riverine macroinvertebrates.

Macroinvertebrate communities of large rivers have experienced dramatic species turnovers in the last decades, which still go on. The analysis of genetic population structure plays a central role in understanding and predicting these biological invasions. Two points of view are considered: the influence of the invasion history on the genetic structuring and the potential implications of genetic structure for future invasibility. Expectations about selectively neutral genetic variation in simple invasion models are compared to case studies of amphipods and Dreissena. The genetic patterns of one amphipod species of the Gammarus fossarum complex yield strong evidence for a stepwise regional colonisation. Other invasive amphipods show similar, but less clear genetic characteristics. Long-distance colonisation is probably common in Dreissena polymorpha, but subsequent downstream swamping of larvae obscures the expected genetic pattern by homogenising neighbouring populations. First, a brief review of general characteristics of riverine invasions is followed by a discussion of the utility of genetic tools for inferring taxon and source population identity.

Journal Article↗
PubMed1993

Assessing the effects of the naked neck gene on chronic heat stress resistance in two genetic populations.

The effect of the naked neck (Na) gene on resistance to chronic heat stress was studied in the F2 generation of two populations of chickens genetically differing in growth. The Na gene was introduced into the Athens-Canadian randombred (ACRB), a small BW population, and into a large BW commercial broiler population. Naked neck and normally feathered birds were maintained in either a chronic heat stress (32 C) environment or a control (21 C) environment from 4 to 8 wk of age. Body weight, BW gain, feed consumption, and feed efficiency were calculated at 4, 6, and 8 wk. The 32 C environment significantly reduced gain and feed consumption at all age intervals in both populations. Feed conversion ratio (FCR) was lower in the 32 C environment in the ACRB population, but in the broiler population FCR either was the same or increased when compared with the 21 C environment. In the F2 generation of both populations the naked neck birds were significantly larger than the normally feathered birds although the two types segregated from the same parents. In the ACRB population the relative growth response was not significantly different between naked neck and normal feathered birds, indicating that the Na gene did not confer resistance to chronic heat stress in the small BW population. In the broiler population, an assessment of the relative growth response in the 32 C environment showed that the naked neck birds had a smaller reduction in BW gain and better feed efficiency than the normally feathered birds, indicating that in the large BW broiler population the Na gene did confer resistance to chronic heat stress.

Animals↗
PubMed2004

Genetic population structure of turbot (Scophthalmus maximus L.) supports the presence of multiple hybrid zones for marine fishes in the transition zone between the Baltic Sea and the North Sea.

Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.

Animals↗
PubMed1998

Population genetics of inversion polymorphism in Drosophila ananassae.

Drosophila ananassae, although a cosmopolitan and domestic species, is largely circumtropical in distribution. It occupies unique status in the whole of genus Drosophila due to certain peculiarities in its genetical behaviour. The most unusual feature of this species is spontaneous male recombination in appreciable frequency. This species is of common occurrence in India. Population genetics of inversion polymorphism has been extensively studied in Indian D. ananassae in our laboratory. The main findings are: (i) Three cosmopolitan inversions namely AL in 2L, DE in 3L and ET in 3R are of frequent occurrence in Indian populations and have become coextensive with the species. (ii) Quantitative data on the frequency of three cosmopolitan inversions in 29 natural populations of D. ananassae suggest that there is a considerable degree of genetic divergence at the level of inversion polymorphism. In general, the populations from south India show more differentiation than those from the north. (iii) These three cosmopolitan inversions exhibit heterosis. Interracial hybridization does not lead to breakdown of heterosis, which suggests that evidence for coadaptation is lacking in geographic populations of D. ananassae. Heterosis appears to be simple luxuriance rather than populational heterosis (coadaptation). (iv) Data on intra- and interchromosomal associations in natural and laboratory populations of D. ananassae show that interchromosomal associations occur randomly indicating no interchromosomal interactions but two inversions of the third chromosome often show strong linkage disequilibria in laboratory populations which is due to epistatic interaction and suppression of crossing over. The role of genetic drift causing linkage disequilibria in isofemale strains of D. ananassae has also been suggested. (v) Mating ability of homo- and hetero-karyotypes due to subterminal (2L) inversion derived from natural populations of D. ananassae in which the frequency of different chromosome arrangements were known, was tested and the results indicate that the chromosome occurring in high frequency is associated with higher mating activity in all the populations analysed and heterokaryotypic males are superior in mating propensity to the corresponding homokaryotypes, indicating the existence of heterosis associated with the AL inversion with respect to male mating activity. Thus inversion polymorphism in D. ananassae may have a partial behavioural basis as has been demonstrated in other species of Drosophila.

Animals↗
PubMed1993

A population genetic study of the evolution of SINEs. I. Polymorphism with regard to the presence or absence of an element.

SINEs are short interspersed repeated DNA elements which are considered to spread throughout genomes via RNA intermediates. Polymorphisms with regard to the presence or absence of SINE are occasionally observed in a specific location of a genome. We modeled the evolution of SINEs with regard to this type of polymorphism. Because SINEs are rarely deleted, multiplication of elements is confined to a certain period, and a few master copies are considered to be responsible for their multiplication, the usual population genetic models of transposable elements assuming the equilibrium state are not applicable to describe the evolution of SINEs. Taking into account these properties and assuming selective neutrality, we computed conditional probabilities of finding a SINE at a specific site given that this site is first found because it is occupied by a SINE in an original sample. Using these probabilities, we investigated ways to estimate the multiplication period and infer relationships among populations. The latter inference procedures are shown to be strongly dependent on the multiplication period.

Animals↗
PubMed1997

Chromosome Y microsatellites: population genetic and evolutionary aspects.

By means of a multicenter study, a large number of males have been characterized for Y-chromosome specific short tandem repeats (STRs) or microsatellites. A complete summary of the allele frequency distributions for these Y-STRs is presented in the Appendix. This manuscript describes in more detail some of the population genetic and evolutionary aspects for a restricted set of seven chromosome Y STRs in a selected number of population samples. For all the chromosome Y STRs markedly different region-specific allele frequency distributions were observed, also when closely related populations were compared. Haplotype analyses using AMOVA showed that when four different European male groups (Germans, Dutch, Swiss, Italians) were compared, less than 10% of the total genetic variability was due to differences between these populations. Nevertheless, these pairwise comparisons revealed significant differences between most population pairs. Assuming a step-wise mutation model and a mutation frequency of 0.21%, it was estimated that chromosome Y STR-based evolutionary lines of descent can be reliably inferred over a time-span of only 1950 generations (or about 49,000 years). This reduces the reliability of the inference of population affinities to a historical, rather than evolutionary time scale. This is best illustrated by the construction of a human evolutionary tree based on chromosome Y STRs in which most of the branches connect in a markedly different way compared with trees based on classical protein polymorphisms and/or mtDNA sequence variation. Thus, the chromosome Y STRs seem to be very useful in comparing closely related populations which cannot probably be separated by e.g. autosomal STRs. However, in order to be used in an evolutionary context they need to be combined with more stable Y-polymorphisms e.g. base-substitutions.

Biological Evolution↗
PubMed1999

Population genetics and paternity in Rasa Aragonesa sheep using DNA fingerprinting.

DNA fingerprinting was used to study the population genetics and paternity of the Rasa Aragonesa sheep (Ovis aries). Using a combination of Hae III and the M13 derived probe pV47, the mean number of bands per individual (5.422 +/- 0.309), the background band sharing coefficient (0.347), the mean population frequency of alleles (0.192) and the mean heterozygosity for bands (0.893) were calculated for 45 individuals from eight different farms in Aragon, northern Spain. Therefore, the estimated probability of missing a wrong paternity was 0.126 for unrelated males, and this probability was 0.438 for full-sibs males. In addition, in a field trial of this technique, paternity was assigned for three ewe-lamb pairs with a probability of 97 per cent in two cases and 77 per cent in one case.

Animals↗
PubMed2006

Isolation by distance within a river system: genetic population structuring of Atlantic salmon, Salmo salar, in tributaries of the Varzuga River in northwest Russia.

An important issue for designing any conservation programme aimed at preserving genetic diversity is estimation of the scale at which genetic structuring occurs. Additional relevant factors include distinguishing whether or not population structuring is expected to be stable as predicted by the member-vagrant hypothesis, or alternatively, whether populations are more prone to local extinction-recolonization processes, as predicted by the metapopulation evolutionary model. In this study, the population genetic structure of Atlantic salmon from 11 locations within or nearby the Varzuga River tributary system was assessed using 17 microsatellites. Mantel tests and spatial autocorrelation analyses revealed a significant isolation-by-distance signal within the tributary system as well as a negative association between the level of genetic diversity and waterway distance from the river mouth, indicating that dispersal is less likely to occur to populations deep in the tributary system. Individual-level spatial autocorrelation analyses indicated that the majority of migration occurred between populations situated within 20 km of each other. The relatively high level of genetic structuring and significant isolation-by-distance signal observed in the Varzuga tributaries are concordant with the predictions of the member-vagrant evolutionary model. However, one subpopulation in particular revealed signs of instability which may be due to its location in the tidal zone, or due to the fact that it is more affected by human impacts. The results suggest that preservation of a number of spawning sites spaced throughout the tributary system is recommendable for ensuring sustainable fishing tourism in the river.

Animals↗
PubMed2006

mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

The mitochondrial genome, contained in the subcellular mitochondrial network, encodes a small number of peptides pivotal for cellular energy production. Mitochondrial genes are highly polymorphic and cataloguing existing variation is of interest for medical scientists involved in the identification of mutations causing mitochondrial dysfunction, as well as for population genetics studies. Human Mitochondrial Genome Database (mtDB) (http://www.genpat.uu.se/mtDB) has provided a comprehensive database of complete human mitochondrial genomes since early 2000. At this time, owing to an increase in the number of published complete human mitochondrial genome sequences, it became necessary to provide a web-based database of human whole genome and complete coding region sequences. As of August 2005 this database contains 2104 sequences (1544 complete genome and 560 coding region) available to download or search for specific polymorphisms. Of special interest to medical researchers and population geneticists evaluating specific positions is a complete list of (currently 3311) mitochondrial polymorphisms among these sequences. Recent expansions in the capabilities of mtDB include a haplotype search function and the ability to identify and download sequences carrying particular variants.

Databases, Nucleic Acid↗
PubMed2006

Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae).

Giant Amazon river turtles, Podocnemis expansa, are indigenous to the Amazon, Orinoco, and Essequibo River basins, and are distributed across nearly the entire width of the South American continent. Although once common, their large size, high fecundity, and gregarious nesting, made P. expansa especially vulnerable to over-harvesting for eggs and meat. Populations have been severely reduced or extirpated in many areas throughout its range, and the species is now regulated under Appendix II of the Convention on International Trade in Endangered Species. Here, we analyse data from mitochondrial DNA sequence and multiple nuclear microsatellite markers with an array of complementary analytical methods. Results show that concordance from multiple data sets and analyses can provide a strong signal of population genetic structure that can be used to guide management. The general lack of phylogeographic structure but large differences in allele and haplotype frequencies among river basins is consistent with fragmented populations and female natal-river homing. Overall, the DNA data show that P. expansa populations lack a long history of genetic differentiation, but that each major tributary currently forms a semi-isolated reproductive population and should be managed accordingly.

Animals↗
PubMed1994

The molecular and population genetics of cyclodiene insecticide resistance.

Cyclodiene resistance has accounted for over 60% of reported cases of insecticide resistance. Understanding of this resistance can therefore help us answer questions relating to the mechanism and origin of representative resistance-associated mutations, questions fundamental to the molecular and populations genetics of pesticide resistance. The cyclodiene resistance gene Rdl (resistance to dieldrin) was cloned from a mutant of the model insect Drosophila resistant to cyclodienes and picrotoxinin. Rdl codes for a subunit of a novel class of GABA gated chloride ion channels and resistance is correlated with replacement of the same amino acid residue in a wide range of species from different insect orders. This single amino acid replacement Ala302 > Ser, within the proposed lining of the chloride ion channel, also confers insensitivity to the blocking action of cyclodienes and picrotoxinin on GABA gated chloride ion channels expressed in Xenopus oocytes. The resistance mechanism involves both changes in cyclodiene binding site affinity and also a change in the rate of receptor desensitization which destabilizes the cyclodiene-favored conformation. Documentation of the resistance associated mutation has allowed for the design of a PCR based molecular monitoring technique. This technique gives more accurate estimates of resistance gene frequency from smaller sample sizes and has shown the frequency of resistance in apparently unselected populations of Drosophila to be as high as 1%. We are still uncertain as to why resistance persists in the apparent absence of selection pressure and any severe reduction in the fitness of resistant strains, besides a paralytic phenotype at high temperature, remains undocumented.

Amino Acid Sequence↗
PubMed2005

Coyote movements and social structure along a cryptic population genetic subdivision.

A recent region-wide study determined that the central California coyote (Canis latrans) population was genetically subdivided according to habitat bioregions, supporting the hypothesis that coyotes exhibit a dispersal bias toward their natal habitat type. Here, we further investigated this hypothesis using radio-collared coyotes captured on a 150-km(2) study site on the border of (i.e. overlapping) two bioregions (Great Valley and Cascade Mountains). As predicted, most coyotes were assigned (based on a priori genetic criteria) to genetic clusters corresponding to one of these two bioregions. All of those assigned to the Great Valley genetic cluster were caught in (and for the most part, remained in) the Great Valley bioregion. However, contrary to expectations, the coyotes assigned to the Cascades genetic cluster occurred commonly in both bioregions. Nearly all resident individuals on the study site, regardless of the particular bioregion, were assigned to the Cascades genetic cluster, whereas a sizable fraction of nonresident (transient or dispersing) coyotes caught in the Great Valley bioregion were assigned to the Great Valley cluster. Even among resident coyotes, interrelatedness of packs was greater within than between bioregions, and packs with territories overlapping both bioregions were more closely related to those with territories completely within the Cascades bioregion than territories completely within the Great Valley bioregion. Finally, direct estimates indicated that gene flow was twice as high from the Cascades bioregion to the Great Valley bioregion than in the reverse direction. Collectively, these findings reveal the anatomy of the genetic subdivision as beginning abruptly at the bioregion boundary and ending diffusely within the Great Valley bioregion.

Animals↗
PubMed2006

Molecular population genetics of the alpha-esterase5 gene locus in original and colonized populations of Drosophila buzzatii and its sibling Drosophila koepferae.

Several studies have suggested that esterase-2 (EST-2) may be the target of natural selection in the cactophilic fly Drosophila buzzatii. In this work, we analyzed nucleotide variation in a fragment of alpha-esterase5 (alphaE5), the gene encoding EST-2, in original (Argentinian) and colonized (Australian) populations of D. buzzatii and in its sibling D. koepferae. Estimates of nucleotide heterozygosity in D. buzzatii were similar in Australia and Argentina, although we detected a loss of singletons in colonized populations, suggesting a moderate founder effect. Interspecific comparisons revealed that D. buzzatii was more polymorphic for nonsynonymous variation, whereas D. koepferae was more variable for synonymous and noncoding sites. The two major chromosomal arrangements (2st and 2j) in D. buzzatii displayed similar levels of nucleotide variation, whereas 2jz3 was monomorphic. The sequenced region allowed the discrimination of a greater number of EST-2 protein variants in the Australian sample than in the Argentinean sample. In D. koepferae, nucleotide variation in alphaE5 does not depart from neutral expectations, although tests of population structure were significant for silent variation. In contrast, D. buzzatii has probably undergone a recent population expansion in its South American range. In addition, the McDonald and Kreitman test revealed an excess of nonsynonymous polymorphism in both original and colonized populations of this species.

Animals↗
PubMed1983

Surnames in Sardinia. I. Fit of frequency distributions for neutral alleles and genetic population structure.

Distributions of surnames were examined using data from about 40 000 individuals from consanguineous marriages (1930-59) in the island of Sardinia. They fit the Karlin-McGregor (1967) distribution for neutral alleles. The logarithmic distribution by Fisher (1943) and the Karlin-McGregor (1967) distribution give practically indistinguishable fits to these data. The two parameters underlying the Fisher distribution, alpha and nu, are fully interdependent, given the sample size N. From the latter and from the number of surnames S, they can be easily and satisfactorily estimated. The quantity nu measures immigration to the area and can be taken as a measure of the richness of the gene pool, being closely related to the quantity theta = Nemu (Ne = effective population size, mu = mutation rate) after the necessary corrections have been taken care of. Surnames behave like genes transmitted by the male line. Differences of female and male migrations require correction for comparison with data from autosomal gene frequencies but there seem to be no important differences between female and male migration in this area, as judged by analysis of pedigrees of consanguineous marriages. It is probable that the migration estimates obtained in this material are lower than real ones, mostly because of a bias characteristic of the particular source of surnames here employed. The distribution of surnames from areas which have very recently undergone economic development is not at equilibrium and is not fitted as well as that of areas which have had less important recent changes. As might be expected, the disturbance is particularly marked in the class most sensitive to effects of recent increases in migration, that of rarest surnames (represented by only one individual). In fact in this material it is noticeable only in this class and correction can be made for it. At equilibrium of migration and drift, the number of surnames in a population sample of given size can give a complete description of the population structure for that sample, in the same sense that the number of alleles is a sufficient statistic for the study of neutral evolution. The study of surnames, given their nature of 'neutral' alleles, the large number of alleles and the ease with which large numbers of individual data can be collected, can be a valuable help in the study of genetic population structure.

Alleles↗
PubMed1991

A population genetic study in Finland: comparison of the Finnish- and Swedish-speaking populations.

In Finland there is a substantial but geographically limited Swedish-speaking minority (in 1980 6.3% of the total population) which originates mainly from Swedish immigrants during the years 1100-1300 AD. The admixture of this population with the neighbouring Finns was studied using more than 20 blood marker loci. The reference populations, Swedes and Finns, in spite of being part of the genetically rather uniform European populations, differ from each other genetically. These quantitative and also qualitative differences in gene frequencies are mostly due to the Finnish population possessing a number of genetic markers absent or rare in the rest of Europe. The results based on a sample of 620 individuals from the Swedish-speaking population in Finland showed a rather high degree of Finnish admixture, which was estimated to about 60%. This admixture most probably occurred at an early stage since it has reached such a high and geographically homogeneous degree.

Autoantigens↗
PubMed2001

Estimation of genetic population variables for six radiographic criteria of hip dysplasia in a colony of Labrador Retrievers.

OBJECTIVE: To estimate genetic population variables for 6 radiographic criteria of canine hip dysplasia (CHD). ANIMALS: 664 full- and half-siblings from a colony of Labrador Retrievers. PROCEDURE: Heritability estimates and genetic correlations were calculated for 6 radiographic criteria of CHD. Two evaluation protocols were compared: the grade of the most severely affected hip joint and the sum of the scores for both hip joints. The predictive performance of estimated breeding values was also evaluated. RESULTS: The overall prevalence of CHD (Federation Cynologique Internationale grades C, D, and E) was 29.6%. Median age at radiographic examination was 377 days. Heritability for the total CHD grade, Norberg angle (NA), coverage of the femoral head (COV), craniodorsal acetabular rim (ACR), subchondral bone sclerosis (SUBCH), shape of the femoral head and neck (FHN), and osteoarthritic changes at the insertion site of the joint capsule (JC) was estimated as follows: 0.44, 0.43, 0.46, 0.37, 0.32, 0.21, and 0.05, respectively. Heritability estimates were slightly higher for the sum of the scores for both hip joints. If NA and COV were included as fixed effects in the model for the dependent variables ACR, SUBCH, FHN, and JC , then heritability of these traits significantly decreased (0.08 to 0.15). High scores of NA and COV lead to a significant increase of the scores of the remaining criteria. CONCLUSIONS AND CLINICAL RELEVANCE: Canine hip dysplasia is heritable to a moderate degree. Signs of subluxation revealed the highest heritability estimates. The criteria ACR, SUBCH, FHN, and JC were strongly influenced by NA and COV.

Animals↗
PubMed1997

Pyrolysis mass spectrometry in epidemiological and population genetic studies of Haemophilus influenzae.

Haemophilus influenzae serotype b (Hib) vaccines have reduced the amount of invasive Hib disease in immunised infants. However, Hib disease remains in unvaccinated infants and adults and non-capsulate H. influenzae (NCHi) still causes infections, including outbreaks of respiratory disease. Characterisation of strains and the bacterial population as a whole is therefore necessary to detect outbreaks of infection with NCHi or changes in the population, for example, to vaccine-resistant clones of Hib. The rapid, simple and objective technique of pyrolysis mass spectrometry (PMS) was investigated as an alternative to current complex, subjective methods. PMS was compared with ribotyping and multilocus enzyme electrophoresis (MLEE) for population genetic analyses of Hib and with ribotyping and protein profiling for epidemiological analyses of NCHi. PMS clustered all the isolates of Hib together whereas MLEE and ribotyping distinguished certain clones - this is probably because the three methods examine different (and unrelated) characteristics of the organisms. The PMS results were essentially similar to those from ribotyping and protein profiling for the epidemiological analyses of outbreaks of NCHi disease. Therefore, PMS is probably unsuitable for comparisons of Hib populations but it is a useful addition to the arsenal of techniques for the characterisation of NCHi.

Adult↗