Reduced genetic variation in Norwegian Peregrine Falcons Falco peregrinus indicated by minisatellite DNA fingerprinting

The Scandinavian Peregrine Falcon Falco peregrinus population went through a severe population bottleneck during the second half of the twentieth century, and was almost extinct during the 1970s. This event may have reduced the amount of genetic variation in the population. With this background, a comparative study, using multilocus, minisatellite DNA fingerprinting, was carried out on broods of the Peregrine Falcon, the Merlin Falco columbarius and the Eurasian Hobby Falco subbuteo from south-east Norway. Band-sharing analysis of DNA fingerprints was used to test whether broods of Peregrine Falcons showed a greater between-nest similarity in their fingerprint profiles than did broods of the two congeneric species breeding in the same region, which have not undergone any recent population bottlenecks. The results show that broods of Peregrine Falcons were significantly more similar to each other genetically than were broods of either Merlins or Eurasian Hobbies. Furthermore, there was a positive correlation between the similarity in minisatellite DNA and the similarity in a set of 11 microsatellite loci analysed for a subset of the Peregrine Falcon samples. The correlation supports the assumption that minisatellite fingerprints provide a reliable indicator of overall genetic similarity, i.e. relatedness, between breeding pairs in the population. Hence we can conclude that broods of Peregrine Falcons were genetically more related to each other than were broods of the other two species. The high similarity in minisatellite DNA between broods indicates a loss of genetic variation in the Peregrine Falcon population caused by the bottleneck, but this explanation can only be verified through a comparative genetic study of individuals sampled before and after the bottleneck event.     

From genes to geography: a genetic similarity rule for arthropod community structure at multiple geographic scales

We tested the hypothesis that leaf modifying arthropod communities are correlated with cottonwood host plant genetic variation from local to regional scales. Although recent studies found that host plant genetic composition can structure local dependent herbivore communities, the abiotic environment is a stronger factor than the genetic effect at increasingly larger spatial scales. In contrast to these studies we found that dependent arthropod community structure is correlated with both the cross type composition of cottonwoods and individual genotypes within local rivers up to the regional scale of 720,000 km(2) (Four Corner States region in the southwestern USA). Across this geographical extent comprising two naturally hybridizing cottonwood systems, the arthropod community follows a simple genetic similarity rule: genetically similar trees support more similar arthropod communities than trees that are genetically dissimilar. This relationship can be quantified with or without genetic data in Populus.     

Genetic diversity in populations of a freshwater ciliate

RAPD fingerprinting with nine different primers revealed that all of 18 E. aediculatus isolates from nine ponds and streams in western Germany, France and the U.S.A. were genetically different. The extent of genetic similarity between genotypes from different waters did not show a significant relationship with the geographical distance among habitats, although genotypes isolated from the same habitat showed a higher genetic similarity than genotypes isolated from different habitats. Phylogenetic analyses of RAPD patterns indicate a separation of E. aediculatus strains into subgroups within one species, but all strains were genetically more similar to one another than to strains from two other Euplotes species. Crossings of the different E. aediculatus strains revealed they belonged to seven mating types of one gene pool. The high genetic diversity observed is explained by a frequent occurrence of conjugation in the studied populations.     

Molecular diversity and relationships among Elymus trachycaulus, E. subsecundus, E. virescens, E. violaceus, and E. hyperarcticus (Poaceae: Triticeae) as determined by amplified fragment length polymorphism.

Morphological similarity among E. trachycaulus, E. virescens, E. violaceus, and E. hyperarcticus has often been noted. Taxonomists have tried to discriminate among these taxa using morphological characters and a number of different relationships among them have been suggested. However, the genetic relationships among these taxa are still unknown. AFLP analysis was used to characterize the molecular diversity of these taxa and to examine genetic relationships among them. A high degree of genetic identity was apparent among 7 accessions of E. virescens. The similarity values ranged from 0.90 to 0.99 with an average of 0.94. The mean similarity values among 3 E. hyperarcticus and among 5 E. violaceus accessions were 0.84 (0.81-0.87) and 0.77 (0.66-0.90), respectively. The similarity values among 17 E. trachycaulus accessions ranged from 0.49 to 0.92 with an average of 0.75. The 5 accessions of E. subsecundus displayed high variation, with similarity values between 0.52 and 0.68 and a mean value of 0.59. Both maximum-parsimony (MP) and neighbor-joining (NJ) analyses showed that all 7 accessions of E. virescens formed a clade, indicating a monophyletic origin. On the other hand, Elymus trachycaulus, E. subsecundus, and E. violaceus were each paraphyletic and separated into different genetically distinct groups. Among these 5 taxa, E. virescens was genetically similar to E. trachycaulus, and E. violaceus was genetically similar to E. hyperarcticus.     

Preliminary study on genetic variability of Dicrocoelium dendriticum determined by random amplified polymorphic DNA

Genetic variability of adult specimens of Dicrocoelium dendriticum has been studied using random amplified polymorphic DNA (RAPD). The worms were collected from the infected livers of different sheep from several localities in León province (NW Spain). DNA fragments were amplified by means of decamer primer oligonucleotides of arbitrary sequence. Some primers produce complex and highly variable patterns of amplified DNA in D. dendriticum. Intra- and inter-population genetic variability of adult parasites were analyzed, scoring polymorphic and monomorphic reproducible bands by means of the Jaccard similarity, and dendrograms showing genetic relationships between individuals were obtained using the FITCH method. Genetic variability seems to be high in this parasite and genetic similarity within a population (worms infecting a single animal) is similar to the average similarity between worms from different sheep. These results suggest that each sheep is infected by numerous genetically different parasites from one or more populations of infected ants.     

Previously unknown and highly divergent ssDNA viruses populate the oceans

Single-stranded DNA (ssDNA) viruses are economically important pathogens of plants and animals, and are widespread in oceans; yet, the diversity and evolutionary relationships among marine ssDNA viruses remain largely unknown. Here we present the results from a metagenomic study of composite samples from temperate (Saanich Inlet, 11 samples; Strait of Georgia, 85 samples) and subtropical (46 samples, Gulf of Mexico) seawater. Most sequences (84%) had no evident similarity to sequenced viruses. In total, 608 putative complete genomes of ssDNA viruses were assembled, almost doubling the number of ssDNA viral genomes in databases. These comprised 129 genetically distinct groups, each represented by at least one complete genome that had no recognizable similarity to each other or to other virus sequences. Given that the seven recognized families of ssDNA viruses have considerable sequence homology within them, this suggests that many of these genetic groups may represent new viral families. Moreover, nearly 70% of the sequences were similar to one of these genomes, indicating that most of the sequences could be assigned to a genetically distinct group. Most sequences fell within 11 well-defined gene groups, each sharing a common gene. Some of these encoded putative replication and coat proteins that had similarity to sequences from viruses infecting eukaryotes, suggesting that these were likely from viruses infecting eukaryotic phytoplankton and zooplankton.     

Odour–genes covariance within a natural population of subterranean Spalax galili blind mole rats

Previous research, using habituation techniques with multiple rodent species as subjects, has demonstrated (from kin to across species) the greater perceptual similarity in the qualities of individual odours of more closely genetically related individuals ('odour–genes covariance', abbreviated 'OGC'). This predictable relationship between individual genotypes and individual odours has only been assessed in rodents in which the genetic similarities and dissimilarities are known either through laboratory breeding or by selecting odour donors from different populations or species. To study OGC within a natural population of rodents, we genotyped Spalax galili blind mole rats using ten microsatellite markers, and conducted pairwise genetic distance comparisons to estimate genetic similarity and to calculate the relatedness coefficient between pairs of individuals. We then used habituation-generalization techniques to assess whether perceived odour similarities covaried with the genetic similarities we had identified. Indeed, animals treated odours from genetically closer donors as more similar than odours from less genetically similar donors. The results suggest an accurate and subtle ability to resolve genetically determined odour distinctions among familially unrelated animals within a population. Graded differential responses to conspecific odours based on degrees of similarity between other individuals' odours and one's own have been demonstrated in kinship and species discriminations and preferences. The evidence presented here provides the basis for hypothesizing a similar process that could promote optimal outbreeding and inclusive fitness within populations of conspecifics. The evolutionary implications of these findings are discussed.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 483–490.     

Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour

Subpopulation genetic structure was studied in a population of the short-lived perennial plant Alkanna orientalis from the Sinai Desert, Egypt. The population investigated was subdivided for sampling into four subpopulations, which were located within three steep-sided wadis and a central plain area. Results from previous studies suggested that bee pollinator behaviour was likely to cause limited gene dispersal within the population and that subpopulations might have diverged from each other genetically. Seven RAPD primers were used to detect polymorphisms in the population. Differences between sub-populations in fragment frequency were found for several of the 45 polymorphic RAPD fragments scored. Population subdivision was evident from cluster analysis, and an analysis of genetic distances showed that there was significant genetic differentiation between all subpopulations. Nevertheless, more extensive gene flow appears to take place within the population than was expected, as demonstrated by a higher level of genetic similarity between subpopulations from two of the narrow wadis and the interconnecting plain. It is suggested that seed transport mediated by periodic flash floods is responsible for this pattern.     

Odour-genes eovariance and differential investigation of individual odours in the Mus species complex

Previous research using habituation techniques has demonstrated that greater genetic similarity between two individuals is associated with more similarity in the qualities of their individual odours ('odour-genes eovariance'). We assessed odour similarities across species in two pairs of genetically close species within the Mus species complex (M. musculus and M. domesticus; M. spicilegus and M. macedonicus). Subjects treated odours within each species pair as similar compared with an odour from the other species pair. Subjects also treated odours of M. spicilegus males from the same population as similar compared with the odour of M. spicilegus males from a different population. This confirms odour-genes eovariance across species and within populations and also supports previous findings that odour similarities are more salient than specific odour markers. When adult males were presented with odours of females from two different heterospecific species, subjects spent more time investigating the odour from his own species pair than the other species pair, indicating greater interest in the odour of the closer heterospecific and demonstrating that odour-genes eovariance is reflected in behavioural responses to odours. Implications of odour-genes eovariance as a basis for identifying degrees of genetic relatedness of unfamiliar individuals through similarities in individual odours are discussed.     

Genetic variability of New Zealand seagrass (Zostera muelleri) assessed at multiple spatial scales

We conducted RAPD analyses at multiple spatial scales to contribute to the conservation and future restoration of New Zealand's seagrass, Zostera muelleri Irmisch ex Asch. (Zosteraceae). Initially we focused on fine-scale genetic variation within two estuaries on the North Island, one on the East coast the other on the West coast. Within each estuary individuals were genetically similar, however, there was clear genetic separation between the two sites (genetic distance D = 0.2965). Genetic variation within a sampling location (m scale) was similar to that observed among sampling locations (km scale) within a site (21% and 28%, respectively) and smaller than that observed between sites (51%). We then expanded our sampling to include a further six populations distributed across almost the entire latitudinal (ca. 15°) gradient of the North and South Islands. At this scale genetic differences were closely correlated with coastal currents. There was a clear separation between North Island and South Island populations and further separation between the East and West coast populations of each Island. Sites located along the same section of coastline were more genetically similar than those from the opposite coast and other Island. Genetic similarity was highest within each of the sites, indicating a low degree of gene flow between populations. We recommend that any future restoration and conservation projects use only locally eco-sourced materials for population augmentations.     

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are

There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records. This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms. Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis. The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are. Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are. The findings here do not conform to these predictions. Neanderthals are more distant to chimpanzees and gorillas than modern humans are. Dinosaurs are more distant to frogs than extant birds are. Mastodons are more distant to opossums than other placental mammals are. The genetic distance between dinosaurs and mastodons is greater than that between extant birds and mammals. Therefore, while the molecular clock hypothesis is consistent with some data from extant organisms, it has yet to find support from ancient fossils. Far more damaging to the hypothesis than data from extant organisms, which merely question the constancy of mutation rate, the study of ancient fossil organisms here challenges for the first time the fundamental premise of modern evolution theory that genetic distances had always increased with time in the past history of life on Earth.     

Phenotypic and genetic divergence among island populations of sika deer (<Emphasis Type="Italic">Cervus nippon</Emphasis>) in southern Japan: a test of the local adaptation hypothesis

Transplant and common garden experiments have been used in studies on local adaptation, but are difficult to be conducted for large animals with long life span. A previous study on the southern Japanese islands demonstrated that relative limb lengths of sika deer (Cervus nippon) were short on islands with steep slopes. We hypothesized that this morphological variation was evidence for local adaptation, and tested this hypothesis by comparing phenotypic divergence with neutral genetic divergence among eight populations of the sika deer in the southern Japanese islands. Divergence patterns differed between the phenotypic and neutral genetic features. Genetic similarity was high among individuals on Kyushu (OI, KGS, and KGK). Individuals on Tanegashima (TN) and Yakushima (YK) also constituted a group, whereas individuals on Tsushima (TS), Wakamatsujima (WM), and Kuchinoerabujima (KE) formed a genetically distinct group. Phenotypic data indicated that individuals from TS, OI, KGS, and KGK exhibited similarity, whereas individuals on YK formed an isolated group that was separated from the other populations. The degree of phenotypic divergence was larger than that of neutral genetic divergence between TN and YK. These results suggest that divergent selection worked between two of the eight island populations (TN and YK). The morphological trait of captive-bred individuals from TN and YK, which had never experienced their original environments, retained their original morphological features. By combining the results of multiple analyses, we found that the difference in relative limb length between the two populations was consistent with local adaptation hypothesis, although conclusive results were not obtained for the other populations.     

Is Mate Choice in Humans MHC-Dependent?

In several species, including rodents and fish, it has been shown that the Major Histocompatibility Complex (MHC) influences mating preferences and, in some cases, that this may be mediated by preferences based on body odour. In humans, the picture has been less clear. Several studies have reported a tendency for humans to prefer MHC-dissimilar mates, a sexual selection that would favour the production of MHC-heterozygous offspring, who would be more resistant to pathogens, but these results are unsupported by other studies. Here, we report analyses of genome-wide genotype data (from the HapMap II dataset) and HLA types in African and European American couples to test whether humans tend to choose MHC-dissimilar mates. In order to distinguish MHC-specific effects from genome-wide effects, the pattern of similarity in the MHC region is compared to the pattern in the rest of the genome. African spouses show no significant pattern of similarity/dissimilarity across the MHC region (relatedness coefficient, R = 0.015, p = 0.23), whereas across the genome, they are more similar than random pairs of individuals (genome-wide R = 0.00185, p<10(-3)). We discuss several explanations for these observations, including demographic effects. On the other hand, the sampled European American couples are significantly more MHC-dissimilar than random pairs of individuals (R = -0.043, p = 0.015), and this pattern of dissimilarity is extreme when compared to the rest of the genome, both globally (genome-wide R = -0.00016, p = 0.739) and when broken into windows having the same length and recombination rate as the MHC (only nine genomic regions exhibit a higher level of genetic dissimilarity between spouses than does the MHC). This study thus supports the hypothesis that the MHC influences mate choice in some human populations.     

Models of spouse influence and their application to smoking behavior

Abstract

Probability models are used to study changes which take place in smoking behavior of married couples over time, especially changes which take place from baseline levels existing at the time the couples first began dating each other. The models focus on the observable effects or outcomes of spouse influence rather than on actual mechanisms, which are remote from our observations. Our analysis of smoking behavior suggests that the spouses do not change independently. Moreover, there is a suggestion that spouses who are initially alike tend either to be more stable in their behavior or more likely to return to their initial status than spouses who are initially dissimilar. This process could tend to perpetuate initial similarity, and therefore stabilize spouse correlation estimates, or may increase levels of similarity if there is a background of considerable cultural change.     

Mutant allele frequencies in domestic cat populations in Arkansas and Tennessee

We conducted surveys of mutant allele frequencies of four cat populations in Arkansas and Tennessee during 2002. Our calculations and analyses support that Southwestern cat populations were relatively more genetically similar to each other than compared to cat populations in other areas of North America. However, the cat population of Fort Smith is slightly different from the other cat populations studied in the Southwestern United States. Although there is a clear significant spatial geographic pattern for many mutant coat allele frequencies in the United States and Canada cat populations (d, l, S, and W), our results revealed that there is not a significant isolation-by-distance model affecting these cat populations. Our data also support the historical migration hypothesis because our calculated allele frequencies were genetically similar to cat populations located in ancestral areas of Europe. Different phenograms, including new European cat genetic profiles, showed that the Southwestern cat populations studied are of a clear British origin. Therefore, migration routes of early Arkansas and Tennessee settlers help explain the similarities of allele frequencies among domestic cat populations.     

Genetic similarity among cultivars of Phyllostachys pubescens

Phyllostachys pubescens is the most important economic bamboo species in China, which grows widely in the South of China. There are more than ten cultivars in this species but their genetic relationship still remains unknown. We used both amplified fragment length polymorphism (AFLP) and inter-simple sequence repeat (ISSR) techniques to determine genetic similarity among ten cultivars of P. pubescens and two related species. Eight hundred and twenty seven bands, in which 495 are polymorphic, were detected using 15 pairs of AFLP primers whereas total 231 bands, in which 154 bands are polymorphic, were scored using 16 ISSR primers. Statistic analysis showed that the genetic similarity matrices obtained from these two sets of molecular markers had a significant correlation (R = 0.959, P = 0.013). The dendrogram generated with AFLP and ISSR markers could clearly genetically identify ten cultivars of P. pubescens that had high similarity with genetic distances ranging from 0.023 to 0.108, and could be divided into three groups based on their genetic variation and similarity. Our results suggest that these molecular markers are useful to genetically classify cultivars or varieties of a species, particularly a bamboo species.     

Dispersal patterns of Lonicera periclymenum determined by genetic analysis

Colonization of Lonicera periclymenum L. (honeysuckle) was studied by RAPD analysis of young ramets in two woodlots planted 20 years ago, and in all ramets in older woodlots within a range of 1 km. Mature ramets that climbed in a particular tree always belonged to one individual. Twenty-five percent of the mature individuals had reproduced vegetatively to other trees or patches nearby, which indicates that the larger part of reproduction is sexual. Some young plants that were growing at close distances from each other were genetically highly similar and shared high similarities to the same mature plants. They may be the product of one dispersal event. Detection of parents of young individuals by exclusion was not successful, because of the dominant nature of the bands. Average distances from young plants to genetically most similar mature plants were variable, due to the small number of colonization events. However, four ways of analysis of genetic similarity among all individuals indicated that exchange of genetic material by seed and pollen occurs to a large extent over small distances and within woodlots: (i) using the Mantel test, pairs of individuals with highest similarity were found significantly more often in the same woodlot than in different woodlots; (ii) genetic similarities between individuals decreased significantly with geographical distance, but only for distances up to 300 m; (iii) individuals of woodlots in the Western part of the study area were hardly related to individuals in the Eastern part of the study area, a distance of 2–3 km; (iv) Φ_ST in the study area was 0.186, indicating a limited gene flow between woodlots. These results are consistent with the dispersal distance as estimated from the average distance between colonized woodlots and the nearest occupied old woodlot in earlier research.     

Geographical variation and diversification in the flightless leaf beetles of the Chrysolina angusticollis species complex (Chrysomelidae, Coleoptera) in northern Japan

Geographical variation and differentiation of flightless leaf beetles of the Chrysolina angusticollis species complex were analysed. Nine morphological groups were recognized on the basis of metric characters relating to body size, shape of hind wing and shape of male genitalia, and binary characters relating to females' elytral surface and larval pubescence. The nine groups were essentially parapatric or allopatric to each other. Five groups occupied a continuous geographical range each, whereas another four groups were disjunctively distributed. Morphometric distance and geographical distance between populations were significantly correlated. Analyses based on 13 allozyme loci demonstrated that six out of the nine morphological groups were further divided into more than one genetically distinct group each. Genetic similarity between populations was significantly correlated with morphometric similarity and geographical closeness. Disjunctively distributed populations of a single morphological group more often resembled geographically adjacent populations of different morphological groups than geographically remote populations of the same group. In a morphological group that occupied a wide continuous range, remote populations substantially differed genetically from each other. The results suggest that there exist at least 19 morphologically and/or genetically differentiated units in the C. angusticollis complex in northern Japan. The C. angusticollis complex is likely a superspecies composed of a number of semispecies. We postulate that the diversification of this species complex might have resulted from the repeated range contraction and expansion during the ice ages. Movement of tension zones that separate two adjacent forms might contribute to enhance their geographical differentiation.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 557–578.     

Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers

Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.     

Conservation genetics of the endangered endemic Hawaiian genus Brighamia (Campanulaceae)

The endemic Hawaiian genus Brighamia (Campanulaceae) comprises two federally endangered, morphologically similar species, B. insignis from Kaua`i and Ni`ihau and B. rockii from Moloka`i. To assist the design of conservation management programs for these taxa, isozyme analyses were performed to assess the levels of genetic diversity at the population and species levels, including comparisons within and among seven natural populations and one ex situ collection each of B. insignis and B. rockii. Our sampling (N = 80) represents ~41% of all known individuals in the wild. Isozyme analyses revealed levels of genetic variation comparable to those reported for other Hawaiian flowering plant taxa but low levels of genetic variation at the population and species levels when compared to flowering plants in general. Ex situ individuals (N = 61) were genetically representative of natural populations and hence may appropriately serve as stock for population augmentations. The two morphologically similar Brighamia species were highly distinct genetically. The combination of morphological and ecological similarity with allozymic dissimilarity observed in Brighamia is unique among the Hawaiian taxa studied to date.