Genetic variability in mitochondrial DNA in a regional population of the great tit (Parus major)

Genetic variation of mitochondrial DNA (mtDNA) in 18 great tits (Parus major) from three neighboring localities in Sweden was investigated with eight tetranucleotide restriction endonucleases. The 18 individuals could be separated into 13 different maternal lineages. The high number of female lineages present in this regional population contrasts with a low level of sequence divergence between the different mtDNA clones, with a mean of 0.19% sequence divergence between all individuals. There was no obvious spatial structuring of mtDNA clones among the three localities. The presence of a high number of different clones with a low degree of sequence divergence could be explained by the effects of a large long-term effective population size, with the mtDNA clones having diverged about 25,000–200,000 years ago.This study was supported by the Swedish Natural Science Research Council, the Erik Philip-Sörensen Foundation, and the Nilsson-Ehle Foundation.     

Unusual mitochondrial DNA polymorphism in two local populations of blue tit Parus caeruleus

Mitochondrial DNA (mtDNA) from 25 blue tits Parus caeruleus sampled from two populations of the Grenoble region (France) was assayed for polymorphism with 17 restriction endonucleases. Nine genotypes were found. Several mtDNA genotypes were also analysed by amplification via the polymerase chain reaction (PCR) and direct sequencing of 903 bp of the cytochrome b gene. The mtDNA polymorphism is greater in P. caeruleus than in other comparable bird species and results from the presence of two clearly differentiated mitochondrial lineages. Using the data of restriction polymorphism, the mean sequence divergence between individuals of the two lineages is 1.23%. Therefore, P. caeruleus should fall into the category II of phylogeographic pattern sensu Avise et al. (1987): discontinuous mtDNA genotypes which co-occur in the same region. P. caeruleus, like humans and other mobile species with high gene flow, seems to have lost its geographic structure in terms of mtDNA phylogeny. This unusual mitochondrial polymorphism can be explained by the recent admixture of two long-term isolated populations. This could be accounted for by two different scenarios. One assumes a simultaneous post-glacial colonization of the Grenoble region by two isolated European populations of P. caeruleus. Alternatively, hybridization between P. caeruleus and P. cyanus could have caused the observed pattern of mtDNA variation.     

Genetic variation of Japanese pink salmon populations inferred from nucleotide sequence analysis of the mitochondrial DNA control region

To estimate genetic variation and structure of pink salmon (Oncorhynchus gorbuscha) populations in Hokkaido, Japan, we analyzed the nucleotide sequence of about 500 bp in a variable portion of the 5′ end of the mitochondrial DNA control region for even- and odd-year broodlines. Sixty-seven haplotypes were detected in the examined individuals. Among these, 25 haplotypes were unique to the even-year broodline, while another 30 haplotypes were unique to the odd-year broodline. Five and three length-heteroplasmic haplotypes were detected in the even-year broodline and odd-year broodline, respectively. The distribution pattern of the 67 haplotypes was different among populations between both broodlines, while not different among populations within the same broodline. The haplotype and nucleotide diversity were higher for even-year broodline populations than for odd-year broodline populations, suggesting greater genetic variation within populations of the even-year broodline. Analysis of molecular variance and pairwise fixation index estimates also demonstrated strong genetic differentiation between even- and odd-year broodlines, although there was no genetic differentiation among populations within the same year broodline. The neutrality tests and mismatch distribution analysis indicate that the demographic history of pink salmon in Japan differs between even- and odd-year populations. Together, these results suggest strong reproductive isolation between the even- and odd-year broodlines of pink salmon, and high gene flow with broodlines due to straying.     

Genetic variation and causes of genotype-environment interaction in the body size of blue tit (Parus caeruleus).

In several studies of natural populations of birds, the heritability of body size estimated by parent-offspring regression has been lower when offspring have developed in poor feeding regimens than when they developed in good feeding regimens. This has led to the suggestion that adaptation under poor regimens may be constrained by lack of genetic variation. We examined the influence of environmental conditions on expression of genetic variation in body size of nestling blue tits (Parus caeruleus) by raising full sibs in artificially reduced and enlarged broods, corresponding to good and poor feeding regimens, respectively. Individuals grown in the poor regimen attained smaller body size than their sibs grown in the good regimen. However, there was among-family variation in response to the treatments--i.e., genotype-environment interactions (GEIs). Partitioning the GEI variance into contributions attributable to (1) differences in the among-family genetic variance between the treatments and (2) imperfect correlation of genotypic values across treatments identified the latter as the main cause of the GEI. Parent-offspring regressions were not significantly different when offspring were reared in the good environment (h2 = 0.75) vs. when they were reared in the poor environment (h2 = 0.63). Thus, there was little evidence that genetic variance in body size was lower under the poor conditions than under the good conditions. These results do not support the view that the genetic potential for adaptation to poor feeding conditions is less than that for adaptation to good conditions, but they do suggest that different genotypes may be favored under the different conditions.     

Paternal leakage of mitochondrial DNA in the great tit (Parus major)

Animal mitochondrial DNA is normally inherited clonally from a mother to all her offspring. Mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype within an individual, can be generated by relatively common somatic mutations within an individual, by heteroplasmy of the oocytes, or by paternal leakage of mitochondria during fertilization of an egg. This biparental inheritance has so far been reported only in mice, mussels, Drosophila, and humans. Here we present evidence that paternal leakage occurs in a bird, the great tit Parus major. The major and minor subspecies groups of the great tit mix in the middle Amur Valley in far-eastern Siberia, where we found a bird that possessed the very distinct haplotypes of the two groups. To our knowledge this is the first report of paternal leakage in birds.     

Phylogeography of the Siberian newt Salamandrella keyserlingii by mitochondrial DNA sequence analysis

Differentiation of geographical populations of the Siberian newt Salamandrella keyserlingii throughout the species range was analyzed using a fragment of the cytochrome b gene. The population of the Primorye region (Russian Far East) is separated to the greatest extent; the Japanese and South Kuril populations are the next most separate. These populations are possibly subspecies. Geographical differentiation of populations in the Siberian part of the species range is lower, lacks a clinal variation, and is irregular. The molecular variation of S. keyserlingii supports the hypothesis that several primary vicarious refugia of pre-Pleistocene differentiation of a common ancestor of Salamandrella occurred in the southeastern part of its current distribution range and that northern and western regions were gradually colonized via repeated steps of expansion and retreat in the Siberian part of the modern species range.     

Variation in personality and behavioural plasticity across four populations of the great tit Parus major

1. Interest in the evolutionary origin and maintenance of individual behavioural variation and behavioural plasticity has increased in recent years. 2. Consistent individual behavioural differences imply limited behavioural plasticity, but the proximate causes and wider consequences of this potential constraint remain poorly understood. To date, few attempts have been made to explore whether individual variation in behavioural plasticity exists, either within or between populations. 3. We assayed 'exploration behaviour' among wild-caught individual great tits Parus major when exposed to a novel environment room in four populations across Europe. We quantified levels of individual variation within and between populations in average behaviour, and in behavioural plasticity with respect to (i) repeated exposure to the room (test sequence), (ii) the time of year in which the assays were conducted and (iii) the interval between successive tests, all of which indicate habituation to novelty and are therefore of functional significance. 4. Consistent individual differences ('I') in behaviour were present in all populations; repeatability (range: 0.34-0.42) did not vary between populations. Exploration behaviour was also plastic, increasing with test sequence - but less so when the interval between subsequent tests was relatively large - and time of year; populations differed in the magnitude of plasticity with respect to time of year and test interval. Finally, the between-individual variance in exploration behaviour increased significantly from first to repeat tests in all populations. Individuals with high initial scores showed greater increases in exploration score than individuals with low initial scores; individual by environment interaction ('I × E') with respect to test sequence did not vary between populations. 5. Our findings imply that individual variation in both average level of behaviour and behavioural plasticity may generally characterize wild great tit populations and may largely be shaped by mechanisms acting within populations. Experimental approaches are now needed to confirm that individual differences in behavioural plasticity (habituation) - not other hidden biological factors - caused the observed patterns of I × E. Establishing the evolutionary causes and consequences of this variation in habituation to novelty constitutes an exciting future challenge.     

Genetic diversity and differentiation of Siberian spruce populations at nuclear microsatellite loci

The results of the study of 21 populations of Siberian spruce (Picea obovata Ledeb.) from different parts of the species natural range by microsatellite (SSR) analysis of nuclear DNA are presented. Using nine loci developed for Picea abies (L.) Karst. and Picea glauca (Moench) Voss and detecting variation in Picea obovata, the parameters of intra- and interpopulation genetic diversity, as well as the degree of population differentiation, were determined. It was demonstrated that the population of Siberian spruce in the study was characterized by a relatively high average level of intrapopulation variability (H_o = 0.408; H_e = 0.423) and low interpopulation differentiation (F_st = 0.048, P = 0.001) at this class of DNA markers. The genetic distance between populations ranged from 0.009 to 0.167, averaging 0.039. The isolated Magadan population, located in the extreme Northeast of Russia at a considerable distance from the main species range and characterized by the lowest genetic diversity among the studied populations, was maximally differentiated from the rest of the spruce populations. In addition, the steppe Ubukun population from Buryatia and the population from the Bogd Khan Uul Biosphere Reserve, Mongolia, were considerably different in the genetic structure from most populations of Siberian spruce, although to a lesser extent than the Magadan population. These findings are consistent with the results of previous studies of this species carried out using allozyme and microsatellite loci of chloroplast DNA and point to the prospects of using nuclear microsatellites as DNA markers to analyze the population genetic structure of Siberian spruce.     

Different population structures in northern and southern populations of the European blue tit (Parus caeruleus)

We sequenced the control region of the mitochondrial DNA from a sample of six European blue tit populations to investigate the phylogeography of Parus species. Along a transect from Barcelona, Spain to Oulu, Finland, the blue tit showed a different phylogeographic structure than the great tit and the willow tit. The southernmost sample from Barcelona consisted of two widely divergent maternal lineages (nucleotide divergence, π = 0.30%), a situation also found earlier in the French Alps. The more northern populations had a relatively uniform structure (π = 0.19%) with distinctive marks of a growing population, thus resembling the great tit populations (π = 0.19%). The amount of genetic variation among blue tits is lower than in the willow tit (π = 0.53%). This probably reflects a smaller long-term effective population size in the great tit and the blue tit than in the willow tit. The different genetic structure of the Barcelona population vs. the rest had an influence on the estimated population parameters, which are calculated based on the assumptions of genetic equilibrium of the populations.     

Phylogeography of the Siberian newt (Salamandrella keyserlingii) by mitochondrial DNA sequence analysis

Differentiation of geographical populations of the Siberian newt Salamandrella keyserlingii throughout the species range was analyzed using a fragment of the cytochrome b gene. The population of the Primorye region (Russian Far East) is separated to the greatest extent; the Japanese and South Kuril populations are the next most separate. These populations are possibly subspecies. Geographical differentiation of populations in the Siberian part of the species range is lower, lacks a clinal variation, and is irregular. The molecular variation of S. keyserlingii supports the hypothesis that several primary vicarious refugia of pre-Pleistocene differentiation of a common ancestor of Salamandrella occurred in the southeastern part of its current distribution range and that northern and western regions were gradually colonized via repeated steps of expansion and retreat in the Siberian part of the modem species range.     

Low variability and absence of phenotypic correlates of Clock gene variation in a great tit Parus major population

Studies of a range of taxa, including birds, have revealed latitudinal clines in allele length at the conserved Clock locus, a gene with known influences on behaviour and physiology. Such clines might reflect adaptation to seasonal variation, a suggestion supported by a recent within‐population analysis of blue tits Cyanistes caeruleus, which found associations between Clock genotype and timing of breeding in females. To test the generality of this pattern, we sequenced the polymorphic poly‐Q locus of the Clock gene in 521 female great tits Parus major, which were selected based on possession of extreme breeding phenotypes. In total, we identified five alleles with one allele accounting for 96% of allelic diversity in the sample set. Overall variability at the poly‐Q locus was very low, and the spatial distribution of Clock alleles across Wytham was highly homogenous. Our data further provide no evidence for a connection between Clock genotype and reproductive timing phenotype in female great tits; further, we found no effect of Clock genotype on reproductive success. Hence, these results are in contrast to the pattern found for the sympatric blue tit population inhabiting the same woodlands, suggesting that phenotypic effects of Clock are not general in passerine birds.     

Genetic variation and differentiation in populations of a threatened tree, Magnolia stellata: factors influencing the level of within-population genetic variation

Genetic variation and differentiation in Magnolia stellata were studied in 20 populations distributed across most of the species' range using 10 microsatellite markers, and the factors influencing their levels of within-population genetic variation were examined. Generally, populations distributed intermittently from southern Gifu to central Aichi Prefectures showed substantially higher levels of genetic variation (exceptions included populations located at unusually high altitude sites or western and southern edges of the range) than more isolated populations on the Atsumi Peninsula of southern Aichi Prefecture and in northern Mie Prefecture. Significant isolation-by-distance patterns were detected in genetic differentiation among the studied populations, and a neighbor-joining tree based on D(A) distances among the populations reflected well the geographical positions of the populations. The level of within-population genetic variation was significantly influenced not only by the size of the populations (represented by the number of reproductive individuals) but also by their degree of isolation (represented by the number of populations within a radius of 0.5 km around them). Therefore, areas within radii of 0.5 km may encompass M. stellata metapopulations, in which gene flow may usually occur. We suggest that this area may be a suitable standard for constructing conservation units for the species.     

Pleistocene climate changes shaped the divergence and demography of Asian populations of the great tit Parus major: evidence from phylogeographic analysis and ecological niche models

Different scales and frequencies of glaciations developed in Europe and Asia during the Pleistocene. Because species’ responses to climate change are influenced by interactive factors including ecology and local topography, the pattern and tempo of species diversification may vary significantly across regions. The great tit Parus major is a widespread Eurasian passerine with a range that encircles the central Asian desert and high‐altitude areas of the Tibetan Plateau. A number of genetic studies have assessed the effect of paleo‐climate changes on the distribution of the European population. However, none have comprehensively addressed how paleo‐climate change affected the distribution of the great tit in China, an apparent hotspot of P. major subspecific diversity. Here, we describe likely paleo‐climatic effects on P. major populations in China based on a combination of phylogeography and ecological niche models (ENMs). We sequenced three mitochondrial DNA markers from 28 populations (213 individuals), and downloaded 112 sequences from outside its Chinese range. As the first step in clarifying the intra‐specific relationships among haplotypes, we attempted to clarify the divergence and demography of populations in China. Phylogeographic analysis revealed that P. major is comprised of five highly divergent clades with geographic breaks corresponding to steep mountains and dry deserts. A previously undescribed monophyletic clade with high genetic diversity, stable niches and a long and independent evolutionary history was detected in the mountainous areas of southwest China. The estimated times at which these clades diverged was traced back to the Early‐Middle Pleistocene (2.19–0.61 mya). Contrary to the post‐LGM (the Last Glacial Maximum) expansion of European populations, demographic history indicates that Asian populations expanded before the LGM after which they remained relatively stable or grew slowly through the LGM. ENMs support this conclusion and predict a similar distribution in the present and the LGM. Our genetic and ecological results demonstrate that Pleistocene climate changes shaped the divergence and demography of P. major in China.     

Genetic variation of mitochondrial DNA in Chinese populations of Pectinophora gossypiella (Lepidoptera: Gelechiidae)

The pink bollworm Pectinophora gossypiella is an invasive pest insect that has successfully established populations in many cotton growing regions around the world. In this study, the genetic diversity and population structure of Chinese populations of P. gossypiella were evaluated using mitochondrial DNA sequence data (COII and Nad4). For comparison, individuals of Pakistan and America were also sequenced at the same two mtDNA regions. Extremely low genetic variation was observed in the two mitochondrial regions among all populations examined. Most of the populations harbored only one to two haplotypes. Although the Nad4 region showed relatively high haplotype diversity and nucleotide variation, ranging from 0.363 to 0.591 and from 0.00078 to 0.00140, respectively, there were only three haplotypes observed in this region. COII and Nad4 haplotype networks shaved one or two common haplotype(s) forming the center of a star-shaped phylogeny. Pairwise tests showed that most of the populations were not significantly differentiated from each other. The Chinese populations were differentiated from the Pakistani and American populations in the Nad4 region. The low level of population genetic variation of P. gossypiella is attributed to invasion bottlenecks, which may have been subsequently strengthened by its nonmigratory biology and the mosaic pattern of agricultural activities.     

Human populations show reduced DNA sequence variation at the factor IX locus

Levels and patterns of human DNA sequence variation vary widely among loci. However, some of this variation may be due to the different populations used in different studies. So far, few studies of diverse human populations have compared different genetic loci for the same samples of populations and individuals. Here, we present new polymorphism data from intron 4 of the Factor IX gene (FIX) sequenced in diverse Old World populations. An explicit comparison is made with another X-linked gene, PDHA1, for which the sampling of individuals was very similar. Despite having a similar amount of divergence from chimpanzees, as do other nuclear genes, FIX has comparatively much less DNA sequence variation among humans. Nucleotide diversity at FIX is the lowest among the existing non-Y chromosome nuclear gene datasets and is less than 10% of the diversity found at PDHA1. Estimates of effective population size based on FIX are 8,558, about half of the value obtained for PDHA1, and the time to the most recent common ancestry among human FIX gene copies (282,000 years) is one of the most recent estimates reported for human genes. Analyses presented here suggest a history for the FIX region that includes recent positive directional selection, or background, selection. The general conclusion emerging is that very large variations can exist between the histories of similar genomic regions, even when sampling differences are minimized.     

Genetic variation and evolutionary demography of Fenneropenaeus chinensis populations, as revealed by the analysis of mitochondrial control region sequences

Genetic variation and evolutionary demography of the shrimp Fenneropenaeus chinensis were investigated using sequence data of the complete mitochondrial control region (CR). Fragments of 993 bp of the CR were sequenced for 93 individuals from five localities over most of the species' range in the Yellow Sea and the Bohai Sea. There were 84 variable sites defining 68 haplotypes. Haplotype diversity levels were very high (0.95 ± 0.03-0.99 ± 0.02) in F. chinensis populations, whereas those of nucleotide diversity were moderate to low (0.66 ± 0.36%-0.84 ± 0.46%). Analysis of molecular variance and conventional population statistics (F(ST) ) revealed no significant genetic structure throughout the range of F. chinensis. Mismatch distribution, estimates of population parameters and neutrality tests revealed that the significant fluctuations and shallow coalescence of mtDNA genealogies observed were coincident with estimated demographic parameters and neutrality tests, in implying important past-population size fluctuations or range expansion. Isolation with Migration (IM) coalescence results suggest that F. chinensis, distributed along the coasts of northern China and the Korean Peninsula (about 1000 km apart), diverged recently, the estimated time-split being 12,800 (7,400-18,600) years ago.     

Genetic variation of the bovine thyroglobulin gene studied at the DNA level

The bovine thyroglobulin gene has been analysed for variation using restriction endonucleases. Six independent restriction fragment length polymorphisms have been identified. One of these results most probably from a 2.5-kb deletion, the others being compatible with point mutations. We determined that an individual taken at random within the Belgian White and Blue breed is, on average, heterozygous for one out of 1700 nucleotides within the thyroglobulin gene.     

BIGSdb: Scalable analysis of bacterial genome variation at the population level

Background  

The opportunities for bacterial population genomics that are being realised by the application of parallel nucleotide sequencing require novel bioinformatics platforms. These must be capable of the storage, retrieval, and analysis of linked phenotypic and genotypic information in an accessible, scalable and computationally efficient manner.     

Components of variance underlying fitness in a natural population of the great tit Parus major

Traits that are closely associated with fitness tend to have lower heritabilities (h2) than those that are not. This has been interpreted as evidence that natural selection tends to deplete genetic variation more rapidly for traits more closely associated with fitness (a corollary of Fisher's fundamental theorem), but Price and Schluter (1991) suggested the pattern might be due to higher residual variance in traits more closely related to fitness. The relationship between 10 different traits for females, seven traits for males, and overall fitness (lifetime recruitment) was quantified for great tits (Parus major) studied in their natural environment of Wytham Wood, England, using data collected over 39 years. Heritabilities and the coefficients of additive genetic and residual variance (CVA and CVR, respectively) were estimated using an "animal model." For both males and females, a trait's correlation (r) with fitness was negatively related to its h2 but positively related to its CVR. The CVA was not related to the trait's correlation with fitness in either sex. This is the third study using directly measured fitness in a wild population to show the important role of residual variation in determining the pattern of lower heritabilities for traits more closely related to fitness.