Who's related to whom? Recent results from molecular systematic studies

Similarities among model systems can lead to generalizations about plants, but understanding the differences requires systematic data. Molecular phylogenetic analyses produce results similar to traditional classifications in the grasses (Poaceae), and relationships among the cereal crops are quite clear. Chloroplast-based phylogenies for the Solanaceae show that tomato is best considered as a species of Solanum, closely related to potatoes. Traditional classifications in the Brassicaceae are misleading with regard to true phylogenetic relationships and data are only now beginning to clarify the situation. Molecular data are also being used to revise our view of relationships among flowering plant families. Phylogenetic data are critical for interpreting hypotheses of the evolution of development.     

Comparison of RFLP and RAPD markers to estimating genetic relationships within and among cruciferous species

Restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers are being used widely for evaluating genetic relationships of crop germplasm. Differences in the properties of these two markers could result in different estimates of genetic relationships among some accessions. Nuclear RFLP markers detected by genomic DNA and cDNA clones and RAPD markers were compared for evaluating genetic relationships among 18 accessions from six cultivated Brassica species and one accession from Raphanus sativus. Based on comparisons of genetic-similarity matrices and cophenetic values, RAPD markers were very similar to RFLP markers for estimating intraspecific genetic relationships; however, the two marker types gave different results for interspecific genetic relationships. The presence of amplified mitochondrial and chloroplast DNA fragments in the RAPD data set did not appear to account for differences in RAPD- and RFLP-based dendrograms. However, hybridization tests of RAPD fragments with similar molecular weights demonstrated that some fragments, scored as identical, were not homologous. In all these cases, the differences occurred at the interspecific level. Our results suggest that RAPD data may be less reliable than RFLP data when estimating genetic relationships of accessions from more than one species.     

Linking Pharmacokinetics and Biomarker Data to Mechanism of Action in Risk Assessment

Incorporating information on metabolism, pharmacokinetics, and DNA and protein biomarkers provides a means to integrate these important factors into the risk assessment process. Such data are useful for species to species extrapolation, high- to low-dose extrapolation and PBPK modeling. In addition, these data are critical for understanding the mode of action for chemical carcinogens. Through the use of mass spectrometry, stable isotopes can be used to unequivocally demonstrate pathways of formation of biomarkers and relationships between exogenous and endogenous processes. This paper reviews what has been learned for two carcinogens, vinyl chloride and butadiene. It is clear that such data play major roles in improving the understanding of how chemicals cause cancer, extending the range of data on exposure-response relationships, and examining interspecies differences and inter-individual differences that may affect susceptibility. As such, it is also clear that these data play a critical role in improving the accuracy of risk assessments.     

Geographical differences in habitat relationships of cetaceans across an ocean basin

The distributions of highly mobile marine species such as cetaceans are increasingly modeled at basin scale by combining data from multiple regions. However, these basin-wide models often overlook geographical variations in species habitat relationships between regions. We tested for geographical variations in habitat relationships for a suite of cetacean taxa between the two sides of the North Atlantic basin. Using cetacean visual survey data and remote sensing data from the western and eastern basin in summer, we related the probability of presence of twelve cetacean taxa from three guilds to seafloor depth, sea surface temperature and primary productivity. In a generalized additive model framework, we fitted 1) basin-wide (BW) models, assuming a single global relationship, 2) region-specific intercepts (RI) models, assuming relationships with the same shape in both regions, but allowing a region-specific intercept and 3) region-specific shape (RS) models, assuming relationships with different shapes between regions. RS models mostly yielded significantly better fits than BW models, indicating cetacean occurrences were better modeled with region-specific than with global relationships. The better fits of RS models over RI models further provided statistical evidence for differences in the shapes of region-specific relationships. Baleen whales showed striking differences in both the shapes of relationships and their mean presence probabilities between regions. Deep diving whales and delphinoids showed contrasting relationships between regions with few exceptions (e.g. non-statistically different shapes of region-specific relationships for harbor porpoise and beaked whales with depth). Our findings stress the need to account for geographical differences in habitat relationships between regions when modeling species distributions from combined data at the basin scale. Our proposed hypotheses offer a roadmap for understanding why habitat relationships may geographically vary in cetaceans and other highly mobile marine species.     

Atlas versus range maps: robustness of chorological relationships to distribution data types in European mammals

Aim Chorological relationships describe the patterns of distributional overlap among species. In addition to revealing biogeographical structure, the resulting clusters of species with similar geographical distributions can serve as natural units in conservation planning. Here, we assess the extent to which temporal, methodological and taxonomical differences in the source of species’ distribution data can affect the relationships that are found. Location Western Europe. Methods We used two data sets – the Atlas of European mammals and polygon range maps from the IUCN Global Mammal Assessment – both as presence–absence data for UTM 50 km × 50 km squares. We performed pairwise comparisons among 156 species for each data set to build matrices of the similarity in distribution across species, using both Jaccard’s and Baroni‐Urbani & Buser’s indices. We then compared these similarity matrices (chorological relationships), as well as the species richness and occurrence patterns from the two data sets. Results As expected, range maps increased both the mean prevalence per species and mean species richness per grid cell in comparison to atlas data, reflecting the general view that these data types respectively over‐ and underestimate species occurrence. However, species richness and occurrence patterns in atlas and range map data were positively associated and, most importantly, the chorological relationships underlying the two data sets were highly similar. Main conclusions Despite many methodological, temporal and taxonomical differences between atlas data and range maps, the chorological relationships encountered between species were similar for both data sets. Chorological analyses can thus be robust to the data source used and provide a solid basis for analytical biogeographical studies, even over broad spatial scales.     

Size correction: comparing morphological traits among populations and environments

Morphological relationships change with overall body size and body size often varies among populations. Therefore, quantitative analyses of individual traits from organisms in different populations or environments (e.g., in studies of phenotypic plasticity) often adjust for differences in body size to isolate changes in allometry. Most studies of among population variation in morphology either (1) use analysis of covariance (ANCOVA) with a univariate measure of body size as the covariate, or (2) compare residuals from ordinary least squares regression of each trait against body size or the first principal component of the pooled data (shearing). However, both approaches are problematic. ANCOVA depends on assumptions (small variance in the covariate) that are frequently violated in this context. Residuals analysis assumes that scaling relationships within groups are equal, but this assumption is rarely tested. Furthermore, scaling relationships obtained from pooled data typically mischaracterize within-group scaling relationships. We discuss potential biases imposed by the application of ANCOVA and residuals analysis for quantifying morphological differences, and elaborate and demonstrate a more effective alternative: common principal components analysis combined with Burnaby’s back-projection method.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Carbon and nitrogen nutrition of nodulated roots of grain legumes

Abstract The spatial and temporal relationships between carbon (C) metabolism and nitrogen (N) nutrition in grain legumes are of great academic interest with the added bonus that any data for economically important species may ultimately prove useful to breeders and growers. So far there are no data which can be used to relate differences in carbon usage by any symbiotic association with differences in economic yield. Much research has focussed on the dependence of dinitrogen fixation on photosynthate supply, on the C–N relationships of nodulated roots and nodules and on diurnal and seasonal profiles of dinitrogen fixation. In all these aspects a plethora of responses have been described, often based on insufficiently proven measurement techniques; consequently unequivocal conclusions cannot be drawn. We know little about within-species differences due to cultivar, strain of Rhi-zobium or environment, or about the proportions of any heritable variations which might be sufficiently large to merit inclusion among the selection criteria of grain legume breeders.     

Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography

We investigated Viburnum phylogeny using separate and combined analyses of DNA sequence data from two chloroplast and three nuclear loci. Separate analyses of nuclear and chloroplast data sets resulted in gene trees that were generally congruent with one another and with trees from two previous analyses. Our gene trees do differ in the position of section Pseudotinus, as well as in species relationships within sections Pseudotinus and Lentago. However, tests for incongruence indicate that differences between the nuclear and chloroplast data are not significant. Furthermore, gene trees from combined analyses were highly similar to those found in separate analyses, suggesting that these localized differences do not affect other parts of the tree. Our analyses provide convincing support for numerous relationships, although there is still uncertainty at the base of the tree. To facilitate future study, we propose informal names for 12 well-supported species groups, as well as for several higher-level clades. We also discuss the biogeographic implications of our phylogeny, focusing on repeated, although apparently temporally incongruent, patterns of disjunction between the Old and New Worlds.     

Genetic code correlations: Amino acids and their anticodon nucleotides

Summary The data here show direct correlations between both the hydrophobicity and the hydrophilicity of the homocodonic amino acids and their anticodon nucleotides. While the differences between properties of uracil and cytosine derivatives are small, further data show that uracil has an affinity for charged species. Although these data suggest that molecular relationships between amino acids and anticodons were responsible for the origin of the code, it is not clear what the mechanism of the origin might have been.     

Differential indicators of loneliness among elderly. The importance of type of partner relationship, partner history, health, socioeconomic status and social relations

Using data from the 1992 NESTOR-survey 'Living arrangements and social networks of older adults' (N = 4494), the aim of the present study is to identify specific categories of older adults who are most vulnerable to loneliness. By looking at different types of partner relationships (first, second, and third marriages; consensual unions; partners who are not household members) and at partner histories (never married, ever divorced, ever widowed, remarried), this study elaborates on previous research which has tended to look only at the presence versus the absence of partner relationships. Findings indicate that different types of partner relationships provide differential protection against loneliness. There appears to be a 'shadow of the past' of a previous divorce or widowhood in second and third partnerships, which accounts for generally higher levels of loneliness. Single men tend to be more lonely than single women. Moreover, there are no differences in loneliness between men who have always been single and those previously married. Among single women, differences in partner history are relevant: never married single women tend to be least vulnerable to loneliness. The differences in loneliness between older adults with different types of partner relationships and partner histories are only partially attributable to network and social participation differences. The latter independently contribute to the explanation of loneliness. The role of non-social determinants (health and socioeconomic position) is also examined. The results underscore the socially isolating effects of sensory impairments. Older adults with functional limitations, and those with visual or auditory problems tend to be more lonely, findings which are only partially attributable to differences in the number and quality of social relationships. Socioeconomic circumstances primarily have an indirect influence on loneliness. Those with higher levels of educational attainment and higher incomes tend to have more extensive social networks and are therefore less prone to loneliness.     

Phylogenetic relationships and remarkable radiation in Parartemia (Crustacea: Anostraca), the endemic brine shrimp of Australia: evidence from mitochondrial DNA sequences

The Australian continent is notable for the faunal radiations which have occurred in its saline inland waters. The endemic brine shrimp genus Parartemia inhabits many of these habitats. The complex pattern of morphological variation in parartemiids has impeded the establishment of a sound scheme of species relationships. The present study provides an explicit hypothesis of relationships for the genus based on nucleotide sequence data from a segment of mitochondrial DNA coding for the large subunit rRNA gene. Phylogenetic analyses indicated that the eight known species are genetically distinct, and revealed the existence of at least two new species. The molecular data support certain morphology-based relationships among species, but are inconsistent with other hypotheses. There is evidence that most members of the genus arose in a short interval, followed by remarkable genetic divergence. Comparisons of levels of mt DNA sequence divergence between lineages from saline inland waters and freshwaters using representative crustacean groups from Australia that included parartemiids indicated profound differences in rates of evolution, with halophiles exhibiting greater rates of change than their counterparts from freshwaters.     

Mitochondrial sequence data and Dipsacales phylogeny: mixed models, partitioned Bayesian analyses, and model selection

Phylogenetic analyses of chloroplast DNA sequences, morphology, and combined data have provided consistent support for many of the major branches within the angiosperm clade Dipsacales. Here we use sequences from three mitochondrial loci to test the existing broad scale phylogeny and in an attempt to resolve several relationships that have remained uncertain. Parsimony, maximum likelihood, and Bayesian analyses of a combined mitochondrial data set recover trees broadly consistent with previous studies, although resolution and support are lower than in the largest chloroplast analyses. Combining chloroplast and mitochondrial data results in a generally well-resolved and very strongly supported topology but the previously recognized problem areas remain. To investigate why these relationships have been difficult to resolve we conducted a series of experiments using different data partitions and heterogeneous substitution models. Usually more complex modeling schemes are favored regardless of the partitions recognized but model choice had little effect on topology or support values. In contrast there are consistent but weakly supported differences in the topologies recovered from coding and non-coding matrices. These conflicts directly correspond to relationships that were poorly resolved in analyses of the full combined chloroplast-mitochondrial data set. We suggest incongruent signal has contributed to our inability to confidently resolve these problem areas.     

Bending for love: losses and gains of sexual dimorphisms are strictly correlated with changes in the mounting position of sepsid flies (Sepsidae: Diptera)

Background  

Sexually dimorphic structures ntribute the largest number of morphological differences between closely related insect species thus implying that these structures evolve fast and are involved in speciation. The current literature focuses on the selective forces that drive these changes, be it 'sexual conflict' or 'female choice'. However, there are only few studies examining the function of sexual dimorphisms and even fewer that investigate how functional changes influence dimorphisms. This is largely due to the paucity of taxa for which the morphology, behavior, and phylogenetic relationships for multiple species are known. Here we present such data for sepsid flies. Sepsids have starkly dimorphic forelegs whose function can be documented under laboratory conditions. We use data from 10 genes to reconstruct the phylogenetic relationships for 33 species and test whether mounting positions are correlated with the presence and absence of sexual dimorphisms in the forelegs.     

Complementary Models of Tree Species–Soil Relationships in Old-Growth Temperate Forests

Ecosystem-level studies identify plant–soil feedbacks as important controls on soil nutrient availability, particularly for nitrogen and phosphorus. Although site- and species-specific studies of tree species–soil relationships are relatively common, comparatively fewer studies consider multiple co-existing species in old-growth forests across a range of sites that vary in underlying soil fertility. We characterized patterns in forest floor and mineral soil nutrients associated with four common tree species across eight undisturbed old-growth forests in Oregon, USA, and used two complementary conceptual models to assess tree species–soil relationships. Plant–soil feedbacks that could reinforce site-level differences in nutrient availability were assessed using the context-dependent relationships model, whereby relative species-based differences in each soil nutrient diverged or converged as nutrient status changed across sites. Tree species–soil relationships that did not reflect strong feedbacks were evaluated using a site-independent relationships model, whereby forest floor and surface mineral soil nutrient pools differed consistently by tree species across sites, without variation in deeper mineral soils. We found that the organically cycled elements carbon, nitrogen, and phosphorus exhibited context-dependent differences among species in both forest floor and mineral soil, and most often followed a divergence model, whereby species differences were greatest at high-nutrient sites. These patterns are consistent with theory emphasizing biotic control of these elements through plant–soil feedback mechanisms. Site-independent species differences were strongest for pools of the weatherable cations calcium, magnesium, potassium, as well as phosphorus, in mineral soils. Site-independent species differences in forest floor nutrients were attributable to one species that displayed significantly greater forest floor mass accumulation. Our findings confirm that site-independent and context-dependent tree species-soil relationships occur simultaneously in old-growth temperate forests, with context-dependent relationships strongest for organically cycled elements, and site-independent relationships strongest for weatherable elements with inorganic cycling phases. These models provide complementary explanations for patterns of nutrient accumulation and cycling in mixed-species old-growth temperate forests.     

Ontogeny, phylogeny, and morphology in anuran larvae: morphometric analysis of cranial development and evolution in Rana tadpoles (Anura: Ranidae)

Comparative studies of chondrocranial morphology in larval anurans are typically qualitative in nature, focusing primarily on discrete variation or gross differences in the size or shape of individual structures. Detailed data on chondrocranial allometry are currently limited to only two species, Rana sylvatica and Bufo americanus. This study uses geometric morphometric and multivariate statistical analyses to examine interspecific variation in both larval chondrocranial shape and patterns of ontogenetic allometry among six species of Rana. Variation is interpreted within the context of hypothesized phylogenetic relationships among these species. Canonical variates analyses of geometric morphometric datasets indicate that species can be clearly discriminated based on chondrocranial shape, even when whole ontogenies are included in the analysis. Ordinations and cluster analyses based on chondrocranial shape data indicate the presence of three primary groupings (R. sylvatica; R. catesbeiana + R. clamitans; and R. palustris + R. pipiens + R. sphenocephala), and patterns of similarity closely reflect phylogenetic relationships. Analysis of chondrocranial allometry reveals that some patterns are conserved across all species (e.g., most measurements scale with negative allometry, those associated with the posterior palatoquadrate tend to scale with isometry or positive allometry). Ontogenetic scaling along similar allometric trajectories, lateral transpositions of individual trajectories, and variable allometric relationships all contribute to shape differences among species. Overall patterns of similarity among ontogenetic trajectories also strongly reflect phylogenetic relationships. Thus, this study demonstrates a tight link between ontogeny, phylogeny, and morphology, and highlights the importance of including both ontogenetic and phylogenetic data in studies of chondrocranial evolution in larval anurans.     

Morphological parameters of abundant and threatened chondrichthyans of the northwestern Mediterranean Sea

The diversity of chondrichthyans in the Mediterranean Sea is relatively high; however, available data indicate that this group is declining in abundance and several species are becoming rare. As a result, the collection of biological data is a priority for demographic models, stock assessments, and food web analysis. In the present study, we report morphological parameters and length–weight relationships of several chondrichthyan species, both abundant and threatened, from the western Mediterranean Sea. Samples were obtained with commercial and scientific bottom trawl vessels between 2001 and 2013. A total of 893 individuals belonging to 11 families and 20 species were weighed and total lengths measured. In addition, seven species of large demersal sharks were measured and length–length relationships obtained to study the relationships between different body length measurements. All species showed positive allometric or isometric growth, except for Centroscymnus coelolepis. The results of the length–weight relationships reveal differences between the western Mediterranean and nearby areas, depending on the species studied.     

QUANTITATIVE CHARACTERS IN PHYLOGENETIC ANALYSIS

Abstract— When analysing phylogcnetic relationships at low laxonomic levels it is often the ease that many of the features that can be used to separate taxa show continuous variation. The theoretical and practical problems for the use of such quantitative characters in phylogenetic analysis arc examined. Three methods of coding continuous data into discrete characters are assessed in detail: simple gap-coding, generalised gap-coding and segment-coding, a form of range-coding. The methods are applied to a data set gathered for Eucatyptus L'Hérit. informal subgenus Symphyomyrtus section Maidenana (Myrtaceae). Each method is capable of distorting relative differences between taxa, but segment-coding produces the least amount of distortion, provided the range of variation of the character is divided into a sufficient number of character states.
Continuous quantitative characters provide data for phylogenetic analysis that arc more noisy than those provided by discrete qualitative characters and should, therefore, only be used when the number of qualitative characters is insufficient for resolution of relationships. The results of such analyses should be recognised as provisional pending the discovery of more readily informative characters.     

Visual exploration of alternative taxonomies through concepts

A graphical user interface is presented that allows users of taxonomic data to explore concept relationships between conflicting but related taxonomic classifications.Ecological analyses that use taxonomic metadata depend on accurate naming of specimens and taxa, and if the metadata involves several taxonomies, care has to be taken to match concepts between them. To perform this accurately requires expert-defined concept relationships, which are more complex yet more representative than the simple one-to-one mappings found through simple name matching, and can accommodate nomenclatural changes and differences in classification technique (cf ‘lumpers’ versus ‘splitters’). In the SEEK-Taxon (Scientific Environment for Ecological Knowledge) project we aim to help users of taxonomic datasets untangle and understand these relationships through a prototype visual interface which graphically displays these relationship structures, allowing users to comprehend such information and more accurately name their data.     

Phylogenetic relationships of bryophytes inferred from nuclear-encoded rRNA gene sequences

We investigate phylogenetic relationships among hornworts, liverworts and mosses, and their relationships to other green plant groups, by analysis of nucleotide variation in complete 18s rRNA gene sequences of three green algae, two hornworts, seven liverworts, nine mosses, and six tracheophytes. Parsimony and maximum-likelihood analyses yield a single optimal tree in which the hornworts are resolved as the basal group among land plants, and the liverworts and mosses are sister taxa that together form the sister clade to the tracheophytes. This phylogeny is internally robust as indicated by decay indices and by comparison (using both parsimony and likelihood criteria) to topologies representing five alternative hypotheses of bryophyte relationships. We discuss some possible reasons for differences between the phylogeny inferred from the rRNA data and those inferred from other character sets.