FREQUENCY-DEPENDENT SELECTION IN DROSOPHILA: ESTIMATION OF NET FITNESS IN PSEUDOHAPLOID POPULATIONS

There is much evidence that the viability of Drosophila larvae depends on the genotypes of other larvae with which they develop. There is, however, little evidence concerning frequency dependence of net fitness. This report documents variation in net fitness among male D. melanogaster from 17 lines studied in 49 discrete-generation populations. The experimental design, which uses attached-X females, eliminates effects of dominance, heterosis, recombination, genetic background, and selection in females. Selection operates only on patroclinously inherited X-chromosomes in males, causing frequency dynamics to mimic those of haploid populations. Analysis of one-generation transitions shows a general pattern of frequency dependence of net fitnesses. Analysis of multigeneration trajectories suggests frequency dependence in 12 populations, but trajectories tend to be heterogeneous among replicates. For a deterministic model in which fitness w(p) is a function of allelic frequency (p), oscillatory dynamics can occur where |dw(p)/dp| > w(p?) (Curtsinger, 1984a). The derivative measures the strength of frequency-dependent selection, and divides models into two categories: dynamically “well-behaved” and “complex.” For the pooled data, this criterion is violated in about half of the frequency space, though several factors probably cause strength to be overestimated. The strength criterion is a useful predictor of evolutionary dynamics: observed oscillations tend to occur most often where frequency dependence is strong, and less often where it is weak.     

IMPLICATIONS OF MORPHOLOGICAL AND ANATOMICAL VARIATION IN ABIES BALSAMEA AND A. LASIOCARPA (PINACEAE) FROM WESTERN CANADA

Abies balsamea and A. lasiocarpa are closely related North American balsam firs that are generally thought to hybridize and intergrade where their ranges overlap in west-central Alberta. To test this hypothesis, a series of collections was made from ten populations along an east-west transect between western Saskatchewan and central British Columbia. Each tree was scored for various vegetative and cone characters. The resulting data were analyzed by Principal Components Analysis and Canonical Variates Analysis. Analyses based on vegetative data produced somewhat different results from analyses based on cone data, indicating that vegetative and sexual features of the trees respond to different selection pressures at the ecologically diverse sample sites. The combined results of analyses of vegetative and sexual data indicate that the ten populations do not represent elements of two morphologically distinct taxa. Instead, the results apparently reflect population differentation within a single, regionally variable complex in response to local selection pressures following east-west gene flow. It is recommended that the separate species designations, A. balsamea and A. lasiocarpa, be retained since: 1) present day elements of the complex are evidently derived from separate refugia isolated by the Rocky Mountains during past glacial periods, and 2) gradual morphological differences exist between populations on each side of the Rocky Mountain crest.     

Complex selection on a regulator of social cognition: Evidence of balancing selection,regulatory interactions and population differentiation in the prairie vole Avpr1a locus

Adaptive variation in social behaviour depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behaviour. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four single nucleotide polymorphisms that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genomewide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favours specific combinations of regulatory polymorphisms, maintains the resulting alleles at population‐specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.     

Genetic variation in the Afromontane tree Prunus africana,an endangered medicinal species

An understanding of the patterns of variation within and among populations of tropical trees is essential for devising optimum genetic management strategies for their conservation and sustainable utilization. Here, random amplified polymorphic DNA (RAPD) analysis was used to partition variation within and among 10 populations of the endangered Afromontane medicinal tree, Prunus africana, sampled from five countries across the geographical range of the species (Cameroon, Ethiopia, Kenya, Madagascar and Uganda). Analysis of molecular variance ( AMOVA ) employed 48 RAPD markers and revealed most variation among countries (66%, P < 0.001). However, variation among individuals within populations and among populations within Cameroon and Madagascar was also highly significant. Analysis of population product frequency data indicated Ugandan material to be more similar to populations from Cameroon than populations from Kenya and Ethiopia, while Malagash populations were most distinct. The implications of these findings for determining appropriate approaches for conservation of the species, particularly in Cameroon and Madagascar, are discussed.     

Variation in the population dynamics of the intertidal pulmonate gastropod Salinator solida Martens (Gastropoda: Amphibolidae) at Towra Point,NSW, Australia

This paper describes variation in the population dynamics of the intertidal pulmonate gastropod solida among mangrove and saltmarsh habitats at Towra Point, NSW, Australia over a two-year period. In general, this paper describes the degree to which the density of the populations fluctuated and the size structure of the populations varied among heights on shore. The density of individuals in the upper mangrove forest was most variable through time and their population size structure was dominated by smaller individuals. The density of populations in the Sarcocornia high on the shore fluctuated least through time and were dominated by large individuals. Those populations found on the mid-shore in the Sarcocornia had population characteristics intermediate to those populations in the upper mangrove forest and the Sarcocornia high on the shore. Analysis of size frequency data indicated that the growth rates of individuals and their annual mortality decreased with increasing height on shore.     

Aggregation and spawning by lampreys (genus Ichthyomyzon) beneath cover

Synopsis Lampreys are generally reported to spawn in shallow water on open, gravel bottoms. During surveys in Wisconsin and Minnesota, we regularly observed aggregations of adult Ichthyomyzon c.f. gagei, I. castaneus, and I. fossor beneath such cover objects as boulders, woody debris, and, at one site, vegetation. In some cases, observations of eggs or rapid quivering by individual lampreys indicated that spawning was occurring. The literature includes scattered anecdotal reports of similar behavior in other populations of Ichthyomyzon. Our data for I. c.f. gagei suggest that aggregations beneath cover objects occur at a greater range of depths than those in the open, but that aggregations in the open can contain greater numbers of individuals. Facultative spawning beneath cover objects may permit lampreys to spawn in deep waters with swift current where spawning could not otherwise occur. Moreover, this behavior may reduce the vulnerability of spawning lampreys to some types of predators.     

Morphological and genetic distinctiveness of metallicolous and non-metallicolous populations of Armeria maritima s.l. (Plumbaginaceae) in Poland

Patterns of morphological, genetic and epigenetic variation (DNA methylation pattern) were investigated in metallicolous (M) and non‐metallicolous (NM) populations of Armeria maritima. A morphological study was carried out using plants from six natural populations grown in a greenhouse. Morphological variation was assessed using seven traits. On the basis of this study, three representative populations were selected for molecular analyses using metAFLP to study sequence‐ and methylation‐based DNA variation. Only one morphological trait (length of outer involucral bracts) was common to both metallicolous populations studied; however, the level of variation was sufficient to differentiate between M and NM populations. Molecular analyses showed the existence of naturally occurring epigenetic variation in A. maritima populations, as well as structuring into distinct between and within population components. We show that patterns of population genetic structure differed depending on the information used in the study. Analysis of sequence‐based information data demonstrates the presence of three well‐defined and genetically differentiated populations. Methylation‐based data show that two major groups of individuals are present, corresponding to the division into M and NM populations. These results were confirmed using different analytical approaches, which suggest that the DNA methylation pattern is similar in both M populations. We hypothesise that epigenetic processes may be involved in microevolution leading to development of M populations in A. maritima.     

Detection and pattern of interspecific hybridization between Gliricidia sepium and G. maculata in Meso-America revealed by PCR-based assays

Gliricidia sepium provides a variety of products important for rural communities in tropical countries. Native populations in Meso-America currently form an important source of seed for distribution to farmers, but concerns centre on mechanisms which may lead to their genetic erosion, including anthropogenic dispersal and subsequent introgression from the related species, G. maculata. Populations of Gliricidia were examined genetically using approaches based on the polymerase chain reaction to test for interspecific hybridization and introgression between G. sepium and G. maculata. Analysis involved 13 RAPD and two RFLP-PCR markers which were identified to have species-diagnostic distributions. Data from both approaches corresponded and indicated three locations where multilocus genotypes were consistent with an hybrid origin. Data at one of these sites was consistent with introgression following hybridization. The hybrid origin of populations was supported by the intermediate geographical location of these sites to ‘pure’ populations of each species. Analysis of maternally inherited organellar DNA, which involved the detection of SSCPs in mitochondrial DNA amplification products, allowed further delineation of genetic structure among Gliricidia populations. Mitochondrial data indicated a high degree of organelle differentiation between sampled locations and identified G. sepium- and G. maculata-diagnostic haplotypes. This data supported the interpretation of genetic structure based on RAPDs and RFLP-PCR. In addition, cytonuclear analysis allowed the directionality of gene transfer during the formation of hybrid populations to be described. Despite evidence for the occurrence of interspecific hybridization and introgression in Gliricidia, important resource populations of G. sepium on the Pacific coast appear to have retained their genetic integrity. Implications in terms of the conservation and utilization of genetic resources within the genus are discussed.     

Microsatellite variation and population genetic structure of the red throat emperor on the Great Barrier Reef

Analysis (using three analytical approaches) of eight microsatellite markers from six locations in three geographic regions of the Great Barrier Reef (GBR), including populations that differed in demographic characteristics, showed no evidence of genetic stock structure in the red throat emperor Lethrinus miniatus. Measures of inter‐population differentiation were non‐significant (P ≥ 0·67). Using a Bayesian clustering approach, ‘admixture’ was detected (mean alpha values >1) with allele frequencies for each of the locations sampled being correlated equally with allele frequencies from all locations sampled. The number of populations (K) identified was one, based on the estimates of the probability of the data at various K values (K = 1, 2, 3, … 6). Additionally, alpha values did not stabilize to relatively constant values in any of the Bayesian analyses performed, indicating that there was no real genetic structure between locations. Analysis of genetic variation as detected by analysis of molecular variance (AMOVA) indicated that almost all of the variance in the data (99·74%, P ≤ 0·023) was within populations, rather than among populations (0·15%, P ≤ 0·176) or amongst regions sampled (0·10%, P ≤ 0·247) on the GBR. F_st statistics identified four individual loci having statistically significant differentiation among populations, but these were only related to one out of 12 pair‐wise comparisons where populations differed demographically. Given these results (albeit using neutral markers), together with the capacity of adults and larvae to be mobile between reefs on the inter‐connected GBR, it is considered unlikely that L. miniatus populations exist as distinct genetic stocks in the GBR. It is therefore not possible, using neutral markers, to reject the null hypothesis that the fishery be managed as a single panmictic stock.     

Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

Evolutionary relationships among populations of chamois (Rupicapra spp.) across their current range from the Caucasus to the Cantabrian Mountains were investigated. The allelic variation in 23 microsatellite loci was assessed in eight geographical populations, recognised as subspecies of the two closely related species R. pyrenaica and R. rupicapra. Analysis of variance in allele frequencies (Fst, statistics) and in repeat numbers (Rst, statistics) showed these data to be highly structured. Two genetic distances between pairs of populations, Ds and (δμ)², were computed and phylogenetic trees were constructed. Similar patterns were produced by the different statistics. All trees indicate a deep divergence between the two recognised species, which is compatible with archaeological data that place their split in the Riss–Würm interglacial period. Genetic distances between pairs of populations are highly correlated with geographical distance. This suggests that the history of the genus during Pleistocene glacial-interglacial periods was dominated by expansions and contractions within limited geographic regions, leading to alternate contact and isolation of contiguous populations. In addition, the alpine barrier has played a substantial role in West–East differentiation.     

Conservation genetics of the endangered endemic Sambucus palmensis Link (Sambucaceae) from the Canary Islands

Five polymorphic microsatellites (simple sequence repeat; SSR) markers were used to estimate the levels of genetic variation within and among natural populations from different islands of the endangered endemic from the Canary Islands Sambucus palmensis Link (Sambucaceae). Genetic data were used to infer potential evolutionary processes that could have led to present genetic differentiation among islands. The levels of genetic variability of S. palmensis were considerably high; proportion of polymorphic loci (P = 100%), mean number of alleles per locus (A = 6.8), average expected heterozygosity (He = 0.499). In spite of its small population size and endemic character, 58 different multilocus genotypes were detected within the 165 individuals analyzed. All samples located in different islands always presented different multilocus genotypes. Principal Coordinates Analysis, genetic differentiation analysis (F _ST and G _ST ′) and Bayesian Cluster Analysis revealed significant genetic differences among populations located in different islands. However, this genetic differentiation was not recorded among Tenerife and La Gomera populations, possibly revealing the uncontrolled transfer of material between both islands. AMOVA analysis attributed 77% of the variance to differences within populations, whereas 8% was distributed between islands. The levels of genetic differentiation observed among populations, and the genetic diversity distribution within populations in S. palmensis, indicate that management should aim to conserve as many of the small populations as possible. Concentrating conservation efforts only on the few large populations would result in the likelihood of loss of genetic variability for the species.     

On the origins,rapid expansion and genetic diversity of native Americans from hunting‐gatherers to agriculturalists

Given the importance of Y‐chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y‐chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai‐Tai, Kungurtug, and Toora‐Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post‐migration population growth in the ubiquitous and diverse Y‐STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural‐ and trade‐based subsistence adopted during the Pre‐Classic, Classic and Post‐Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median‐joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y‐ STR average gene diversity indices. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.     

Analysis of microsatellite variation in the rainbow trout <Emphasis Type="Italic">Parasalmo (Oncorhynchus) mykiss</Emphasis> from Kamchatka

Genetic variation of Kamchatka rainbow trout Parasalmo (O.) mykiss was examined using 10 microsatellite DNA loci, and phylogeographic comparison with other representatives of the species across the distribution range was performed. It was demonstrated that Kamchatka populations differed from other geographic groups of rainbow trout in a number of microsatellite loci. These populations also displayed distinct clustering and were characterized by lower genetic diversity. Analysis of a set of 26 different microsatellite loci (personal and literature data) demonstrated that most of the populations within the Kamchatka region were separated from one another, characterized by marked geographic differentiation, and affiliation to certain river basins. In Kamchatka rainbow trout, with high degree of probability, three geographic clusters (northwestern, southwestern, and eastern) were identified. In general, analysis of microsatellite DNA supported the data on low genetic diversity of the Kamchatka group Parasalmo (O.) mykiss, based on the variation estimates for a number of genes of nuclear and mitochondrial DNA, and allozyme loci.     

Genetic Structure of Przewalski’s Rock Partridge (Alectoris magna) Populations in the Longzhong Loess Plateau, China

In this paper, we have analyzed the nuclear DNA of Alectoris magna samples, collected from the Longzhong Loess Plateau. We used allelic variation at eight microsatellite markers to describe the genetic structure of A. magna populations. The primary goal of this study was to examine the population genetic structure and determine the extent of population differentiation among populations of A. magna. The average value of H _E (0.455) was smaller than H _O (0.477), and there was a heterozygote deficit at the MCW135 locus in the Lanzhou population and the Beidao population. The AB063167 locus in each population (except that of Jingyuan) was not in equilibrium (P < 0.05). The Lixian edge population had a lower proportion of genetic diversity than the central geographic populations; the Haiyuan and Jingyuan populations had higher genetic diversity than the central geographic populations. Analysis of population structure revealed clear differentiation among the eight populations of A. magna, suggesting strong isolation of these populations and correspondingly low levels of migration or gene flow. The A. magna populations of Longzhong Loess Plateau are separated into eastern and western populations by a clustering chart. Genetic data indeed suggest that patterns of speciation and population diversification of A. magna in the Longzhong Plateau have been affected by the stability of the climate, natural selection, and human intervention.     

Elliptic Fourier Analysis of leaf outline shape in forest fragment populations of <Emphasis Type="Italic">Anthurium sinuatum</Emphasis> and <Emphasis Type="Italic">A. pentaphyllum</Emphasis> (Araceae) from Northeast Brazil

A field-based comparative study of leaflet outline shape in five populations of Anthurium sinuatum Benth. ex Schott from Amazonia and humid brejo forests of Ceará, Northeast Brazil, and ten populations of A. pentaphyllum (Aubl.) G. Don var. pentaphyllum from Amazonia and the Brazilian Atlantic forest is reported. 1,120 leaflets from 561 individuals in 15 populations were sampled. Using images, leaflet outlines were captured by digitisation and subjected to Elliptic Fourier Analysis (EFA) to produce matrices of Fourier coefficients based on 40 harmonics; lateral and central leaflets were analysed separately. Twelve shape variables, extracted from the Fourier coefficient matrices, described the leaflet outlines of 531 individuals. Between-population relationships were estimated using cluster analysis, Canonical Variates Analysis and non-parametric MANOVA. Amazonian populations showed the greatest within-population variability. In A. sinuatum the Pacatuba population was the most distinct in Ceará and the Pará population (Amazonia) was not significantly different from those at Ibiapaba and Maranguape (both Ceará). In A. pentaphyllum 80% of population pairs were significantly different and three significantly different groups of populations were observed. Although the populations of A. pentaphyllum displayed considerable variation, the morphological patterns did not correlate with previously reported molecular ones. The two species were found to be slightly but significantly different on leaf outline data.     

Superoxide dismutase polymorphism in field populations of the potato cyst nematodes Globodera rostochiensis and G. pallida

Superoxide dismutase (SoDase) polymorphism in reference populations of potato cyst nematodes (PCN) was studied by isoelectric focusing and compared with the banding pattern obtained from 26 English field populations of PCN. Qualitative and quantitative differences were found between the reference populations: a band detected only in the G. rostochiensis Ro4 and Ro5 reference populations was found in four field populations of varying pathotype composition and two field populations of G. rostochiensis Rol possessed extra bands that were not detected in the other field populations. Analysis of the band differences showed little correlation between pathotype and banding pattern in the field populations.     

Phylogeography of Wild Musk Shrew (Suncus Murinus) Populations in Asia Based on Blood Protein/Enzyme Variation

The musk shrew (Suncus murinus) is an insectivore species that inhabits tropical and subtropical Asia widely. To clarify the genetic relationship among wild musk shrew populations, we examined the electrophoretic variants of biparentally inherited genetic markers at 10 loci coding for eight blood proteins/enzymes in a total of 639 animals and compared the results obtained from the mitochondrial DNA data. The principal-component analysis performed using the allele frequency data revealed that the 17 populations could be divided into two major groups, a South Asian group and a Southeast Asian group that includes several island populations bound by Myanmar. The degrees of genetic divergence among populations were higher within the Southeast Asian group than within the South Asian group. This finding was incongruent with the mtDNA diversity. Analysis conducted at the individual level showed that a shrew from the central region in Myanmar that carries a South Asian type of mtDNA showed the electrophoretic variants specific to the Southeast Asian group, suggesting that this region is a contact zone between the two major groups.     

MODE OF SWARMING IN RELATION TO REPRODUCTIVE ISOLATION IN MAYFLIES

Mayfly males swarm, that is they fly in a fixed pattern by a specific object, the swarm marker. Females orientate to the same markers. Leptophlebia marginata mayflies were observed to orientate to two kinds of objects in a single locality in central Finland: to trees and to horizontal pale objects on the ground; when dispersed or moved to the other type of marker, they returned to their former orientation. Tree swarming is by far the most common mode of swarming, but some horizontally orientating populations were found. Sympatric populations are genetically and morphologically distinct, whereas other populations appear to have some gene flow between the swarming types. The tree-swarming mode appears to be primitive and the horizontal mode derived; wind rather than predation is the factor favoring swarming close to the ground. Swarming constitutes an effective mechanism of premating isolation in mayflies.     

Population genetic structure of the endangered crayfish Austropotamobius pallipes in France based on microsatellite variation: biogeographical inferences and conservation implications

1. One important goal in conservation biology is to characterise evolutionary lineages within endangered species before management decisions are taken. Here, we assess population differentiation in the freshwater crayfish Austropotamobius pallipes, an endangered species endemic to western Europe and provide valuable information for the conservation of French populations. 2. Analysis of five microsatellite loci in 44 populations revealed very different within population levels of genetic diversity (0.000 < H₀ < 0.564). Two groups, corresponding to northern and southern French populations, showed a high degree of genetic differentiation in both allele frequencies and allele sizes. Comparison of these results with previous studies of A. pallipes strongly suggests that the divergence between northern and southern populations could have occurred during the last glaciation period of the Pleistocene from one Atlantic and one Mediterranean refuge. 3. Evidence for genetic admixture between these two lineages was revealed by correspondence analyses in southern populations, probably as the result of artificial translocations. 4. French populations appeared significantly differentiated among the different river drainages and were highly structured within rivers. The impact of population size, population bottlenecks and founder events on the population genetic differentiation are discussed. 5. Based on these results, we propose the designation of two evolutionarily significant units for A. pallipes in France. Our data also support the maintenance of separate demographic management strategies for crayfish inhabiting different river systems. However, genetic analyses will have to be combined with demographic and ecological data for sustainable conservation programmes.     

INTRASPECIFIC VARIATION IN ABIES LASIOCARPA FROM BRITISH COLUMBIA AND WASHINGTON

Sixteen natural stands of Abies lasiocarpa (Hook.) Nutt. were sampled from British Columbia and Washington to investigate patterns of intraspecific variation in this species and to evaluate Hunt and von Rudloff's recognition of two species of subalpine fir. Principal components analysis and canonical variates analysis were performed separately on seed-cone data, needle morphology data, and needle flavonoid data. Analysis of cone data indicated no geographical patterning of populations, but eastern and western groups of populations were segregated in both the needle morphology and flavonoid analyses. With the exception of the Vancouver Island population, three geographic groups were discerned based on their needle morphology: 1) populations from the coastal mountains of British Columbia, 2) those from the Cascade Mountains of Washington, and 3) those from the eastern interior of British Columbia. Although the Vancouver Island population was grouped with the interior British Columbia populations based on needle morphology, it was similar to the other coastal populations based on flavonoid data. These inconsistent results among the three different types of taxonomic evidence underscore the need to consider a variety of traits when drawing taxonomic conclusions in Abies. Although the delineation of eastern and western groups is not wholly consistent for the different data sets, the results support recognition of coastal and interior varieties of subalpine fir.