Isozyme variation in Silene pratensis: a response to different environments

The isozymes of nine enzyme systems were screened and the frequencies of the flavone glycosylating genes were determined in an outdoor experiment with 70 populations of European S. pratensis and an indoor experiment with 30 populations of the same species. Cluster analysis (using Ward's cluster criterion) were performed on all data sets. In the outdoor experiment, cluster analysis of the flavonoid data gave the same pattern that we obtained in an ealier survey of a larger set of populations and showed clearly that there are eight chemical races in European S. pratensis. No comparable geographic distributiion could be found in the isozyme data set, although the dendrogram showed two very clearly separated groups. The two groups represented the two years in which the populations were grown. This result indicates that isozyme variation in European S. pratensis is largely determined by environmental factors. Observations on changes in isozyme patterns during ontogeny and on differences between indoor and outdoor grown plants of the same F2 crosses confirm this. Differences in isozyme patterns can be caused by very small differencs in environment as is shown by the results of the indoor experiment, in which a slight gradient in environmental conditions was present in the greenhouses. The cluster analysis of the isozyme data from the indoor experiment revealed three distinct groups of populations that could be related to location within the greenhouses. As in the outdoor experiment, the dendrogram for the flavonoids gave the same geographic pattern as found with the earlier survey.     

Geographic trends in flavone-glycosylation genes and seed morphology in EuropeanSilene pratensis (Caryophyllaceae)

Three of the loci controlling isovitexin glycosylation inSilene pratensis are polymorphic and show geographic trends which are compared with geographic trends in seed morphology (and other phenotypic characters) as demonstrated by multivariate analysis. Various lines of evidence support the hypothesis thatS. pratensis spread into Europe from at least two genetically differentiated sources.S. dioica, by contrast, shows little interpretable geographic variation in morphology or flavonoid content.     

Is geographic variation within species related to macroevolutionary patterns between species?

The relationship between microevolution and macroevolution is a central topic in evolutionary biology. An aspect of this relationship that remains very poorly studied in modern evolutionary biology is the relationship between within‐species geographic variation and among‐species patterns of trait variation. Here, we tested the relationship between climate and morphology among and within species in the salamander genus Plethodon. We focus on a discrete colour polymorphism (presence and absence of a red dorsal stripe) that appears to be related to climatic distributions in a common, wide‐ranging species (Plethodon cinereus). We find that this trait has been variable among (and possibly within) species for >40 million years. Furthermore, we find a strong relationship among species between climatic variation and within‐species morph frequencies. These between‐species patterns are similar (but not identical) to those in the broadly distributed Plethodon cinereus. Surprisingly, there are no significant climate–morphology relationships within most other polymorphic species, despite the strong between‐species patterns. Overall, our study provides an initial exploration of how within‐species geographic variation and large‐scale macroevolutionary patterns of trait variation may be related.     

Genetic signatures of plant resistance genes with known function within and between species

Plant disease resistance (R) genes have undergone significant evolutionary divergence to cope with rapid changes in pathogens. These highly variable evolutionary patterns may have contributed to diversity in R gene protein families or structures. Here, the evolutionary patterns of 76 identified R genes and their homologs were investigated within and between plant species. Results demonstrated that nucleotide binding sites and leucine-rich-repeat genes located in loci with complex evolutionary histories tended to evolve rapidly, have high variation in copy numbers, exhibit high levels of nucleotide variation and frequent gene conversion events, and also exhibit high non-synonymous to synonymous substitution ratios in LRR regions. However, non-NBS-LRR R genes are relatively well conserved with constrained variation and are more likely to participate in the basic defense system of hosts. In addition, both conserved and highly divergent evolutionary patterns were observed for the same R genes and were consistent with inter- and intra-specific distributions of some R genes. These results thus indicate either continuous or altered evolutionary patterns between and within species. The present investigation is the first attempt to investigate evolutionary patterns among all clearly functional R genes. The results reported here thus provide a foundation for future plant disease studies.     

Phylogenetic analysis of Lappula Moench (Boraginaceae) based on molecular and morphological data

Lappula Moench includes ca. 70 species and exhibits a wide range of nutlet variation. Currently, the evolutionary relationships among species of Lappula have not been examined; therefore, to elucidate phylogenetic relationships and morphological evolution within Lappula and related genera, we conducted phylogenetic analyses with matrices that include 48 species as well as four DNA regions (ITS, trnL-trnF, rpS16 and psbA-trnH) and 18 morphological characters. These matrices were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference methods. Analyses of the combined molecular and morphological data result in a phylogeny that is better resolved than that based solely on molecular sequence data. Phylogenetic results suggest that the current infrageneric classification of Lappula, at least at the subsectional and series level, is artificial. The evolutionary patterns of 18 morphological characters are investigated in a phylogenetic context. In Lappula, nutlet homomorphism and small corollas are resolved as ancestral, while nutlet heteromorphism and larger corollas are derived.     

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species.     

Effects of salinity and clipping on biomass and competition between a halophyte and a glycophyte

Global climate change will likely result in the reduction of water levels in intermountain wetlands and ponds, and the vegetation communities associated with these wetlands are an important forage source for livestock. Lowered water levels will not only constrict wetland plant communities, it will potentially change aquatic and soil salt concentrations. Such an increase in salinity can reduce plant growth and potentially affect competitive interactions between plants. A greenhouse experiment examined the effects of salinity and competition on the growth of two wet meadow grass species, Poa pratensis (a glycophyte) and Puccinellia nuttalliana (a halophyte). The following hypotheses based on published data were tested: (1) Biomass of both species will decrease with increasing concentration of salt; (2) root:shoot (R:S) ratio of P. pratensis will decrease with increasing salt concentration while R:S ratio of P. pratensis and P. nuttalliana will increase with clipping; (3) competitive importance will decrease for P. pratensis and P. nuttalliana with increasing salt concentration because salt induces a stress response and competitive importance is reduced in stressed environments. A factorial design included 3 plant treatments (P. nuttalliana alone, P. pratentsis alone, P. nuttalliana + P. pratensis) × 4 salinity rates (control; 5, 10, 15 g/L NaCl) × 2 clipping intensities (plants clipped or not clipped) for a total of 24 combinations replicated 6 times over a period of 90 days. We found a reduction in dry biomass as salinity increased, and this effect was greatest for P. pratensis. (1.94 g (SE 0.13) at 0 g/L NaCl to 0.22 g (SE 0.11) at 15 g/L NaCl). The R:S ratio of P. pratensis was reduced by salinity, but not for P. nuttalliana. Competitive importance of both species was reduced by clipping and by salinity, but the effect was greater and more consistent for P. pratensis. We conclude that salt concentration reduces plant growth and the effect of competition.     

Uncoupled geographical variation between leaves and flowers in a South-Andean Proteaceae

Background and Aims

Geographical variation in foliar and floral traits and their degree of coupling can provide relevant information on the relative importance of abiotic, biotic and even neutral factors acting at geographical scales as generators of evolutionary novelty. Geographical variation was studied in leaves and flowers of Embothrium coccineum, a species that grows along abrupt environmental gradients and exhibits contrasting pollinator assemblages in the southern Andes.

Methods

Five foliar and eight floral morphological characters were considered from 32 populations, and their patterns of variation and covariation were analysed within and among populations, together with their relationship with environmental variables, using both univariate and multivariate methods. The relationships between foliar and floral morphological variation and geographical distance between populations were compared with Mantel permutation tests.

Key Results

Leaf and flower traits were clearly uncoupled within populations and weakly associated among populations. Whereas geographical variation in foliar traits was mostly related to differences in precipitation associated with geographical longitude, variation in floral traits was not.

Conclusions

These patterns suggest that leaves and flowers responded to different evolutionary forces, environmental (i.e. rainfall) in the case of leaves, and biotic (i.e. pollinators) or genetic drift in the case of flowers. This study supports the view that character divergence at a geographical scale can be moulded by different factors acting in an independent fashion.Key words: Embothrium coccineum, Proteaceae, geographical variation, foliar morphology, floral morphology, uncoupling, selective forces, environmental conditions, pollinators, south Andes     

Patterns of Evolutionary Divergence and Convergence in the Bushy-Tailed Woodrat (Neotoma cinerea) Across Western North America

The degree of concordance between patterns of divergence in genetic and morphological characters provides insight into the process of evolutionary diversification. We analyzed species-wide morphological variation in a broadly distributed species of small mammal, the bushy-tailed woodrat (Neotoma cinerea), for comparison against a recently developed mitochondrial phylogeny. We focused our analyses on patterns of qualitative and quantitative craniodental morphological variation throughout the distribution of this taxon. We found strong concordance between the morphology of one prominent craniodental feature (sphenopalatine vacuity) and the major mitochondrial lineages, but only minimal differentiation in overall morphometric variation between these clades. Further, in contrast to the largely east–west subdivision of mitochondrial and sphenopalatine vacuity variation, cluster analyses of morphometric variation revealed a north–south morphological subdivision irrespective of mitochondrial clade. Our combined character sets are best explained by a deep history of evolutionary divergence within this taxon accompanied or followed by broad-scale convergent or parallel evolution.     

Microhabitat selection by ovipositing females and pre-diapause larvae of a Welsh population of <Emphasis Type="Italic">Euphydryas aurinia</Emphasis> (Lepidoptera: Nymphalidae)

Habitat requirements of the marsh fritillary Euphydryas aurinia have been studied intensively in recent years in order to inform conservation action on this rapidly declining species. Autecological studies have been undertaken on various spatial scales to account for differences in mobility between life stages. It has become clear that resource utilisation by the species varies between different geographic areas and also on a local scale. We studied the microhabitat surrounding Succisa pratensis plants chosen for oviposition and around resulting larval webs in a key Welsh population, UK. Microhabitat preferences were shown to differ between ovipositing females and pre-diapause larval groups. For oviposition, females showed a preference for host plants within clusters of S. pratensis surrounded by a relatively low sward. In contrast, larval webs were found in relatively high vegetation with relatively low S. pratensis cover in the immediate vicinity. The marked difference between oviposition and larval web microhabitat was achieved through very long distance dispersals undertaken by the pre-diapause larval groups. This gives rise to questioning the common assumption that pre-diapause larval web location can be used as a proxy for oviposition location. It also underpins the importance of managing E. aurinia habitats for maximum structural variability on a small scale.     

Environmental versus Anthropogenic Effects on Population Adaptive Divergence in the Freshwater Snail Lymnaea stagnalis

Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q _ST -F _ST comparisons. Despite strong neutral differentiation (mean F _ST = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.     

Molecular phylogeny of the neotropical genus Christensonella (Orchidaceae, Maxillariinae): species delimitation and insights into chromosome evolution

Background and Aims

Species'' boundaries applied within Christensonella have varied due to the continuous pattern of variation and mosaic distribution of diagnostic characters. The main goals of this study were to revise the species'' delimitation and propose a more stable classification for this genus. In order to achieve these aims phylogenetic relationships were inferred using DNA sequence data and cytological diversity within Christensonella was examined based on chromosome counts and heterochromatin patterns. The results presented describe sets of diagnostic morphological characters that can be used for species'' identification.

Methods

Phylogenetic studies were based on sequence data of nuclear and plastid regions, analysed using maximum parsimony and maximum likelihood criteria. Cytogenetic observations of mitotic cells were conducted using CMA and DAPI fluorochromes.

Key Results

Six of 21 currently accepted species were recovered. The results also support recognition of the ‘C. pumila’ clade as a single species. Molecular phylogenetic relationships within the ‘C. acicularis–C. madida’ and ‘C. ferdinandiana–C. neowiedii’ species'' complexes were not resolved and require further study. Deeper relationships were incongruent between plastid and nuclear trees, but with no strong bootstrap support for either, except for the position of C. vernicosa. Cytogenetic data indicated chromosome numbers of 2n = 36, 38 and 76, and with substantial variation in the presence and location of CMA/DAPI heterochromatin bands.

Conclusions

The recognition of ten species of Christensonella is proposed according to the molecular and cytogenetic patterns observed. In addition, diagnostic morphological characters are presented for each recognized species. Banding patterns and chromosome counts suggest the occurrence of centric fusion/fission events, especially for C. ferdinandiana. The results suggest that 2n = 36 karyotypes evolved from 2n = 38 through descendent dysploidy. Patterns of heterochromatin distribution and other karyotypic data proved to be a valuable source of information to understand evolutionary patterns within Maxillariinae orchids.Key words: Chromosome number, Christensonella, Cymbidieae, cytotaxonomy, fluorochrome staining, Maxillaria, Maxillariinae, molecular phylogenetics, species delimitation     

Molecules and morphology suggest cryptic species diversity and an overall complex taxonomy of fish scale geckos, genus Geckolepis

The current classification of the Malagasy-Comoroan geckos of the genus Geckolepis recognizes three valid species and is based on morphological differences only. Species allocation of individuals is difficult, mainly because of the insufficiently known degree of variation and the frequent partial loss of the integument in preserved specimens. Here we study Geckolepis specimens from almost their entire known range. We combine molecular and morphological data to estimate species richness in the genus, and to assess the taxonomic validity of the morphological differences proposed. Analyses of mitochondrial (12S, ND4) and nuclear (RAG1, CMOS) gene sequences support three major clades in addition to the morphologically distinct G. polylepis (included for 12S only), and the presence of various divergent lineages within these clades, some occurring in sympatry. Among lineages, the external morphology seems to be comparatively conservative, and differences are faint in many cases. For each major lineage, we summarize the most diagnostic morphological characters that distinguish it from other lineages. The combined molecular and morphological data strongly indicate the presence of highly divergent lineages, three of which are tentatively referred to the names Geckolepis maculata, G. polylepis and G. typica, whereas three other major lineages are considered Confirmed Candidate Species. Among the remaining lineages, differentiation is shallower, and these may qualify for Deep Conspecific Lineages. In conclusion, our analysis provides evidence for an underestimation of species richness in the genus and a complex evolutionary history, not reflected by current Geckolepis species-level taxonomy.     

Effects of Mitochondrial DNA Rate Variation on Reconstruction of Pleistocene Demographic History in a Social Avian Species,Pomatostomus superciliosus

Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (T_MRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in T_MRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of T_MRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.     

A pattern analysis of the geographical distribution of flavone-glycosylating genes in Silene pratensis

The three flavone glycosylating genes in European Silene pratensis shows a distinct geographical variation. Three genetically different races can be distinguished on the basis of gene frequencies. Pattern recognition techniques and cluster analysis have been used on the data set of frequencies of the flavone-glycosylating genes in 285 European populations of S. pratensis. The combined results of these analyses confirm the previously recognized races and reveal a steep cline between races 7 and 2(+3) and a wide wide transition zone between races 2 and 3.     

Fuzzy Boundaries: Color and Gene Flow Patterns among Parapatric Lineages of the Western Shovel-Nosed Snake and Taxonomic Implication

Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.     

Looking beneath the tip of the iceberg: diversification of the genus <Emphasis Type="Italic">Epimeria</Emphasis> on the Antarctic shelf (Crustacea,Amphipoda)

The amphipod genus Epimeria is very speciose in Antarctic waters. Although their brooding biology, massive and heavily calcified body predict low dispersal capabilities, many Epimeria species are documented to have circum-Antarctic distributions. However, these distribution records are inevitably dependent on the morphological species definition. Yet, recent DNA evidence suggests that some of these Epimeria species may be complexes of species with restricted distributions. Mitochondrial COI and nuclear 28S rDNA sequence data were used to infer evolutionary relationships among 16 nominal Epimeria species from the Antarctic Peninsula, the eastern Weddell Sea and the Adélie Coast. Based on this phylogenetic framework, we used morphology and the DNA-based methods GMYC, bPTP and BPP to investigate species boundaries, in order to revise the diversity and distribution patterns within the genus. Most of the studied species appeared to be complexes of pseudocryptic species, presenting small and previously overlooked morphological differences. Altogether, 25 lineages were identified as putative new species, increasing twofold the actual number of Antarctic Epimeria species. Whereas most of the species may be geographically restricted to one of the three studied regions, some still have very wide distribution ranges, hence suggesting a potential for large-scale dispersal.     

Genetic Diversity of Neotropical Myotis (Chiroptera: Vespertilionidae) with an Emphasis on South American Species

Background

Cryptic morphological variation in the Chiropteran genus Myotis limits the understanding of species boundaries and species richness within the genus. Several authors have suggested that it is likely there are unrecognized species-level lineages of Myotis in the Neotropics. This study provides an assessment of the diversity in New World Myotis by analyzing cytochrome-b gene variation from an expansive sample ranging throughout North, Central, and South America. We provide baseline genetic data for researchers investigating phylogeographic and phylogenetic patterns of Myotis in these regions, with an emphasis on South America.

Methodology and Principal Findings

Cytochrome-b sequences were generated and phylogenetically analyzed from 215 specimens, providing DNA sequence data for the most species of New World Myotis to date. Based on genetic data in our sample, and on comparisons with available DNA sequence data from GenBank, we estimate the number of species-level genetic lineages in South America alone to be at least 18, rather than the 15 species currently recognized.

Conclusions

Our findings provide evidence that the perception of lower species richness in South American Myotis is largely due to a combination of cryptic morphological variation and insufficient sampling coverage in genetic-based systematic studies. A more accurate assessment of the level of diversity and species richness in New World Myotis is not only helpful for delimiting species boundaries, but also for understanding evolutionary processes within this globally distributed bat genus.     

PCR-Denaturing Gradient Gel Electrophoresis Profiling of Inter- and Intraspecies 18S rRNA Gene Sequence Heterogeneity Is an Accurate and Sensitive Method To Assess Species Diversity of Arbuscular Mycorrhizal Fungi of the Genus Gigaspora

Despite the importance of arbuscular mycorrhizal fungi in the majority of terrestrial ecosystems, their ecology, genetics, and evolution are poorly understood, partly due to difficulties associated with detecting and identifying species. We explored the inter- and intraspecies variations of the 18S rRNA genes of the genus Gigaspora to assess the use of this marker for the discrimination of Gigaspora isolates and of Gigasporaceae populations from environmental samples. Screening of 48 Gigaspora isolates by PCR-denaturing gradient gel electrophoresis (DGGE) revealed that the V3-V4 region of the 18S rRNA gene contained insufficient variation to discriminate between different Gigaspora species. In contrast, the patterns of 18S ribosomal DNA (rDNA) heterogeneity within the V9 region of this marker could be used for reliable identification of all recognized species within this genus. PCR-DGGE patterns provided insight into some putative misidentifications and could be used to differentiate geographic isolates of G. albida, G. gigantea, and G. margarita but not G. rosea. Two major clusters were apparent based upon PCR-DGGE ribotype patterns, one containing G. albida, G. candida, G. ramisporophora, and G. rosea and the other containing G. decipiens and G. margarita. Dissection of the DGGE patterns by cloning, DGGE screening, and sequencing confirmed these groupings and revealed that some ribotypes were shared across species boundaries. Of the 48 isolates examined, only two displayed any spore-to-spore variation, and these exceptions may be indicative of coisolation of more than one species or subspecies within these cultures. Two Brazilian agricultural soils were also analyzed with a Gigasporaceae-specific nested PCR approach, revealing a dominance of G. margarita within this family.