Isolation of polymorphic tetranucleotide microsatellite markers in the satin bowerbird,Ptilonorhynchus violaceus

We isolated 13 polymorphic microsatellite markers from the satin bowerbird, Ptilonorhynchus violaceus from a genomic library enriched in (AAGG)_n repetitive elements and characterized them in 20 individuals. The number of alleles ranged from two to 18 per locus with the observed heterozygosity ranging from 0.15 to 1.00. These markers will be useful for analysing questions concerning parentage, population genetic structure and models of speciation.     

Female signals enhance the efficiency of mate assessment in satin bowerbirds (Ptilonorhynchus violaceus)

Recent evidence suggests that males adjust their sexually selecteddisplay traits in response to female behaviors during courtships.Little is known, however, about whether females signal to influencemale displays and whether females benefit from this interaction.Male courtship displays in the satin bowerbird (Ptilonorhynchusviolaceus) are highly intense and aggressive. Females may usethese displays as indicators of mating benefits, but these displaysoften startle females and disrupt courtship. Previous studieshave shown that successful males decrease female startling byadjusting their display intensity according to female crouchingbehaviors, suggesting that crouching behaviors function as signals.Here we address whether female crouching is a signal by usingobservations of natural courtship behaviors. In addition, weexamine why females differ in signaling and whether femalesbenefit from signaling. First, we find that female crouchingis related to the likelihood that females will be startled bymale displays, suggesting that crouching signals the degreeof display intensity that females will tolerate from a malewithout being startled. Second, we find that female tolerancefor intense display increases during successive courtships asfemales assess potential mates, and that female tolerance mayalso be affected by age and condition. Third, we find evidencethat females that reduce startling by signaling their intensitytolerance are more efficient in mate searching. These resultssuggest that females signal to influence how males display theirsexually selected traits, and by doing so, females may increasetheir benefits in mate choice.     

Stealing behavior and the maintenance of a visual display in the satin bowerbird

Honest signals that indicate male quality have been observedin many species and are thought to have evolved to allow malesto assess rivals accurately and respond to "cheaters." Femalescould potentially also use the same honest signals as reliableindicators of male quality. In bowerbirds, the numbers of specificbower decorations may serve as an honest signal of male quality:this study investigates whether decoration stealing among malesatin bowerbirds at the Bunya Mountains, Australia, may alsoinvolve honest signals. In this study, we aimed to determine1) predictors for the degree to which individual male satinbowerbirds steal, and are stolen from, and 2) predictors forwhy some male pairs interact by stealing, whereas other pairsdo not. We also assessed how experimentally standardizing thenumber of decorations on bowers would affect the 1) frequencyof stealing, 2) specific interactions among males, and 3) distributionof decorations across bowers. Bower decorations were labeledand tracked through one breeding season. Males that were successfulstealers, stole from other successful stealers, had many feathersand bottle tops on their bowers and painted their bower wallsoften. Male pairs were more likely to interact by stealing iftheir bowers were in close proximity. Most of the stealing observedwas of a reciprocal nature. After we standardized the numbersand types of decorations on a small group of males' bowers,the mean number of daily stealing gains and the total numberof males interacting by stealing did not change. In addition,no significant novel stealing interactions were initiated afterthe manipulation. The average number of all bower decorationsand the average number of rosella feathers on a given male'sbower prior to the manipulation were proportional to the averagenumbers for the period after the manipulation. Furthermore,males that originally had better collections of decorationstended to suffer fewer losses due to stealing after the manipulation.Our results suggest that the total number of decorations, thetotal number of rosella feathers on a male's bower, and possiblystealing behavior, may form part of the basis of an honest signalindicating male quality and therefore might be correlated withmating success.     

Genetic variation and population structure in the endangered greater horseshoe bat Rhinolophus ferrumequinum

Following a dramatic decline last century, the British population of the endangered greater horseshoe bat Rhinolophus ferrumequinum is highly fragmented. To examine the consequences of fragmentation and limited dispersal on patterns of genetic structure and variation, we used microsatellite markers to screen bats from around 50% of the known maternity colonies in Britain, and two areas from continental Europe. Analyses revealed that Welsh and English colonies were genetically isolated. This, and lower variability in Britain than north France, may result from either genetic drift, or the species' colonization history. Gene flow among most neighbouring colonies was not generally restricted, with one exception. These findings have important implications for the ongoing conservation management of this species.     

Phylogeography of an east Australian wet-forest bird, the satin bowerbird (Ptilonorhynchus violaceus), derived from mtDNA, and its relationship to morphology

Australian wet forests have undergone a contraction in range since the mid-Tertiary, resulting in a fragmented distribution along the east Australian coast incorporating several biogeographical barriers. Variation in mitochondrial DNA and morphology within the satin bowerbird was used to examine biogeographical structure throughout almost the entire geographical extent of these wet forest fragments. We used several genetic analysis techniques, nested clade and barrier analyses, that use patterns inherent in the data to describe the spatial structuring. We also examined the validity of the two previously described satin bowerbird subspecies that are separated by well-defined biogeographical barriers and tested existing hypotheses that propose divergence occurs within each subspecies across two other barriers, the Black Mountain corridor and the Hunter Valley. Our data showed that the two subspecies were genetically and morphologically divergent. The northern subspecies, found in the Wet Tropics region of Queensland, showed little divergence across the Black Mountain corridor, a barrier found to be significant in other Wet Tropics species. Biogeographical structure was found through southeastern Australia; three geographically isolated populations showed genetic differentiation, although minimal divergence was found across the proposed Hunter Valley barrier. A novel barrier was found separating inland and coastal populations in southern New South Wales. Little morphological divergence was observed within subspecies, bar a trend for birds to be larger in the more southerly parts of the species' range. The results from both novel and well-established genetic analyses were similar, providing greater confidence in the conclusions about spatial divergence and supporting the validity of these new techniques.     

Genetic variation and population structure of the mosquito Anopheles jeyporiensis in southern China

Genetic differentiation among populations of Anopheles jeyporiensis was examined using 76 mtDNA COII sequences from 16 sites throughout southern China and northern Vietnam. The COII sequences are AT-rich (74.58%) and reveal high levels of diversity with 39 of 685 sites polymorphic and 50 different haplotypes present. Genetic variation is high within populations and significant geographical structure was detected at both population and regional levels. In the larger samples, the distributions of haplotypes suggest recent population expansion.     

Microsatellite variation and fine-scale population structure in the wood frog (Rana sylvatica)

We investigated genetic population structure in wood frogs (Rana sylvatica) from a series of Prairie Pothole wetlands in the northern Great Plains. Amphibians are often thought to exist in demographic metapopulations, which require some movement between populations, yet genetic studies have revealed strong subdivision among populations, even at relatively fine scales (several km). Wood frogs are highly philopatric and studies of dispersal suggest that they may exhibit subdivision on a scale of approximately 1-2 km. We used microsatellites to examine population structure among 11 breeding assemblages separated by as little as 50 m up to approximately 5.5 km, plus one population separated from the others by 20 km. We found evidence for differentiation at the largest distances we examined and among a few neighbouring ponds, but most populations were strikingly similar in allele frequencies, suggesting high gene flow among all but the most distant populations. We hypothesize that the few significant differences among neighbouring populations at the finest scale may be a transient effect of extinction-recolonization founder events, driven by periodic drying of wetlands in this hydrologically dynamic landscape.     

Genetic variation and population structure ofCarex breviculmis (Cyperaceae) in Korea

We determined the genetic diversity and population structures ofCarex breviculmis (Cyperaceae) populations in Korea, using genetic variations at 23 allozyme loci.C. breviculmis is a long-lived herbaceous species that is widely distributed in eastern Asia. A high level of genetic variation was found in 15 populations. Twelve enzymes revealed 23 loci, of which 11 were polymorphic (47.8%). Genetic diversity at the speciesand population levels were 0.174 and 0.146, respectively. Total genetic diversity (H_T = 0.363) and within-population genetic diversity (H_s = 0.346) were high, whereas the extent of the population divergence was relatively low (G_ST = 0.063). Deviation from random mating (Fis) within the 15 populations was 0.206. An indirect estimate of the number of migrants per generation(Nm = 3.69) indicated that gene flow was extensive among Korean populations of this species. Analysis of fixation indices revealed a substantial heterozygote deficiency in some populations and at some loci. Genetic identity between popu-lations was high, exceeding 0.956.     

Genetic variation and population structure of interleukin genes among seven ethnic populations from Karnataka,India

The extent of genetic variation and the degree of genetic differentiation among seven ethnic populations from Karnataka, India (Bunt, Havyak, Iyengar, Lingayath, Smartha, Vaishya, Vokkaliga), was investigated using four single nucleotide polymorphisms (SNPs: IL-1A 4845, IL-1B 3954, IL-1B 511 and IL-1RA 2018) of the interleukin gene cluster. Allele frequencies varied by threefold among these populations, which also differed for gene diversity and heterozygosity levels. The average degree of population subdivision among these castes was low (F _ST = 0.02). However, pair-wise interpopulation differentiation ranged from 0–7%, indicating no detectable differentiation to moderate differentiation between specific populations. The results of phylogenetic analysis based on genetic distances between populations agreed with known social and cultural data on these ethnic groups. Variation in the allele frequencies, as well as differentiation, may be attributed to differential selection and demographic factors including consanguinity among the ethnic groups. Information on the distribution of functionally relevant polymorphisms among ethnic populations may be important towards developing community medicine and public health policies.     

Genetic variation and bill size dimorphism in a passerine bird, the reed bunting Emberiza schoeniclus

In passerine birds morphological differentiation in bill size within species is not commonly observed. Bill size is usually associated with a trophic niche, and strong differences in it may reflect the process of genetic differentiation and, possibly, speciation. We used both mitochondrial DNA (mtDNA) and nuclear microsatellites to study genetic variation between two subspecies of reed bunting, Emberiza schoeniclus schoeniclus and E.s. intermedia , along their distributional boundary in western Europe. These two subspecies are characterized by a high dimorphism in bill size and, although breeding populations of the two subspecies are found very close to each other in northern Italy, apparently no interbreeding occurs. The observed morphological pattern between the two subspecies may be maintained by geographically varying selective forces or, alternatively, may be the result of a long geographical separation followed by a secondary contact. MtDNA sequences of cytochrome b and ND5 (515 bp) showed little variation and did not discriminate between the two subspecies, indicating a divergence time of less than 500 000 years. The analysis of four microsatellite loci suggested a clear, although weak, degree of genetic differentiation in the large- and small-billed populations, as indicated by F _ST and R _ST values and genetic distances. The correlation between bill size and genetic distance between populations remained significant after accounting for the geographical distances between sampling localities. Altogether, these results indicate a very recent genetic differentiation between the two bill morphs and suggest that a strong selection for large bills in the southern part of the breeding range is probably involved in maintaining the geographical differentiation of this species.     

Genetic structure of the annual weed Senecio vulgaris in relation to habitat type and population size

Throughout the world, the highly selfing annual common groundsel, Senecio vulgaris (Asteraceae) is a common weed. Recently, it has also colonized ecological compensation areas in agro-ecosystems. We investigated the genetic structure of S. vulgaris using random amplified polymorphic DNA (RAPD) profiles of 80 plants from nine populations representing three habitat types in two regions in Switzerland. RAPD variation among regions (19.8%), among populations within regions (19.2%) and within populations (61.1%) was highly significant (ANOVA; P < 0.001). Gene flow estimated from the observed differentiation among populations (PhiST = 0.382) was low (assuming Wright's island model, Nem = 0.404). Genetic distances between pairs of populations were significantly correlated with geographical distances (Mantel test; r = 0.37, P < 0.03). Molecular variance obtained with AMOVA was lowest in the small populations in compensation areas (1.13), intermediate in vineyard populations (2.49), all located in northern Switzerland and highest in the larger vegetable field populations from western Switzerland (3.41; P < 0.05). Overall, there was a positive correlation of molecular variance and population size (P < 0.05), as expected under genetic drift. However, molecular variance was negatively correlated with population size among populations in ecological compensation areas, suggesting that selection was also important. We also applied triazine herbicide to leaves of three offspring of each of the 80 plants. Plants from populations of compensation areas showed higher mean levels and reduced variation in the resistance to triazine herbicide than plants from vineyards and vegetable fields. This suggests that compensation areas were colonized from adjacent corn fields, in which there has been selection for herbicide resistance. We discuss the implications of our results for the biological control of S. vulgaris.     

Genetic population structure, fitness variation and the importance of population history in remnant populations of the endangered plant Silene chlorantha (Willd.) Ehrh. (Caryophyllaceae)

Habitat fragmentation can lead to a decline of genetic diversity, a potential risk for the survival of natural populations. Fragmented populations can become highly differentiated due to reduced gene flow and genetic drift. A decline in number of individuals can result in lower reproductive fitness due to inbreeding effects. We investigated genetic variation within and between 11 populations of the rare and endangered plant Silene chlorantha in northeastern Germany to support conservation strategies. Genetic diversity was evaluated using AFLP techniques and the results were correlated to fitness traits. Fitness evaluation in nature and in a common garden approach was conducted. Our analysis revealed population differentiation was high and within population genetic diversity was intermediate. A clear population structure was supported by a Bayesian approach, AMOVA and neighbour-joining analysis. No correlation between genetic and geographic distance was found. Our results indicate that patterns of population differentiation were mainly caused by temporal and/or spatial isolation and genetic drift. The fitness evaluation revealed that pollinator limitation and habitat quality seem, at present, to be more important to reproductive fitness than genetic diversity by itself. Populations of S. chlorantha with low genetic diversity have the potential to increase in individual number if habitat conditions improve. This was detected in a single large population in the investigation area, which was formerly affected by bottleneck effects.     

Clonal population structure and genetic variation in sand-shinnery oak,Quercus havardii (Fagaceae)

We investigated clonal population structure and genetic variation in Quercus havardii (sand-shinnery oak), a deciduous rhizomatous shrub that dominates vegetation by forming uninterrupted expanses of ground cover over sandy deposits on the plains of western Texas, western Oklahoma, and eastern New Mexico. Isozyme electrophoresis (15 loci coding 11 enzymes) was used to recognize and map clones arrayed in a 2000-m transect (50-m sample intervals) and a 200 × 190 m grid (10-m sample intervals). Ninety-four clones were discovered, 38 in the transect and 56 in the grid, resulting in an estimated density of ～15 clones per hectare. Clones varied greatly in size (～100-7000 m), shape, and degree of fragmentation. The larger clones possessed massive interiors free of intergrowth by other clones, while the smaller clones varied in degree of intergrowth. The population maintained substantial levels of genetic variation (P = 60%, A = 2.5, H(exp) = 0.289) comparable to values obtained for other Quercus spp. and for other long-lived perennials. The population was outcrossing as evidenced by conformance of most loci to Hardy-Weinberg expected genotype proportions, although exceptions indicated a limited degree of population substructuring. These data indicate that despite apparent reproduction primarily through vegetative means, Q. havardii possesses conventional attributes of a sexual population.     

Molecular genetic variation and population structure in morphologically differentiated cave and surface populations of the freshwater amphipod Gammarus minus

Gammarus minus is an important component of surface spring and cave ecosystems throughout Appalachia, and is a useful indicator of the hydrology and gene flow in freshwater communities. Gammarus minus populations occupying large cave passages (> 2 km) are usually troglomorphic, having reduced eyes, fewer ommatidia, larger body size, longer antennae, and reduced pigmentation relative to surface populations. We surveyed five cave stream and 10 surface spring populations for DNA sequence variation in the cytochrome c oxidase I (COI) and internal transcribed spacer 1 (ITS-1) genes with an aim towards characterizing phylogeographical structure and comparing the nature of genetic variation in cave vs. surface populations. Although standing variation at both loci was rather low within populations, a significant degree of divergence and spatial structuring of populations was observed. Levels of genetic variation within cave and spring populations differed substantially, with caves harbouring significantly less variation at the COI locus than surface springs. Codon usage bias was significantly lower in caves, indicating that cave streams harbour smaller and/or more recently colonized populations. Overall these data indicate limited gene flow among populations and suggest that the cave populations sampled in this study are prone to bottlenecks, possibly due to larger temperature fluctuations and more frequent incidence of drought conditions associated with these particular cave habitats.     

Fine‐scale genetic structure and helping decisions in a cooperatively breeding bird

In animal societies, characteristic demographic and dispersal patterns may lead to genetic structuring of populations, generating the potential for kin selection to operate. However, even in genetically structured populations, social interactions may still require kin discrimination for cooperative behaviour to be directed towards relatives. Here, we use molecular genetics and long‐term field data to investigate genetic structure in an adult population of long‐tailed tits Aegithalos caudatus, a cooperative breeder in which helping occurs within extended kin networks, and relate this to patterns of helping with respect to kinship. Spatial autocorrelation analyses reveal fine‐scale genetic structure within our population, such that related adults of either sex are spatially clustered following natal dispersal, with relatedness among nearby males higher than that among nearby females, as predicted by observations of male‐biased philopatry. This kin structure creates opportunities for failed breeders to gain indirect fitness benefits via redirected helping, but crucially, most close neighbours of failed breeders are unrelated and help is directed towards relatives more often than expected by indiscriminate helping. These findings are consistent with the effective kin discrimination mechanism known to exist in long‐tailed tits and support models identifying kin selection as the driver of cooperation.     

Genetic variation versus recombination rate in a structured population of mice

The correlation between genetic variation and recombination rate was investigated in a structured mouse population. Nucleotide sequence data from 19 autosomal DNA loci from eight inbred strains of mouse (Mus musculus) sampled from three major subspecies were analyzed. The recombination rate was estimated from the comparison of genetic and physical map distances between markers flanking a 10-cM region of each locus. The strains were categorized into four groups (subpopulations) based on geography. By partitioning the genetic diversity into within-group and among-group variation, we detected a positive correlation between the recombination rate and nucleotide diversity within groups. The level of nucleotide differentiation among groups (G(ST)) showed a negative correlation with the rate of recombination. There was no significant correlation between recombination rate and nucleotide diversity when data from different subpopulations were pooled. No correlation was detected between recombination rate and nucleotide divergence of M. musculus and M. spicilegus. These patterns deviate from the strict neutral expectation under the constant nucleotide substitution rate, and they are likely to have been formed either by a hitchhiking effect of positively selected mutants or by background selection of deleterious mutants occurring in a subdivided population. Our series of comparisons show that because a real population always has some structure, incorporation of its information is important in detecting non-neutral evolution.     

Genetic population structure of the German cockroach, Blattella germanica: Absence of geographical variation

The genetic structure of 31 populations of the German cockroach, Blattella germanica (L.), located in two French cities 900 km apart, was estimated by enzyme gel electrophoresis. A set of 41 loci was analysed. Eight loci (4 Est, 3 Lap and 1 Got) were polymorphic. Diversity was estimated at different geographical levels: the overall population, between cities and within a city. Hierarchical F-statistics indicated significant genetic differentiation between all populations and among populations within each city, but no differentiation between cities. F_ST values for populations within each city and for the overall sample were substantially dissimilar. In addition, a cluster analysis did not separate populations according to their geographical origin but according to the predominance of either of the two alternative Est-4 alleles. The results of this analysis point to the absence of genetic differentiation on a large geographical scale: no large-scale geographical distance effect was detected. However, we evidenced strong genetic substructuring on a local scale, within cities.     

Genetic diversity and population structure in the outcrossing populations of Equisetum arvense and E. hyemale (Equisetaceae)

An allozyme examination was conducted to study the mating systems and genetic differentiation of populations of Equisetum arvense and E. hyemale. The study revealed that the rate of intragametophytic selfing in these homosporous pteridophytes is very low, i.e., on average 0.020 and 0.019, respectively, despite the potential hermaproditism and selfing of the gametophytes. Most populations consisted of numerous genotypes, and the average heterozygosities of E. arvense and E. hyemale equalled 0.092 and 0.134, respectively. The commonly observed excess of the heterozygote genotypes indicates that there are interclonal differences in the frequency of vegetative reproduction. The level of genetic divergence among populations was considerable even within a limited geographic area. It is suggested that the life history of Equisetum, characterized by the inefficiency of spore germination and gametophyte reproduction in noncolonizing situations, limits the level of gene flow and leads to a great genetic divergence between populations.