Age determination in roe deer — a new approach to tooth wear evaluated on known age in dividuals

A novel, simple, and objective method is presented for ageing roe deerCapreolus capreolus (Linnaeus, 1758) evaluated on 471 lower jaws from roe deer of known age (351 with permanent premolars). It is based on tooth eruption patterns and presence/absence of wear characters in jaws from roe deer integrated in a scoring system. Permanent cheek teeth emerge in May–July in the year af ter birth, which enables precise age determination of individuals with deciduous premolars. For individuals with permanent cheek teeth, the method provides the correct age for all individ uals younger than 13 months and > 80% of all individuals between 13 and 24 months old. For older in dividuals the accuracy decreases, but decent accuracy is achieved to the age of 48 months. Males have higher wear rates than females corroborating recent documentation of sex-specific life history tactics in ungulates. The data originate from two separated Danish roe deer populations exposed to contrasting habitats, but no difference in wear rate is found between populations. Thus, previous concern about the validity of age determination methods based on tooth wear may have been overstated. The findings demonstrate that objective measures of tooth wear can provide the basis for age determination in ungulate species that are otherwise difficult to age.     

Cryptic species of cardinalfish with evidence for old and new divergence

Larval dispersal and limited knowledge of physical boundaries challenge our understanding of the processes that drive genetic divergence and potential speciation in the marine environment. Divergence, both within and between populations of marine taxa, is not uncommon, but spatial and temporal stability of observed genetic structure is not well known. Previously, we detected large genetic differences among populations of the cardinalfish species Ostorhinchus doederleini inhabiting adjacent coral reefs. Here, we determined the spatial and temporal persistence of these genetic structures over the course of ten consecutive generations. Using microsatellite markers, we detected large changes (genetic population distance, D _est, ranged from 0.04 to 0.46) in the genetic structure in some years, but some reefs maintained the same populations for nearly all sampling years. As this species’ life span does not exceed 1 yr, persistence of distinct reef populations suggests natal homing. Mitochondrial identity based on two mtDNA markers corroborates the nuclear genetic evidence for genetic differences large enough to constitute different clades and even cryptic species in O. doederleini, which, based on gross morphology, was thought to be a single taxon. Habitat specialization was observed in one clade that exclusively inhabited reef lagoons, while all clades could be observed on reef slopes. We suggest that local habitat recognition combined with local population recognition and selection against hybrids can form barriers that maintain a cryptic species complex.     

Affinities between contemporary and skeletal Jewish and non-Jewish groups based on tooth morphology

Samples from five Jewish and six non-Jewish populations were compared in terms of the frequencies of 19 dental morphological variables. All but one of the samples came from Europe, North Africa, or the Middle East. Nine were from contemporary populations, and two were skeletal. Of the skeletal groups, one was Jewish, excavated on Mount Zion, Jerusalem, and dated at around 3,000 years old; and the other non-Jewish, excavated on the east coast of Australia, and dated at between 1,000 and 200 years old. Assessment of affinity between the different groups was based on smallest space analysis and cluster analysis. The results demonstrated relative proximity of the Jewish groups (with one exception), despite the fact that they came from a wide geographical area. In particular, the sample from Mount Zion showed greater affinity with three of the four living Jewish populations than with most non-Jewish groups. The skeletal Australian sample formed a cluster of its own, distinct from all the other groups. For six of the groups, the relationships based on tooth morphology showed good correspondence with known relationships based on single locus polymorphisms. The similarity of the Jewish groups to each other in terms of both tooth morphology and single locus polymorphisms was of special interest, since differences in other morphological and anthropometric characteristics, thought to be the result of selection, are known to exist between the Jewish populations.     

Ecotypes and genetic structure of Rhinanthus alectorolophus (Orobanchaceae) in southwestern Germany

European annual species of the genus Rhinanthus often exhibit seasonal ecotypic variation, a phenomenon also known from related genera of hemiparasitic Orobanchaceae. Populations with different flowering times exist, correlated with differences in a number of morphological characters. The present study evaluates the correlation of morphological characters and genetic differentiation of populations of Rhinanthus alectorolophus. Thirty-nine populations of three different subspecies from southwestern Germany were sampled. A total of 798 individuals were used for morphological analyses and 187 of these for AFLP analyses. Principal component analysis showed that morphological variation is mostly continuous. In a discriminant analysis based on morphological characters, only 89.7 % of all individuals were correctly assigned to their previously determined subspecies, indicating that subspecies identification is ambiguous for some populations. Using AFLP data and Bayesian assignment analysis, the sampled individuals could be grouped in three genetic clusters which do not correspond to the three subspecies. Instead, the clustering shows a clear geographic pattern and a Mantel test likewise revealed a significant correlation between genetic and geographic distances. Correlations of genetic distances with differences in morphological characters were weak and mostly insignificant. The results indicate that the subspecies of R. alectorolophus do not form discrete entities and that the character combinations distinguishing them are homoplastic.     

Morphological and Genetic Traits of Pikeperch <Emphasis Type="Italic">Sander lucioperca</Emphasis> of the Volga–Akhtuba Aquatic System: on the Spatial Structure of a Species in the Lower Volga Basin

Characters of external morphology and ten loci of microsatellite DNA are investigated in pikeperch Sander lucioperca from the Volga–Akhtuba water system on sites of the Akhtuba and the Volga situated 150 km from the beginning of the Volga Delta and 300 km from the dam of the Volgograd Power Plant. Significant differences in plastic characters are found between samples from the Akhtuba and the Volga. Differences are also found in the genetic diversity of pikeperch: the found alleles are more numerous in most loci and the mean value of allele diversity is higher in the sample from the Akhtuba. At the same time, the calculated distance between samples of pikeperch is not certain. However, this may follow from limitations accompanying the calculation of differentiation parameters. The allele diversity and heterosis of pikeperch from the Akhtuba and the Volga are higher than those in populations from the Baltic basin and Western Europe. The known differences in external morphology and in genetic characters indicate to the present day partial separation of the Volga pikeperch from the Akhtuba pikeperch and that the found polymorphism of morphological and genetic characters reflects the ecological plasticity of the species, which is an adaptive response to changing environmental conditions.     

Morphological divergence of lake and stream Phoxinus of Northern Italy and the Danube basin based on geometric morphometric analysis

Minnows of the genus Phoxinus are promising candidates to investigate adaptive divergence, as they inhabit both still and running waters of a variety of altitudes and climatic zones in Europe. We used landmark‐based geometric morphometric methods to quantify the level of morphological variability in Phoxinus populations from streams and lakes of Northern Italy and the Danube basin. We analyzed body shape differences of populations in the dorsal, lateral, and ventral planes, using a large array of landmarks and semilandmarks. As the species identification of Phoxinus on morphological characters is ambiguous, we used two mitochondrial genes to determine the genetic background of the samples and to ensure we are comparing homogenous groups. We have found significant body shape differences between habitats: Minnow populations inhabiting streams had a deeper body and caudal peduncle and more laterally inserted pectoral fins than minnows inhabiting lakes. We have also found significant body shape differences between genetic groups: Italian minnows had deeper bodies, deeper and shorter caudal peduncles, and a shorter and wider gape than both groups from the Danube. Our results show that the morphology of Phoxinus is highly influenced by habitat and that body shape variation between habitats was within the same range as between genetic groups. These morphological differences are possibly linked to different modes of swimming and foraging in the respective habitats and are likely results of phenotypic plasticity. However, differences in shape and interlandmark distances between the groups suggest that some (though few) morphometric characters might be useful for separating Phoxinus species.     

Density dependence and population differentiation of genetic architecture in Impatiens capensis in natural environments

We identified environment-dependent constraints on the evolution of plasticity to density under natural conditions in two natural populations of Impatiens capensis. We also examined the expression of population divergence in genetic variance-covariance matrices in these natural environments. Inbred lines, originally collected from a sunny site with high seedling densities and a woodland site with low seedling densities, were planted in both original sites at natural high densities and at low density. Morphological and life-history characters were measured. More genetic variation for plastic responses to density was expressed in the sun site than in the woodland site, so the evolutionary potential of plasticity was greater in the sun site. Strong genetic correlations between the same character expressed at different densities and correlations among different characters could constrain the evolution of plasticity in both sites. Genetically based trade-offs in meristem allocation to vegetative growth and reproduction were apparent only in the high-resource environment with no overhead canopy and no intraspecific competition. Therefore, genetic constraints on the evolution of plasticity depended on the site and density in which plants were grown, and correlated responses to selection on plastic characters are also expected to differ between sites and densities. Population differentiation in genetic variance-covariance matrices was detected, but matrix structural differences, as opposed to proportional differences, were detected between populations only in the sun site at natural high density. Thus, population divergence in genetic architecture can occur rapidly and on a fine spatial scale, but the expression of such divergence may depend on the environment.     

The impact of species-specific traits and phylogenetic relatedness on allozyme diversity inCarex sect.Phyllostachys (Cyperaceae)

Allozyme variation was examined inCarex sect.Phyllostachys (Cyperaceae) to study the effects of species-specific traits and phylogenetic relatedness on genetic structure. In contrast to the findings of similar studies, genetic variability in thePhyllostachys is poorly correlated with geographic range and putative differences in breeding systems (as inferred from morphology). This suggests that other patterns of evolution, colonization, and gene flow characterize the species found in this section. Fixation indices are negative for all populations suggesting that mechanisms such as disassortative mating and selection are maintaining heterozygous excess within populations. Closely related taxa often exhibit different genetic variability statistics. In some instances, however, clades (e.g.C. jamesii andC. juniperorum) display very similar levels of genetic variability despite marked differences in species-specific traits. Recent speciation coupled with the ability to maintain historical levels of variation within populations may be factors accounting for this phenomenon. Contrary to similar studies, species restricted to known glacial refugia have lower genetic diversity than those species that underwent mass migrations in response to deglaciation. Narrowly endemic species were found to partition their genetic diversity within, as opposed to between populations. The opposite trend was evident in wider ranging congeners.     

Morphological differentiation among local trout (Salmo trutta) populations

The trout (Salmo trutta) has been divided into three forms: sea-run trout, lake-run brown trout, and resident brown trout. They differ in their living environment, migratory behaviour, growth and appearance. As local trout populations are often isolated, and gene flow between them is minimal, differentiation between populations can be expected. The morphology of 1-year-old trout from ten populations representing all three forms was studied in a common-garden experiment. The fish were reared under similar environmental conditions, and 20 morphometric characters were measured from each individual fish. Marked morphological differentiation was found, and differences between populations were greater than differences between forms. The results suggest that the differences have a genetic basis, and they are likely to indicate adaptation to local environmental conditions in the native habitat of the trout.     

DIFFERENTIATION AMONG NINE POPULATIONS OF PHLOX. I. ELECTROPHORETIC AND QUANTITATIVE VARIATION

The organization of genetic variation in Phlox drummondii was investigated using both allozyme electrophoresis and quantitative genetics. Variation at five polymorphic enzyme loci was characterized in nine populations, and variation in 16 morphological and life-history characters was examined using an analysis of full- and half-sibs in seven populations. Significant levels of genetic variation were found at enzyme loci and for metric characters. Significant heritabilities were observed for 15 of the 16 characters examined. Genetic differences among populations were revealed both by Nei's genetic distance and by phenotypic differences, summarized by discriminant analysis. Partitioning variance in allozyme frequencies among hierarchical levels of genetic organization indicated that 94% of this variance lay within populations, 4% between populations within varieties, and 2% between varieties. Partitioning phenotypic variance for metric characters indicated that 73% lay within populations, 24% lay between populations within varieties, and 3% lay between varieties. Thus, both electrophoretic and metric characters indicated that despite extensive genetic differentiation among populations, most of the evolutionary potential of the species lies within populations.     

Morphometrics Parallel Genetics in a Newly Discovered and Endangered Taxon of Galápagos Tortoise

Galápagos tortoises represent the only surviving lineage of giant tortoises that exhibit two different types of shell morphology. The taxonomy of Galápagos tortoises was initially based mainly on diagnostic morphological characters of the shell, but has been clarified by molecular studies indicating that most islands harbor monophyletic lineages, with the exception of Isabela and Santa Cruz. On Santa Cruz there is strong genetic differentiation between the two tortoise populations (Cerro Fatal and La Reserva) exhibiting domed shell morphology. Here we integrate nuclear microsatellite and mitochondrial data with statistical analyses of shell shape morphology to evaluate whether the genetic distinction and variability of the two domed tortoise populations is paralleled by differences in shell shape. Based on our results, morphometric analyses support the genetic distinction of the two populations and also reveal that the level of genetic variation is associated with morphological shell shape variation in both populations. The Cerro Fatal population possesses lower levels of morphological and genetic variation compared to the La Reserva population. Because the turtle shell is a complex heritable trait, our results suggest that, for the Cerro Fatal population, non-neutral loci have probably experienced a parallel decrease in variability as that observed for the genetic data.     

Dobzhansky's rule and reinforcement of pre-zygotic reproductive isolation in zones of secondary contact

It is well known that closely related sympatric species are usually more different in characters involved in species recognition (e.g., in visual and acoustic signals) than allopatric species of the same evolutionary age. In this article I call this phenomenon Dobzhansky's rule in accordance with the name of the scientist who first discovered it. There are two alternative explanations for this pattern. Under hypothesis of reinforcement by Dobzhansky, these species-specific differences evolve in situ, exactly in zone of overlap between two populations. Under hypothesis of differential fusion by Templeton, the differences originate in geographically separated regions, and only those populations that have evolved such differences can persist in secondary sympatry. These evolutionary scenarios are significantly different. The scenario by Dobzhansky is an essentially sympatric model, in which natural selection reinforces pre-zygotic isolation between divergent populations by selecting against unfit hybrids. The scenario by Templeton is based on classic allopatric speciation model that consider the formation of reproductive isolation to be a by-product of divergent evolution. In this work we show that the sympatric distribution of sister taxa of Agrodiaetus butterflies strongly correlates with differences in male wing colour. We also use a new quantitative phylogenetic test to distinguish between the models by Dobzhansky and by Templeton and to demonstrate that the pattern observed is, most likely, the result of reinforcement.     

Population genetic structure and its implications for adaptive variation in memory and the hippocampus on a continental scale in food-caching black-capped chickadees

Food-caching birds rely on stored food to survive the winter, and spatial memory has been shown to be critical in successful cache recovery. Both spatial memory and the hippocampus, an area of the brain involved in spatial memory, exhibit significant geographic variation linked to climate-based environmental harshness and the potential reliance on food caches for survival. Such geographic variation has been suggested to have a heritable basis associated with differential selection. Here, we ask whether population genetic differentiation and potential isolation among multiple populations of food-caching black-capped chickadees is associated with differences in memory and hippocampal morphology by exploring population genetic structure within and among groups of populations that are divergent to different degrees in hippocampal morphology. Using mitochondrial DNA and 583 AFLP loci, we found that population divergence in hippocampal morphology is not significantly associated with neutral genetic divergence or geographic distance, but instead is significantly associated with differences in winter climate. These results are consistent with variation in a history of natural selection on memory and hippocampal morphology that creates and maintains differences in these traits regardless of population genetic structure and likely associated gene flow.     

Dental health and lifestyle in four early mediaeval juvenile populations: Comparisons between urban and rural individuals, and between coastal and inland settlements

Dental stress markers such as enamel hypoplasia and caries are suitable indicators of population health and lifestyle, although they must be recorded and interpreted carefully. To date, they have been predominantly studied in adult samples, whereas juvenile remains are also affected by these lesions. In this study, dental enamel hypoplasia and caries were both evaluated on 613 non-adult individuals from four early mediaeval Moravian and Frankish skeletal series, who had experienced contrasting environments and lifestyles. The aim of this study is to assess the relationship between these biological traits and living conditions, and how this is manifested in the juvenile dental remains.Significant differences between populations were found in stress markers, dental lesions and the way these were manifested. Exposure to stressful conditions varies between urban and rural populations and is related to age groups. Although the children under investigation seem to have had different diets, it is difficult to distinguish the biological contribution (different enamel susceptibility) from the lifestyle contribution (different food, environment) in the formation of caries. Moreover, such studies must be interpreted carefully due to the possibility of intra- and inter-observer errors and the subjectivity of the scoring techniques.Nevertheless, this study also demonstrates that results of an investigation of juvenile skeletal remains can be as informative as a study of adults and that juvenile skeletons can be included in large bioarchaeological population studies.     

Some problems of the study and representation of Siberian flora biodiversity in connection with its conservation

The present knowledge of flora of Siberia is quite insufficient, which is a considerable obstacle to the detection of its biodiversity for conserving the gene pool. Planning conservation measures should be focused not only on species, but also on intraspecific taxa and their phylogenetic uniqueness. In the absence of genetic data, available morphological and geographical methods should be used, so that, when it is impossible to establish the actual origin and relationship of taxa, the existing morphological diverstity is at least represented, as far as it is known to be based on genetic diversity. Phenetic maps can be of much use in the study of intraspecific morphological diversity. The estimation of geographic variability and morphological diversity, as well as the evaluation of territories, can be based on such maps. To represent adequately the biodiversity existing within poorly studied, presumably hybrid plant groups, until actual origin and relationship are known, they should probably be forcedly and provisionally considered as a special type of hybrid complexes, representing the unclear present day taxonomic situation. Such complexes could include populations and individuals with morphological characters of two or more different species, until the systematic position of such populations and individuals is further explored. Until the actual taxonomic status and relationship of the components are established, they could be regarded as subspecies permitted by the Code, or as certain recorded morphological deviations from the type, without assigning any taxonomic status to them--depending on the available data on variability and distribution. In the future, the resulting provisional information on morphological diversity would help to concentrate the efforts of biologists, in possession of the newest methods, on the most important objects, and serve as the scientific base for effective measures aimed at the conservation and management of the vast gene pool of the Siberian flora.     

Genetic classification of populations using supervised learning

There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case-control studies and quality control (when participants in a study have been genotyped at different laboratories). This latter application is of particular importance in the era of large scale genome wide association studies, when collections of individuals genotyped at different locations are being merged to provide increased power. The traditional method for detecting structure within a population is some form of exploratory technique such as principal components analysis. Such methods, which do not utilise our prior knowledge of the membership of the candidate populations. are termed unsupervised. Supervised methods, on the other hand are able to utilise this prior knowledge when it is available.In this paper we demonstrate that in such cases modern supervised approaches are a more appropriate tool for detecting genetic differences between populations. We apply two such methods, (neural networks and support vector machines) to the classification of three populations (two from Scotland and one from Bulgaria). The sensitivity exhibited by both these methods is considerably higher than that attained by principal components analysis and in fact comfortably exceeds a recently conjectured theoretical limit on the sensitivity of unsupervised methods. In particular, our methods can distinguish between the two Scottish populations, where principal components analysis cannot. We suggest, on the basis of our results that a supervised learning approach should be the method of choice when classifying individuals into pre-defined populations, particularly in quality control for large scale genome wide association studies.     

Genomic Background and Generation Time Influence Deleterious Mutation Rates in Daphnia

Understanding how genetic variation is generated and how selection shapes mutation rates over evolutionary time requires knowledge of the factors influencing mutation and its effects on quantitative traits. We explore the impact of two factors, genomic background and generation time, on deleterious mutation in Daphnia pulicaria, a cyclically parthenogenic aquatic microcrustacean, using parallel mutation-accumulation experiments. The deleterious mutational properties of life-history characters for individuals from two different populations, and for individuals maintained at two different generation times, were quantified and compared. Mutational properties varied between populations, especially for clutch size, suggesting that genomic background influences mutational properties for some characters. Generation time was found to have a greater effect on mutational properties, with higher per-generation deleterious mutation rates in lines with longer generation times. These results suggest that differences in genetic architecture among populations and species may be explained in part by demographic features that significantly influence generation time and therefore the rate of mutation.     

Spatial genetic structure in natural populations of the overexploited tree Eremanthus erythropappus (DC.) macleish (Asteraceae)

Management and genetic conservation plans require knowledge of spatial genetic structure (SGS) to ensure the long-term maintenance of genetic variability in natural populations. This study uses spatial statistical analyses to assess the SGS in nine locations with diverse landscape characteristics where Eremanthus erythropappus occurs at varying densities. This species, commonly known as candeia, is widely distributed throughout Minas Gerais State, Brazil, and its wood has high economic value due to its natural durability and production of oil containing the active ingredient alpha-bisabolol. The species has undergone intense exploitation without adequate management planning. Our analyses were based on polymorphism at nine inter-simple sequence repeat (ISSR) loci. We observed SGS in five of the nine populations. The data indicate different degrees of SGS in the populations, which supports the premise that conservation plans and seed collection strategies should be informed by genetics studies.     

Systematics of the genus Floridichthys

Samples representing the three nominal subspecies of Floridichthys carpio were examined electrophoretically. Although the populations in Florida could not be distinguished completely from the populations in Yucatan by morphology, 5 of the 30 electrophoretic characters demonstrated fixed differences between Florida and Yucatan populations. Based on the observed genetic differentiation between Florida and Yucatan populations and the absence of genetic differentiation within those populations, we conclude that the Yucatan population has diverged to the species level. We, therefore, propose to elevate the nominal Yucatan subspecies Floridichthys carpio polyommus to a species status.     

Morphological similarity and molecular divergence of Trochulus striolatus and T. montanus,and their relationship to sympatric congeners (Gastropoda: Pulmonata: Hygromiidae)

Shell morphology has played an important role in the differentiation of mollusc species. However, extensive morphological variation and the lack of readily available diagnostic characters often lead to confusion and controversy in taxonomy of closely related species, such as the genus Trochulus. Two nominal species Trochulus striolatus and T. montanus show only subtle differences in their reproductive systems and are indistinguishable on the basis of sole conchological traits. Therefore, we performed molecular and morphological analyses to establish robust species limits among the taxa. The canonical discriminant analysis (CDA) of shell characters confirmed strong similarity between the species. It also revealed high intraspecific variability of the shell morphology, which allowed the distinguishing of some populations as two extremely distinct forms, while simultaneously making it difficult to discriminate between the two species. Analysis of the genital morphology indicated that differences were continuous and practically negligible among the species. In contrast, phylogenetic analyses based on newly obtained 114 Trochulus sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and 55 homologues retrieved from the GenBank database showed clear genetic divergence between T. striolatus and T. montanus. Moreover, they revealed a close relationship between some T. montanus, some T. caelatus and T. clandestinus samples, which formed a monophyletic group. Some of their haplotypes were even identical. It suggested that their recent common origin or recurrent gene flow occurred between these populations. However, T. sericeus sequences were split into independent diverged lineages, which were separated by many unidentified Trochulus species. It suggested that this taxon may represent a paraphyletic species complex.