Genetic relationships among populations of wild resident, and wild and hatchery anadromous brook charr

To determine the genetic relationship of anadromous and resident life-history types within and among drainages, and compare several hatchery strains to their progenitor populations, brook charr Salvelinus fontinalis were examined for allozyme and mitochondrial DNA variation. Greater genetic similarity of sympatric anadromous and resident charr was found compared to similar life-history forms allopatrically, suggesting the two life-history types are not reproductively isolated. Low divergence among the mtDNA haplotypes suggests that the two life-history types are members of the same evolutionary lineage. Population differentiation from mtDNA data exceeded that from estimates based on allozymes. Genetic deviations from expectations suggest that the hatchery strains were derived from few individuals.     

Genetic diversity and relationships among wild and cultivated Stenocereus queretaroensis populations in western Mexico

Stenocereus queretaroensis is an endemic, chiropterophilous, columnar cactus of economic importance in Mexico. To investigate the effect of artificial selection on genetic diversity, inter-simple sequence repeat (ISSR) markers were used to estimate the genetic variation of wild, orchard, and backyard populations of S. queretaroensis from two regions in western Mexico. Six primers were used to generate 62 bands, of which 39 were polymorphic (62.9%). The total genetic diversity was similar in the wild (H_T = 0.296) and orchard (H_T = 0.291) groups, and slightly lower in the backyard group (H_T = 0.281). Wild populations (F_ST = 0.13) were less differentiated than backyard (F_ST = 0.17) and orchard (F_ST = 0.21) populations. The wild and backyard groups were genetically closer (0.015) than the wild and orchard (0.018) groups. A Mantel test revealed a positive correlation between genetic and geographic distances (r = 0.433, p = 0.002). In conclusion, gene flow and the prevailing management system have efficiently maintained genetic diversity and facilitated inter-population differentiation in S. queretaroensis.     

Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines

The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model‐based approach implemented in the software structure , we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.     

The relationships between Apocrita wasp populations and flowering plants in Maine's wild lowbush blueberry agroecosystems

This was the first study to have surveyed the spatial and temporal structure of Apocrita wasps in lowbush blueberry fields, a unique native agricultural landscape in Maine and eastern Canada. The relative abundances of wasps associated with lowbush blueberry (Vaccinium angustifolium Ait.) were investigated in 33 blueberry fields throughout Washington County, Maine, USA. Native wasps were captured during the springs and summers of 1997 and 1998 in Malaise traps erected along a transect in each field. Vegetation sampling was also conducted along these transects to quantify available floral resources. Data indicate the abundance of the total wasp community was positively associated with the abundance of sheep laurel (Kalmia angustifolia L.). Relationships between trap capture of 13 wasp morphospecies and other flowering weeds were also investigated. Most taxa in 1998 were positively associated with one or more of the following flowering plants: bunchberry (Cornus canadensis L.), bush honeysuckle (Diervilla lonicera P. Mill.), dogbane (Apocynum androsaemifolium L.), sheep laurel, and witherod (Viburnum nudum var. cassinoides L.). Similar results were not evident in 1997 because the method used to sample vegetation was not as extensive as that used in 1998. However, sheep laurel was positively associated with the wasp genera Microplitis spp. and Phanerotoma spp. during both years.     

Social recognition in wild fish populations

The ability of animals to gather information about their social and physical environment is essential for their ecological function. Odour cues are an important component of this information gathering across taxa. Recent laboratory studies have revealed the importance of flexible chemical cues in facilitating social recognition of fishes. These cues are known to be mediated by recent habitat experience and fishes are attracted to individuals that smell like themselves. However, to be relevant to wild populations, where animals may move and forage freely, these cues would have to be temporally flexible and allow spatial resolution. Here, we present data from a study of social recognition in wild populations of three-spined sticklebacks (Gasterosteus aculeatus). Focal fish preferentially associated with conspecifics from the same habitat as themselves. These preferences were changed and updated following translocation of the focal fish to a different site. Further investigation revealed that association preferences changed after 3 h of exposure to different habitat cues. In addition to temporal flexibility, the cues also allowed a high degree of spatial resolution: fish taken from sites 200 m apart produced cues that were sufficiently different to enable the focal fish to discriminate and associate with fish captured near their own home site. The adaptive benefits of this social recognition mechanism remain unclear, though they may allow fish to orient within their social environment and gain current local information.     

Reconstructing the deep-branching relationships of the papilionoid legumes

Resolving the phylogenetic relationships of the deep nodes of papilionoid legumes (Papilionoideae) is essential to understanding the evolutionary history and diversification of this economically and ecologically important legume subfamily. The early-branching papilionoids include mostly Neotropical trees traditionally circumscribed in the tribes Sophoreae and Swartzieae. They are more highly diverse in floral morphology than other groups of Papilionoideae. For many years, phylogenetic analyses of the Papilionoideae could not clearly resolve the relationships of the early-branching lineages due to limited sampling. In the eight years since the publication of Legumes of the World, we have seen an extraordinary wealth of new molecular data for the study of Papilionoideae phylogeny, enabling increasingly greater resolution and many surprises. This study draws on recent molecular phylogenetic studies and a new comprehensive Bayesian phylogenetic analysis of 668 plastid matK sequences. The present matK phylogeny resolves the deep-branching relationships of the papilionoids with increased support for many clades, and suggests that taxonomic realignments of some genera and of numerous tribes are necessary. The potentially earliest-branching papilionoids fall within an ADA clade, which includes the recircumscribed monophyletic tribes Angylocalyceae, Dipterygeae, and Amburanae. The genera Aldina and Amphimas represent two of the nine main but as yet unresolved lineages comprising the large 50-kb inversion clade. The quinolizidine-alkaloid-accumulating Genistoid s.l. clade is expanded to include Dermatophyllum and a strongly supported and newly circumscribed tribe Ormosieae. Sophoreae and Swartzieae are dramatically reorganized so as to comprise monophyletic groups within the Core Genistoid clade and outside the 50-kb inversion clade, respectively. Acosmium is excluded from the Genistoids s.l. and strongly resolved within the newly circumscribed tribe Dalbergieae. By providing a better resolved phylogeny of the earliest-branching papilionoids, this study, in combination with other recent evidence, will lead to a more stable phylogenetic classification of the Papilionoideae.     

Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data

Class Demospongiae (phylum Porifera) encompasses most of sponges' morphological and species diversity. It also represents one of the most challenging and understudied groups in animal phylogenetics, with many higher-level relationships still being unresolved. Among the unanswered questions are the most fundamental, including those about the monophyly of the Demospongiae and the relationships among the 14 recognized orders within the class. The lack of resolved phylogeny hampers progress in studies of demosponge biology, evolution and biodiversity and may interfere with the efficient conservation and economic use of this group. We addressed the question of demosponge relationships using mitochondrial genomic data. We assembled a mitochondrial genomic dataset comprising all orders of demosponges that includes 17 new and five previously published complete demosponge mitochondrial genomes. To test for the congruence between mtDNA-based and nuclear rRNA-based phylogenies, we also determined and analyzed 18S rRNA sequences for the same set of species. Our results provide strong support for five major clades within the Demospongiae: Homoscleromorpha=G0 (order Homosclerophorida), Keratosa=G1 (orders Dendroceratida, Dictyoceratida, and Verticillitida), Myxospongiae=G2 (orders Chondrosida, Halisarcida, and Verongida), marine Haplosclerida=G3 and the rest of demosponges=G4 (orders Agelasida, Astrophorida, Hadromerida, Halichondrida, Poecilosclerida, Spirophorida, and freshwater Haploscerida), and for the (G0((G1+G2)(G3+G4)) relationships among these clades. Conversely, mitochondrial genomic data do not support the monophylies of traditional subclasses Ceractinomorpha and Tetractinomorpha as well as several currently recognized orders of demosponges. Furthermore, we demonstrate that mitochondrial gene arrangements can also be informative for the inference of order-level demosponge relationships and propose a modified method for the analysis of gene order data that works well when translocation of tRNA genes are more frequent than other rearrangements.     

Pedigree reconstruction in wild cichlid fish populations

It is common practice to use microsatellites to detect parents and their offspring in wild and captive populations, in order to reconstruct a pedigree. However, correct inference is often constrained by a number of factors, including the absence of demographic data and ignorance regarding the completeness of parental sampling. Here we present a new Bayesian estimator that simultaneously estimates the pedigree and the size of the unsampled population. The method is robust to genotyping error, and can estimate pedigrees in the absence of demographic data. Using a large-scale microsatellite assay in four wild cichlid fish populations of Lake Tanganyika (1000 individuals in total), we assess the performance of the Bayesian estimator against the most popular assignment program, Cervus. We found small but significant pedigrees in each of the tested populations using the Bayesian procedure, but Cervus had very high type I error rates when the size of the unsampled population was assumed to be lower than what it was. The need of pedigree relationships to infer adaptive processes in natural populations places strong constraints on sampling design and identification of multigenerational pedigrees in natural populations.     

Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations

Nucleotide sequences of mitochondrial DNA (mtDNA) cytochrome B gene (1140 bp) and control region (707 bp) were used to determine the phylogenetic relationships among 51 pig samples representing ancient and current varieties of Iberian pigs (26), Spanish wild boars (seven) and other domestic pigs (18) of cosmopolitan (Duroc, Large White, Landrace, Pietrain and Meishan) and local (Spotted Black Jabugo, Basque and Mangalitza) breeds. A neighbour-joining tree constructed from pairwise distances provide evidence of the European origin of both Iberian pigs and Spanish wild boars. The introgression of Asian mtDNA haplotypes in the genetic pool of the Iberian breed seems unlikely. Four estimates of sequence divergence between European and Asian clades were calculated from the two main domains of the D-loop region and the synonymous and nonsynonymous nucleotide substitutions in the cytochrome B gene. The time since the divergence of pig ancestors was estimated at about 600,000 years before present.     

Evidence of melanoma in wild marine fish populations

The increase in reports of novel diseases in a wide range of ecosystems, both terrestrial and marine, has been linked to many factors including exposure to novel pathogens and changes in the global climate. Prevalence of skin cancer in particular has been found to be increasing in humans, but has not been reported in wild fish before. Here we report extensive melanosis and melanoma (skin cancer) in wild populations of an iconic, commercially-important marine fish, the coral trout Plectropomus leopardus. The syndrome reported here has strong similarities to previous studies associated with UV induced melanomas in the well-established laboratory fish model Xiphophorus. Relatively high prevalence rates of this syndrome (15%) were recorded at two offshore sites in the Great Barrier Reef Marine Park (GBRMP). In the absence of microbial pathogens and given the strong similarities to the UV-induced melanomas, we conclude that the likely cause was environmental exposure to UV radiation. Further studies are needed to establish the large scale distribution of the syndrome and confirm that the lesions reported here are the same as the melanoma in Xiphophorus, by assessing mutation of the EGFR gene, Xmrk. Furthermore, research on the potential links of this syndrome to increases in UV radiation from stratospheric ozone depletion needs to be completed.     

Alkaloid variability in Leucojum aestivum from wild populations

Leucojum aestivum (summer snowflake) is a plant species used for the extraction of galanthamine, an acetylcholinesterase inhibitor for the treatment of Alzheimer's disease. Extracts from bulbs collected from 18 Bulgarian populations and from shoot-clumps obtained in vitro from 8 different populations showed variations in their alkaloid composition. Nineteen alkaloids were detected in the studied samples by GC-MS. Typically, the alkaloid fractions of L. aestivum bulbs were dominated by galanthamine type compounds, but lycorine, haemanthamine and homolycorine type alkaloids were also found as dominant compounds in some of the samples. Extracts from the shoot-clumps obtained in vitro were found to contain galanthamine or lycorine as main alkaloids. The galanthamine content ranged from 28 to 2104 microg/g dry weight in the bulbs, and from traces to 454 microg/g dry weight in the shoot-clumps.     

Genetic diversity in wild populations of Paulownia fortunei

The genetic diversities of 16 Paulownia fortunei populations involving 143 individuals collected from 6 provinces in China were analyzed using amplified fragment length polymorphism (AFLP). A total of 9 primer pairs with 1169 polymorphic loci were screened out, and each pair possessed 132 bands on average. The percentage of polymorphic bands (98.57%), the effective number of alleles (1.2138–1.2726), Nei’s genetic diversity (0.1566–0.1887), and Shannon’s information index (0.2692–0.3117) indicated a plentiful genetic diversity and different among Paulownia fortune populations. The genetic differentiation coefficient between populations was 0.2386, while the gene flow was 1.0954, and the low gene exchange promoted genetic differentiation. Analysis of variance indicated that genetic variation mainly occurred within populations (81.62% of total variation) rather than among populations (18.38%). The 16 populations were divided by unweighted pair-group method with arithmetic means (UPGMA) into 4 groups with obvious regionalism, in which the populations with close geographical locations (latitude) were clustered together.     

Testing evolutionary theories of aging in wild populations

Classic theories for the evolution of senescence predict that rates of aging should be highest in populations in which extrinsic mortality is high. This predication is called into question in new work by David Reznick and co-workers, who found that guppies Poecilia reticulata derived from natural populations with high levels of predation live the longest in the laboratory. This study illustrates that the effect of mortality on aging might depend on how we define aging, and on the particular cause of increased mortality.     

Phylogenetic relationships among wild and cultivated Tartary buckwheat (Fagopyrum tataricum Gaert.) populations revealed by AFLP analyses

Phylogenetic relationships among cultivated landraces and natural populations of wild subspecies of Tartary buckwheat were investigated at the individual level by constructing a phylogenetic tree based on amplified fragment length polymorphism (AFLP) markers. Seven individuals from seven cultivated landraces and 35 individuals from 21 natural populations of wild subspecies were utilized for AFLP analyses. Three groups were recognized: (1) all cultivated landraces and wild subspecies from northern Pakistan, central and eastern Tibet, and northwestern Yunnan, (2) wild subspecies from central and southern Sichuan, (3) wild subspecies from northern Sichuan and eastern Tibet. It was concluded that cultivated Tartary buckwheat probably originated in eastern Tibet or northwestern Yunnan in China.     

Original birthplace of cultivated common buckwheat inferred from genetic relationships among cultivated populations and natural populations of wild common buckwheat revealed by AFLP analysis

The genetic relationships among seven cultivated populations and eight natural populations of wild common buckwheat were analyzed using amplified fragment length polymorphism (AFLP). The genetic distance was estimated for each pair of the 15 populations based on the AFLP data, and a phylogenetic tree was constructed using the neighbor-joining (NJ) method based on the genetic distance. All the cultivated populations were grouped in a cluster. The natural populations were grouped into two clusters composed of (1) the Sanjiang group (three populations from eastern Tibet and one population from Adong village of Yunnan province) and (2) two populations from Yunnan province and two populations from Sichuan province. The Sanjiang group is more closely related to cultivated populations. These results indicate that the direct ancestor of common buckwheat was natural populations of wild common buckwheat from the Sanjiang area.     

Kin assortment in juvenile shoals in wild guppy populations

Grouping provides many potential benefits to individuals in terms of foraging and anti-predator protection. However, it has been suggested that individuals could gain additional benefits in terms of indirect fitness by grouping with kin. Surprisingly, the genetic composition of wild fish shoals and the importance of kin-associated shoaling remain poorly understood. The Trinidadian guppy (Poecilia reticulata) has life history traits that might promote kin structure of shoals such as internal fertilisation and small brood size in contrast to many other fish species. Even though previous studies did not find any indication of kin structure in shoals of adult guppies, it is possible that related juveniles remain together in shoals, partly because of lower mobility and because the advantages of kin association may change with age. Using 10 microsatellite markers, we conducted a genetic analysis on 40 shoals from four populations. Pair-wise relatedness was inferred using a modified version of the software package COLONY and permutation tests were conducted to test the hypothesis that kin occur together in juvenile shoals more often than expected by chance. The frequency of sib dyads among juveniles within shoals was significantly larger than that between shoals in two high predation populations but not in two low predation populations. This finding contributes to the understanding of factors underlying shoal composition and highlights the potential of recent methodological advances for detecting such relationships.     

Phylogenetic relationships and genetic polymorphisms in wild Indian mice

Randomly amplified polymorphic DNA (RAPD) analysis was used to examine the extent of variability in 11 Indian wild derived commensal house mice (Mus musculus) populations and compared with inbred strains of musculus and domesticus subspecies as well as commonly used laboratory inbred strains C57BL/6J and DBA/2J. Arbitrary designed 10 mer oligonucleotide primers with 60-70% (G+C) content were used to amplify DNA template. Out of 52 primers screened initially on the laboratory strains, 20 were selected for analysis on the basis of amplification product in the size range of 200-1400 bp. Among 353 total polymorphic bands, 220 bands (64%) were found to be polymorphic in Indian wild mice, 85 bands (25%) in wild derived inbred strains and 37 bands (11%) in laboratory mice strains. The amplification patterns produced by primers were statistically analysed by Jaccard's similarity coefficient the value of which ranged from 0.56 to 0.80. High level of genetic diversity was seen in the Indian wild mice populations as compared to the controls. The UPGMA phenogram grouped mice population into two major clusters except Bikaner [BIK], Bilaspur [BIL] and Ranikhet [RK] populations which were placed outside the close-knit clusters. Inspite of low values of bootstrap estimates obtained by Wagner and Dollo parsimony analysis, the results were comparable with UPGMA phenogram when constitution of the populations in the major cluster was considered. Indian mice populations appeared to be diverse from laboratory inbred mice strains.