Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta‐analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode of life and habitat. First, after correcting for study effort and accounting for higher taxonomic affinities and biogeographical region of origins, our results do not support the hypothesis that cryptic taxa are more frequent among parasitic than free‐living taxa. Second, in contrast, the results support the hypothesis that cryptic taxa are more common in certain habitats than others: for a given study effort, more cryptic taxa are found in freshwater than in terrestrial or marine taxa. These findings suggest that the greater heterogeneity and fragmentation of freshwater habitats may promote higher rates of genetic differentiation among its inhabitants, a general pattern with serious implications for freshwater conservation biology.     

Approaches to the resolution of contradictions between phylogenetic reconstructions based on morphofunctional and genetic data

Essential differences between genetic and morphofunctional characteristics as sources of information about evolutionary development are discussed using examples of mammal taxa. The approaches to combined analysis of data characterizing different levels of biological organization in phylogenetic reconstructions are considered using examples of certain mammalian taxa.     

Alien species as a driver of recent extinctions

We assessed the prevalence of alien species as a driver of recent extinctions in five major taxa (plants, amphibians, reptiles, birds and mammals), using data from the IUCN Red List. Our results show that alien species are the second most common threat associated with species that have gone completely extinct from these taxa since AD 1500. Aliens are the most common threat associated with extinctions in three of the five taxa analysed, and for vertebrate extinctions overall.     

Revisiting the Estimation of Dinosaur Growth Rates

Previous growth-rate studies covering 14 dinosaur taxa, as represented by 31 data sets, are critically examined and reanalyzed by using improved statistical techniques. The examination reveals that some previously reported results cannot be replicated by using the methods originally reported; results from new methods are in many cases different, in both the quantitative rates and the qualitative nature of the growth, from results in the prior literature. Asymptotic growth curves, which have been hypothesized to be ubiquitous, are shown to provide best fits for only four of the 14 taxa. Possible reasons for non-asymptotic growth patterns are discussed; they include systematic errors in the age-estimation process and, more likely, a bias toward younger ages among the specimens analyzed. Analysis of the data sets finds that only three taxa include specimens that could be considered skeletally mature (i.e., having attained 90% of maximum body size predicted by asymptotic curve fits), and eleven taxa are quite immature, with the largest specimen having attained less than 62% of predicted asymptotic size. The three taxa that include skeletally mature specimens are included in the four taxa that are best fit by asymptotic curves. The totality of results presented here suggests that previous estimates of both maximum dinosaur growth rates and maximum dinosaur sizes have little statistical support. Suggestions for future research are presented.     

HOMOPLASY AS PATTERN: MULTIVARIATE ANALYSIS OF MORPHOLOGICAL CONVERGENCE IN ANSERIFORMES

Abstract— A multivariatc model for taxa and characters is presented that represents taxa as points in an ordination space such that shared derived character states define groups of taxa or regions in this space. This model is compared, in terms of concepts of information content and explanatory power, to the eladistie model that relates characters and taxa to a hierarchical pattern. While a cladogram may be identified with a phylogenetic hypothesis, the ordination pattern may be equated with hypotheses about similarities among the taxa in habitat, feeding mode, or other ecological factors.
This basic data-pattern model is appropriate for the explanation of the character convergences implied by a particular phylogenetic hypothesis. Under the assumptions of the model, the underlying ordination pattern may be inferred from the observed character data using robust ordination procedures recently developed in community ecology.
As an illustration of the method, the morphological convergences derived from a recent phylogenetic hypothesis for genera of Anseriformes are analysed. In the resulting two-dimensional ordination, the genera are arranged such that the convergenlly derived states form regions in the space. While this pattern implies that some of the taxa that are close together in the space are phylogcnetically dissimilar , taxa that are close together in the space are found to be similar in their mode of feeding. Thus, the ordination demonstrates that taxa sharing these morphological convergences tend to utilize habitat in the same way in terms of mode of feeding.
The explanatory power of the pattern and the degree of recovery of habitat information are tested against null hypotheses using Monte Carlo simulations.
Extensions of the method are discussed, including applications to studies of parasite—host relationships and to biogeography.     

Correction to: An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago

The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset covering 97.9% of the taxa. Spatial distribution of species richness and phylogenetic diversity was visualized. Apomixis was observed in 11.0% of the native taxa whose reproductive modes are known. The number of sexually reproducing polyploid taxa (n = 199) is less than sexual diploids (n = 241), and 30 of them are evidently allopolyploid, in contrast with the low number of possible autopolyploids (n = 4). Apomictic taxa were found to have smaller latitudinal ranges than sexual taxa or taxa with multiple reproductive modes. A morphological character dataset in Lucid format is provided for taxonomic identification of the native taxa.

     

Systematic biostratigraphy: A solution to problematic classification systems in biostratigraphy

Systematic biostratigraphy is based on the exclusive use of monophyletic marker taxa. Non-monophyletic, or artificial, marker taxa have been shown to change biostratigraphic correlations, a situation that can be rectified by using systematics to ensure that marker taxa are monophyletic or natural. Both hypothetical and real examples demonstrate the validity of the methodology. The foraminiferal genera Praemurica and Parvularugoglobigerina are examples of non-monophyletic marker taxa. Cladistic results permit the reclassification of both genera, and a revision of foraminiferal biostratigraphy. Systematic biostratigraphy ensures the use of monophyletic marker taxa, preventing artificial classifications from hindering biostratigraphic correlations and producing more accurate, and stable, biostratigraphic zonations.     

Reassessment of diversity and analysis of distribution in Tulipa (Liliaceae) in Uzbekistan

The diversity and distribution of the genus Tulipa in Uzbekistan are discussed; 34 taxa of Tulipa are recognized in Uzbekistan. The taxa were mapped using GIS software and their distributions were analyzed. Six species are endemic to the country. A national check‐list of Tulipa was created based on the classification developed by Zonneveld (2009). ‘Hot spot’ areas of tulip diversity in Uzbekistan are western Tien‐Shan (18 taxa), the western Pamir–Alay mountains (18 taxa) and the Turan lowland (5 taxa). An assessment of rare tulip species according to IUCN red list categories and criteria was performed for the first time for Uzbekistan. Evaluation of the latest classification of Tulipa clearly shows that further studies are required to arrive at a natural classification of the genus.     

Molecular systematics,GISH and the origin of hybrid taxa in Nicotiana (Solanaceae)

Phylogenetic relationships in the genus Nicotiana were investigated using parsimony analyses of the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA (nrDNA). In addition, origins of some amphidiploid taxa in Nicotiana were investigated using the techniques of genomic in situ hybridization (GISH), and the results of both sets of analyses were used to evaluate previous hypotheses about the origins of these taxa. Phylogenetic analyses of the ITS nrDNA data were performed on the entire genus (66 of 77 naturally occurring species, plus three artificial hybrids), comprising both diploid and polyploid taxa, and on the diploid taxa only (35 species) to examine the effects of amphidiploids on estimates of relationships. All taxa, regardless of ploidy, produced clean, single copies of the ITS region, even though some taxa are hybrids. Results are compared with a published plastid (matK) phylogeny using fewer, but many of the same, taxa. The patterns of relationships in Nicotiana, as seen in both analyses, are largely congruent with each other and previous evolutionary ideas based on morphology and cytology, but some important differences are apparent. None of the currently recognized subgenera of Nicotiana is monophyletic and, although most of the currently recognized sections are coherent, others are clearly polyphyletic. Relying solely upon ITS nrDNA analysis to reveal phylogenetic patterns in a complex genus such as Nicotiana is insufficient, and it is clear that conventional analysis of single data sets, such as ITS, is likely to be misleading in at least some respects about evolutionary history. ITS sequences of natural and well-documented amphidiploids are similar or identical to one of their two parents-usually, but not always, the maternal parent-and are not in any sense themselves 'hybrid'. Knowing how ITS evolves in artificial amphidiploids gives insight into what ITS analysis might reveal about naturally occurring amphidiploids of unknown origin, and it is in this perspective that analysis of ITS sequences is highly informative.     

A reexamination of infraspecific taxa of a wild potato,Solanum microdontum (Solanum sect.Petota:Solanaceae)

Current taxonomic interpretations ofSolanum microdontum Bitter partition the species into two or three infraspecific taxa, variously recognized as subspecies or varieties. The present study reexamines these taxa using morphological data from four individuals each of 69 accessions from most of the range of the species, planted in a common field plot. Our results show that the character states used to recognize infraspecific taxa inS. microdontum often vary within accessions and have no correlation with geography. We conclude that past hypotheses have used typological concepts and that infraspecific taxa are not warranted. This study questions other hypotheses of infraspecific taxa in sect.Petota.     

Taxonomy of the Carex flava complex (Cyperaceae) in Finland

The morphological variation in the Carex flava complex (sect. Ceratocystis ) in Finland, particularly taxa described by Alvar Palmgren as endemic to northern Europe, was studied using numerical analyses. Discriminant analyses were used to maximize the separation of the taxa. However, the separation of the taxa described by Palmgren was weak. The taxonomic treatment of the C. flava complex in Finland based on morphology, ecology, distribution and hybridization of the taxa is presented. Four species are recognized: Carex flava (the lectotype is selected here), C. lepidocarpa, C. demissa and C. viridula. C. lepidocarpa includes ssp. lepidocarpa and ssp. jemtlandica . In the polymorphic C. viridula , three taxa are recognized: var. viridula , var. bergrothii and var. pulchella . A key to the taxa is presented. The distribution of the taxa in Finland is presented, and their ecology is briefly discussed.     

Selection of nontarget arthropod taxa for field research on transgenic insecticidal crops: using empirical data and statistical power

One of the possible adverse effects of transgenic insecticidal crops is the unintended decline in the abundance of nontarget arthropods. Field trials designed to evaluate potential nontarget effects can be more complex than expected because decisions to conduct field trials and the selection of taxa to include are not always guided by the results of laboratory tests. Also, recent studies emphasize the potential for indirect effects (adverse impacts to nontarget arthropods without feeding directly on plant tissues), which are difficult to predict because of interactions among nontarget arthropods, target pests, and transgenic crops. As a consequence, field studies may attempt to monitor expansive lists of arthropod taxa, making the design of such broad studies more difficult and reducing the likelihood of detecting any negative effects that might be present. To improve the taxonomic focus and statistical rigor of future studies, existing field data and corresponding power analysis may provide useful guidance. Analysis of control data from several nontarget field trials using repeated-measures designs suggests that while detection of small effects may require considerable increases in replication, there are taxa from different ecological roles that are sampled effectively using standard methods. The use of statistical power to guide selection of taxa for nontarget trials reflects scientists' inability to predict the complex interactions among arthropod taxa, particularly when laboratory trials fail to provide guidance on which groups are more likely to be affected. However, scientists still may exercise judgment, including taxa that are not included in or supported by power analyses.     

Composition and similarity of bovine rumen microbiota across individual animals

The bovine rumen houses a complex microbiota which is responsible for cattle's remarkable ability to convert indigestible plant mass into food products. Despite this ecosystem's enormous significance for humans, the composition and similarity of bacterial communities across different animals and the possible presence of some bacterial taxa in all animals' rumens have yet to be determined. We characterized the rumen bacterial populations of 16 individual lactating cows using tag amplicon pyrosequencing. Our data showed 51% similarity in bacterial taxa across samples when abundance and occurrence were analyzed using the Bray-Curtis metric. By adding taxon phylogeny to the analysis using a weighted UniFrac metric, the similarity increased to 82%. We also counted 32 genera that are shared by all samples, exhibiting high variability in abundance across samples. Taken together, our results suggest a core microbiome in the bovine rumen. Furthermore, although the bacterial taxa may vary considerably between cow rumens, they appear to be phylogenetically related. This suggests that the functional requirement imposed by the rumen ecological niche selects taxa that potentially share similar genetic features.     

Can Global Weed Assemblages Be Used to Predict Future Weeds?

Predicting which plant taxa are more likely to become weeds in a region presents significant challenges to both researchers and government agencies. Often it is done in a qualitative or semi-quantitative way. In this study, we explored the potential of using the quantitative self-organising map (SOM) approach to analyse global weed assemblages and estimate likelihoods of plant taxa becoming weeds before and after they have been moved to a new region. The SOM approach examines plant taxa associations by analysing where a taxon is recorded as a weed and what other taxa are recorded as weeds in those regions. The dataset analysed was extracted from a pre-existing, extensive worldwide database of plant taxa recorded as weeds or other related status and, following reformatting, included 187 regions and 6690 plant taxa. To assess the value of the SOM approach we selected Australia as a case study. We found that the key and most important limitation in using such analytical approach lies with the dataset used. The classification of a taxon as a weed in the literature is not often based on actual data that document the economic, environmental and/or social impact of the taxon, but mostly based on human perceptions that the taxon is troublesome or simply not wanted in a particular situation. The adoption of consistent and objective criteria that incorporate a standardized approach for impact assessment of plant taxa will be necessary to develop a new global database suitable to make predictions regarding weediness using methods like SOM. It may however, be more realistic to opt for a classification system that focuses on the invasive characteristics of plant taxa without any inference to impacts, which to be defined would require some level of research to avoid bias from human perceptions and value systems.     

Categorizing locally rare plant taxa for conservation status

Locally rare taxa are those that are rare or uncommon within a local geographical boundary while more common outside of that boundary. In addition to the rare taxa identified by global, national, and state/provincial levels, locally rare taxa are important for the preservation of species diversity and ecological processes, and therefore require effective and recognizable conservation status. Currently, there are no specific local rarity criteria in use to categorize taxa at regional jurisdictional levels. To address this need, we developed criteria for categorizing locally rare plant taxa by using the framework the Natural Heritage Network’s Element Ranking System combined with attributes of the World Conservation Union’s Red List Criteria. We then tested the efficacy of our classification system (called L-ranks) on the flora of Napa County using a geographic information system and available plant distribution data for the State of California. Results indicated that 89 taxa from 34 families met the area of occupancy criteria for local rarity status. Our findings demonstrated that with available geographic data, the proposed criteria for classifying locally rare plants can be usefully applied at the county level to identify significant peripheral plant populations. The proposed L-rank system was specifically designed to be compatible with existing multi-scale conservation programs and will augment the current systems in use by local organizations. By systematically classifying locally rare plants, current regulations that are applicable to locally rare taxa may be used more effectively in conservation planning and prioritizing at the county scale.     

Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.     

Large-scale phylogenies and measuring the performance of phylogenetic estimators

Performance measures of phylogenetic estimation methods such as accuracy, consistency, and power are an attempt at summarizing an ensemble of a given estimator's behavior. These summaries characterize an ensemble behavior with a single number, leading to a variety of definitions. In particular, the relationships between different performance measures such as accuracy and consistency or accuracy and error depend on the exact definition of these measures. In addition, it is relatively common to use large-sample behavior to infer similar behavior for small samples. In fact, large-sample results such as the claimed asymptotic efficiency of the maximum-likelihood estimator are often uninformative for small samples. Conversely, small-sample behavior using simulations is sometimes used to imply large-sample behavior such as consistency. However, such extrapolation is often difficult. How the performance of a phylogenetic estimator scales with the addition of taxa must be qualified with respect to whether the whole tree is being estimated or a fixed subset of taxa is being estimated. It must also be qualified with respect to how tree models are sampled. Over the ensemble of all possible trees of a given size, the performance of the estimators for the whole tree estimate suffers when the tree size becomes larger. However, under certain models of cladogenesis, the estimate can improve with the addition of taxa. In fact, at all numbers of taxa there are subsets of tree models that are easier to estimate than others. This suggests that with judicious addition or subtraction of taxa we can move from tree models that are more difficult to estimate at one number of taxa to those that are easier to estimate at another number of taxa.     

Investigation of hybridization between Asclepias speciosa and A. syriaca using alkanes,fatty acids and triterpenoids

Individuals of Asclepias speciosa and A. syriaca from Kansas and Nebraska were sampled and their alkanes, fatty acids and triterpenoids analyzed. Analysis of variance for 30 compounds yielded four significant and seven highly significantly quantitative differences between the taxa. No qualitative differences were found. Analyses of the components using Well's hybrid distance diagram and principal coordinate analysis confirmed that hybridization as well as introgression is occurring between these taxa in this region. Data from isozymes revealed that the two taxa are almost identical. These data, taken together, are indicative of a closer (perhaps conspecific) relationship between these taxa than previously suggested.     

Assessing the ecological value of small testate amoebae (<45 μm) in New Zealand peatlands

Methodological advances are essential for robust ecological research. Quantitative reconstructions of environmental conditions using testate amoebae rely on sound taxonomy. While the taxonomy of large species is relatively well resolved, this is not the case for most small taxa (typically <45 μm long). In New Zealand, peatlands contain a diversity of both cosmopolitan and characteristic large southern endemic taxa, but also have a high abundance of small taxa. The latter are often lumped into morphotypes reducing their value as ecological indicators. In this study, we demonstrate how (a) lumping small taxa versus splitting them into unique types, and (b) including or excluding them from community analysis influenced their ecological inference. We assessed testate amoeba composition in six peat bogs from New Zealand, three that were moderately-to-highly impacted, and three that were non-impacted. Environmental variables were measured at each sampling site and the surface testate amoeba community patterns and community-environment relationships compared. We found a clear division between impacted and non-impacted sites. Several distinct small taxa were more strongly related to water-table depth and conductivity, while the larger taxa were more correlated to pH. These results show that improved taxonomic resolution of small taxa can provide more informed environmental assessment.     

Rarity in the tropics: biogeography and macroecology of the primates

Aim To describe rarity and elucidate its biology in a tropical mammalian order, the Primates. Location Africa, Central and South America, Asia, Madagascar. Methods A review of the literature, with some additional analyses using data from the literature. A variety of definitions of rarity are used in order to describe it and to investigate its biology by correlating the degree of rarity with a variety of biological traits indicative of resource use (e.g. size of annual home range), reproductive rate (e.g. birth interval)and specialization (e.g. number of habitat types used). Results Few primate taxa occur outside the tropics, and most taxa are rare (small geographical range size or latitudinal extent, low density or both). Latitudinal extent is narrower at lower latitudes in Africa and Asia, but the potential resultant packing of taxa appears not to explain the taxonomic diversity gradient. Whilst primate species do not show the common, positive density by range size relationship, primate genera show a significant shallow slope, and primate families/subfamilies a strongly positive slope. Rare taxa are specialized, but neither use more resources nor breed more slowly than common taxa. The correlation of rarity and specialization is via geographical range: taxa with small ranges, or small ranges for their density, are specialized, but not taxa at low density. Common taxa are generalized because they consist of more differently specialized subtaxa, not because each subtaxon is generalized. Main conclusions Most primate taxa are rare, in which case most are presumably likely to go extinct. Rare primates are specialized, but do not necessarily use more resources, nor breed more slowly. Specialization as an explanation for rarity appears to work via constriction of range size, not of density. Common primates might be common (large range size) not because subtaxa or individuals are generalized, but because they are composed of more subtaxa. A consequence could be that persistence of even common taxa will depend on conservation of several populations scattered across the taxon's geographical range.