Taxonomic Congruence Research Articles

Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name Asgardarchaeota lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2TS, proposed to serve as the nomenclatural type for the species Asgardarchaeum abyssiTS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that A. abyssi AB3033_2TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for Asgardarchaeota using established Thermoproteota lineages in the GTDB r207 reference tree, we establish a robust classification and propose Asgardarchaeum as the type genus for the family Asgardarchaeaceae (fam. nov)., the order Asgardarchaeales (ord. nov.), the class Asgardarchaeia (class. nov.), and the phylum Asgardarchaeota (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.

Evolution of flower allometry and pigmentation in Mammillaria haageana (Cactaceae)

BackgroundA puzzle in evolution is the understanding of how the environment might drive subtle phenotypic variation, and whether this variation is adaptive. Under the neutral evolutionary theory, subtle phenotypes are almost neutral with little adaptive value. To test this idea, we studied the infraspecific variation in flower shape and color in Mammillaria haageana, a species with a wide geographical distribution and phenotypic variation, which populations are often recognized as infraspecific taxa.ResultsWe collected samples from wild populations, kept them in the greenhouse for at least one reproductive year, and collected newly formed flowers. Our first objective was to characterize tepal natural variation in M. haageana through geometric morphometric and multivariate pigmentation analyses. We used landmark-based morphometrics to quantify the trends of shape variation and tepal color-patterns in 20 M. haageana accessions, belonging to five subspecies, plus 8 M. albilanata accessions for comparison as the sister species. We obtained eight geometric morphometric traits for tepal shape and color-patterns. We found broad variation in these traits between accessions belonging to the same subspecies, without taxonomic congruence with those infraspecific units. Also the phenetic cluster analysis showed different grouping patterns among accessions. When we correlated these phenotypes to the environment, we also found that solar radiation might explain the variation in tepal shape and color, suggesting that subtle variation in flower phenotypes might be adaptive. Finally we present anatomical sections in M. haageana subsp. san-angelensis to propose some of the underlying tepal structural features that may give rise to tepal variation.ConclusionsOur geometric morphometric approach of flower shape and color allowed us to identify the main trends of variation in each accession and putative subspecies, but also allowed us to correlate these variation to the environment, and propose anatomical mechanisms underlying this diversity of flower phenotypes.

A Study of Correlation between Morphology and Evolution of Euphorbiaceae s.l. using Taxonomic Congruence and Total Evidence

Euphorbiaceae is one of the largest family of flowering plants, in our study different species were collected from different localities of Mizoram, the collected specimens were studied and their morphological features noted. 34 genera of Euphorbiaceae s.l were used in the study. Cladistic analysis was performed in Mesquite software and Phenetic analysis was done in NTsys software. Both analyses produce a pictorial representation in a form of a tree; cladistic analysis produce phylogenetic tree (evolutionary relationship) while phenetic analysis produce phenogram (morphological relationship). The results of the aforementioned analyses were further analysed by total evidence technique and taxonomic congruence, a phylogenetic software PAUP is used for this purpose. The resultant trees were very different and comparison was done to find correlation between evolution and morphological characters. The research finds various correlation among characters like the number of locule in ovule, phyllanthoid branching and support the inclusion of genus like Breynia, Sauropus into Phyllanthus.

Redesigning the Trading Zone between Systematics and Conservation: Insights from Malagasy mouse lemur classifications, 1982 to present

Translating information between the domains of systematics and conservation requires novel information management designs. Such designs should improve interactions across the trading zone between the domains, herein understood as the model according to which knowledge and uncertainty are productively translated in both directions (cf. Collins et al. 2019). Two commonly held attitudes stand in the way of designing a well-functioning systematics-to-conservation trading zone. On one side, there are calls to unify the knowledge signal produced by systematics, underpinned by the argument that such unification is a necessary precondition for conservation policy to be reliably expressed and enacted (e.g., Garnett et al. 2020). As a matter of legal scholarship, the argument for systematic unity by legislative necessity is principally false (Weiss 2003, MacNeil 2009, Chromá 2011), but perhaps effective enough as a strategy to win over audiences unsure about robust law-making practices in light of variable and uncertain knowledge. On the other side, there is an attitude that conservation cannot ever restrict the academic freedom of systematics as a scientific discipline (e.g., Raposo et al. 2017). This otherwise sound argument misses the mark in the context of designing a productive trading zone with conservation. The central interactional challenge is not whether the systematic knowledge can vary at a given time and/or evolve over time, but whether these signal dynamics are tractable in ways that actors can translate into robust maxims for conservation. Redesigning the trading zone should rest on the (historically validated) projection that systematics will continue to attract generations of inspired, productive researchers and broad-based societal support, frequently leading to protracted conflicts and dramatic shifts in how practioners in the field organize and identify organismal lineages subject to conservation. This confident outlook for systematics' future, in turn, should refocus the challenge of designing the trading zone as one of building better information services to model the concurrent conflicts and longer-term evolution of systematic knowledge. It would seem unreasonable to expect the International Union for Conservation of Nature (IUCN) Red List Index to develop better data science models for the dynamics of systematic knowledge (cf. Hoffmann et al. 2011) than are operational in the most reputable information systems designed and used by domain experts (Burgin et al. 2018). The reasonable challenge from conservation to systematics is not to stop being a science but to be a better data science. In this paper, we will review advances in biodiversity data science in relation to representing and reasoning over changes in systematic knowledge with computational logic, i.e., modeling systematic intelligence (Franz et al. 2016). We stress-test this approach with a use case where rapid systematic signal change and high stakes for conservation action intersect, i.e., the Malagasy mouse lemurs (Microcebus É. Geoffroy, 1834 sec. Schüßler et al. 2020), where the number of recognized species-level concepts has risen from 2 to 25 in the span of 38 years (1982–2020). As much as scientifically defensible, we extend our modeling approach to the level of individual published occurrence records, where the inability to do so sometimes reflects substandard practice but more importantly reveals systemic inadequacies in biodiversity data science or informational modeling. In the absence of shared, sound theoretical foundations to assess taxonomic congruence or incongruence across treatments, and in the absence of biodiversity data platforms capable of propagating logic-enabled, scalable occurrence-to-concept identification events to produce alternative and succeeding distribution maps, there is no robust way to provide a knowledge signal from systematics to conservation that is both consistent in its syntax and acccurate in its semantics, in the sense of accurately reflecting the variation and uncertainty that exists across multiple systematic perspectives. Translating this diagnosis into new designs for the trading zone is only one "half" of the solution, i.e., a technical advancement that then would need to be socially endorsed and incentivized by systematic and conservation communities motivated to elevate their collaborative interactions and trade robustly in inherently variable and uncertain information.

No background in biology is assumed

No background in biology is assumed

Diversity and distribution of the intertidal Mollusca of the State of Kuwait, Arabian Gulf

A total of 271 species of Mollusca from 5 classes, 26 orders, and 87 families were identified in the intertidal macrofauna survey along Kuwaiti coastal areas. A total of 36 sites along Kuwait’s mainland and island areas were sampled quantitatively and qualitatively during late autumn and winter season from December 2013 to December 2015. Of the 271 species, 211 were collected alive; the Gastropoda (104 species) ranked first, followed by the Bivalvia with 100; three species were recorded for the Polyplacophora, and two each for the Scaphopoda, and Cephalopoda. As many as 61 species, notably the micro-molluscs, are probably new records for Kuwait and many of may also be new to science.The most frequently occurring species included Brachidontes pharaonis, Ergalatax junionae, Planaxis savignyi, Leiosolenus tripartitus and Pinctada radiata. Mollusca diversity was higher in rocky-sandy areas than intertidal mudflats. The highest species richness was found in the area of south Kuwait Bay and coastal area around Failaka Island.Comparisons with previous surveys dating back to 1984 indicated that the dominant species composition was relatively unchanged. There are indications of the adverse affects of industrial impacts on the intertidal fauna, including eutrophication and increased turbidity. However, differences in methodology made any quantitative assessment impossible.Wider comparisons with the molluscan faunas of the Arabian Gulf and Arabian region suggest that the fauna of Kuwait has some unique elements not found elsewhere. Taxonomic problems surrounding some of the dominant elements such as the number of species of oysters (Ostreiidae) and mud snails (Cerithiidae) were recognised. The lack of taxonomic congruence between studies and the incomplete taxonomy of the molluscs in general made such comparisons inconclusive but did highlight the need for a revised identification guide to the Mollusca of the Arabian Gulf and Arabian Sea.

Phylogenetic Utility of Mammalian Postcranial Characters

In phylogenetic studies of extinct species, researchers often exclude postcranial data because postcranial elements are missing, underrepresented, or difficult to assign to particular species. However, in some cases these decisions revolve around the idea that postcranial data are inappropriate for phylogenetic analyses because they are functionally or developmentally integrated or otherwise “prone to homoplasy.” In this study, we used a character congruence approach to test the hypothesis that postcranial data cannot be used to reconstruct phylogenies instead of the taxonomic congruence approaches most often employed in paleoanthropological studies. We identified 98 published mammalian phylogenetic datasets that included sufficient numbers of characters from the skull, dentition, and postcranium to be included in the analysis. We calculated partitioned Bremer support (PBS) values for each data partition on each strict consensus cladogram using the programs Phylogenetic Analysis Using Parsimony (PAUP) v. 4.0b10 and TreeRot.v3, calculated partition congruence indices (PCI), and assessed significant differences between data partitions using Fischer's least significant difference test. Averaged across each cladogram, postcranial PBS values are greater than, or not significantly different from, 69.4% of skull PBS values (68 studies) and 64.3% of dental PBS values (63 studies). Postcranial data provided primary support (“winning sites”) at 301/1448 nodes (20.8%), exhibited positive values at 710/1483 nodes (47.9%), and “do no harm” at 1196/1483 nodes (80.6%). There is no correlation between PBS values and data partition size as long as there are at least ten characters in each data partition. These results highlight the potential for using postcranial data to construct hominin phylogenies and argue against their exclusion from phylogenetic analyses for a priori reasons.Support or Funding InformationUndergraduate student research in this study was supported by the Benedictine University Natural Science Summer Research Program.

Two Influential Primate Classifications Logically Aligned.

Classifications and phylogenies of perceived natural entities change in the light of new evidence. Taxonomic changes, translated into Code-compliant names, frequently lead to name:meaning dissociations across succeeding treatments. Classification standards such as the Mammal Species of the World (MSW) may experience significant levels of taxonomic change from one edition to the next, with potential costs to long-term, large-scale information integration. This circumstance challenges the biodiversity and phylogenetic data communities to express taxonomic congruence and incongruence in ways that both humans and machines can process, that is, to logically represent taxonomic alignments across multiple classifications. We demonstrate that such alignments are feasible for two classifications of primates corresponding to the second and third MSW editions. Our approach has three main components: (i) use of taxonomic concept labels, that is name sec. author (where sec. means according to), to assemble each concept hierarchy separately via parent/child relationships; (ii) articulation of select concepts across the two hierarchies with user-provided Region Connection Calculus (RCC-5) relationships; and (iii) the use of an Answer Set Programming toolkit to infer and visualize logically consistent alignments of these input constraints. Our use case entails the Primates sec. Groves (1993; MSW2–317 taxonomic concepts; 233 at the species level) and Primates sec. Groves (2005; MSW3–483 taxonomic concepts; 376 at the species level). Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every concept pair in the Primates sec. MSW2/MSW3. The complete alignment, and various partitions thereof, facilitate quantitative analyses of name:meaning dissociation, revealing that nearly one in three taxonomic names are not reliable across treatments—in the sense of the same name identifying congruent taxonomic meanings. The RCC-5 alignment approach is potentially widely applicable in systematics and can achieve scalable, precise resolution of semantically evolving name usages in synthetic, next-generation biodiversity, and phylogeny data platforms.

Dispelling five myths about hypothesis testing in biological systematics

The emphasis on testing phylogenetic hypotheses has been prominent since the English language introductions of Willi Hennig’s Phylogenetic Systematics (1966) and Karl Popper’s (1959) Logic of Scientific Discovery. While the mechanics of hypothesis and theory testing are well established in other fields of science, adherence to those prescriptions in biological systematics has rarely been formally recognized. The consequence has been the development of potentially contradictory approaches to empirically evaluating phylogenetic hypotheses under the guise of testing. In his brief review of the topic, Assis (Cladistics, 30:240–242, 2014) identified five different views on phylogenetic hypothesis testing: (1) total evidence, (2) taxonomic congruence, (3) reciprocal illumination, (4) homology assessment, and (5) taxa sampling. The present paper examines the validity of these views against the actual inferential steps required to infer hypotheses and subsequently engage in testing, i.e., abduction, deduction, and induction (sensu stricto), respectively. It is shown that none of the tests discussed by Assis are valid, and while it is straightforward to outline what is required to properly test phylogenetic hypotheses, the feasibility of accomplishing such tests is operationally impractical in most instances.

With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast.

The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.

Heuristic optimization for global species clustering of DNA sequence data from multiple loci

Summary Hierarchical clustering of molecular data is commonly used for estimation of species diversity in all forms of life. Parameters appropriate for species‐level clustering are usually derived from reference data and applied for the delineation of sequences of unknown species membership, although it is not clear how this should be carried out in a multilocus scenario. We introduce a novel means of concurrent clustering parameter optimization and delineation for multilocus data. A simulated annealing heuristic search is performed, whereby clustering thresholds are independently varied for each locus, but optimized according to the recovery of expected taxonomic species globally over loci. For each iteration of the search, one or more loci are randomly selected and a different threshold is separately proposed to cluster each, then the loci are linked to form global species units. Where the set of thresholds group the reference (species labelled) data with high taxonomic congruence, they are adopted for clustering of the subject (nonlabelled) sequences into global molecular operational taxonomic units (global MOTU). Four mined test data sets composed of both reference and subject sequences are combined with a newly sequenced three gene Apoidea data set, and subject to the proposed method. Even optimizing four loci and thousands of sequences, the approach rapidly convergences on a set of parameters with maximal optimality score, although the method masks a high degree of incongruence, and does not always converge on a single set of thresholds. For example, of the 476 Apoidea sequences, 70 global MOTU were inferred over the heuristic search, although the number of single gene MOTU were much lower for the 28S RNA locus, and a range of equally optimal clustering thresholds were observed for the CytB gene. We demonstrate the approach as a scalable species delineation solution for heterogeneous data sets composed of incompletely and inconsistently labelled data from public DNA data bases, for newly sequenced multilocus data, or both. The delineation over a heuristic search of clustering parameters facilitates the estimation of species diversity in multilocus data, giving species estimates that take into account uncertainty regarding choice of clustering thresholds.

Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence

The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.

Unravelling phylogenetic relationships among regionally co-existing species: Hydropsyche species (Trichoptera: Hydropsychidae) in the Loire River

Taxonomy is undoubtedly complementary to other fields in biology such as ecology, and both ecologists and taxonomists increasingly acknowledge that they can profit from phylogenetic ecology or ecological phylogeny, respectively. However, such mutual relations between these disciplines are constrained by traditional focuses on different operational scales: taxonomists are more familiar with large scales (e.g., global, continental, many species of a given clade), whereas ecologists are more familiar with small scales (regional, ecosystems, habitats, few species of a given clade). To foster mutually fruitful, 2-way exchanges between taxonomy and ecology at such smaller scales requires assessments of the small-scale performance of taxonomic practices so far used at larger scales. Such assessments are the objective of this study. To combine quantified ecology and phylogeny at the smaller scale, we designed a research project using 9 species of Hydropsyche (Trichoptera) from the Loire River (i.e., we focus on the regional scale). Here, we tried to unravel the phylogenetic relationships of this regional set of species using (1) many different characters (molecular and morphological characters of larvae and adults), (2) taxonomic congruence instead of total evidence (as the former provides more opportunities for future research on links between different data sets), and (3) an explicit data matrix and analysis methods that are commonly recommended for phylogenetic studies (e.g., maximum parsimony, maximum likelihood, bootstrapping), and we also included traditional, parsimonious, phylogenetic reasoning. Combining these elements, we obtained the following information for the regional Hydropsyche representatives from the Loire: (1) phylogenetic clusters of the species, (2) phylogenetic distances among the species, and (3) phylogenetic polarities of characters (plesioto apomorphies) in the species tree. For our future ecological studies, this will enable (1) establishment of priorities in species selections for experimental approaches, (2) establishment of relationships between ecological and phylogenetic distances, and (3) interpretation of ecological response gradients across the species in the context of evolutionary processes such as adaptation, niche conservatism, or fitness. These future ecological studies will provide elements that in turn should be useful for taxonomists wishing to include small-scale ecological data into their analyses.

Catching the phylogenic history through the ontogenic hourglass: a phylogenomic analysis of Drosophila body segmentation genes

The phylogenetic information content of different developmental stages is a long-standing issue in the study of development and evolution. We performed phylogenetic analyses of 51 body segmentation genes in 12 species of Drosophila in order to investigate the impact of the mode of evolution of development on phylogeny inference. Previous studies of these genes in Drosophila using pairwise phenetic comparisons at the species group level revealed the presence of an "hourglass model" (HG), wherein mid-embryonic stages are the most evolutionarily constrained. We utilized two character-based approaches: taxonomic congruence using the relative consensus fork index (RCFI), in which phylogenies are inferred from each gene separately and compared with a total evidence tree (TET), and partitioned simultaneous analysis using several indices such as branch support (BS) and localized incongruence length difference (LILD) test. We also proposed a new index, the recapitulatory index (R), which divides the number of synapomorphies on the total number of informative characters in a data set. Polynomial adjustment of both BS and R indices showed strong support for the hourglass model regardless of the taxonomic level (species subgroup vs. subgenera), showing less phylogenetic information content for mid-developmental stages (mainly the zygotic segment polarity stage). Significant LILD scores were randomly distributed among developmental stages revealing the absence of differential selective constraints, but were significantly related to chromosomal location showing physical (linkage) impact on phylogenetic incongruence. RCFI was the most sensitive measure to taxonomic level, having a convex parabola at the species subgroup level in support of the hourglass model and a concave parabola at the subgeneric level in support of the adaptive penetrance model. This time-dependent discrepancy of best fit developmental model parallels previous conflicting results from the vertebrates. Because of the quasi-phenetic nature of this index, we argue that the discrepancy is due to the evolutionary rate heterogeneity of developmental genes rather than to fundamental differences among organisms. We suggest that simultaneous character-based analyses give better macroevolutionary support to the hourglass model of the developmental constraints on genome evolution than pairwise phenetic comparisons.

Formalizing reliability in the taxonomic congruence approach

In the ‘total evidence’ approach to phylogenetics, the reliability of a clade is implicitly measured by its degree of support, often embodied in a robustness index such as a bootstrap proportion. In the taxonomic congruence approach, the measurement of reliability has been implemented by various consensus or supertree methods, but was seldom explicitly discussed as such. We explore a reliability index for clades using their repetition across independent data sets. All possible combinations of the elementary data sets are used to compose the sets of independent data sets, across which the repetitions are counted. The more a clade occurs across such independent combinations, the higher its index. However, if other repeated clades occur that are incompatible with that clade, its index is decreased to take into account the uncertainty resulting from conflicting hypotheses. Results can be summarized through a greedy consensus tree in which clades appear according to their repetition indices. This index is tested on a 73 acanthomorph taxa data set composed of five independent molecular markers and multiple combinations of them. On this particular application, we confirm that reliability as defined here and robustness (estimated by bootstrap proportions obtained from a ‘total evidence’ approach) should be clearly distinguished.

RNF213, a new nuclear marker for acanthomorph phylogeny

We show that RNF213 is a nuclear gene suitable for investigating large scale acanthomorph teleosteans interrelationships. The gene recovers many clades already found by several independent studies of acanthomorph molecular phylogenetics and considered as reliable. Moreover, we performed phylogenetic analyses of three other independent nuclear markers, first separately and then of all possible combinations (Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71–85. URL http://dx.doi.org/10.1017/S0954102004) of the four genes. This was coupled with an assessment of the reliability of clades using the repetition index of Li and Lecointre ( Li, B., Lecointre, G., 2008. Formalizing reliability in the taxonomic congruence approach. Article accepted by Zoologica Scripta. URL http://dx.doi.org/10.1111/j.1463-6409.2008.00361.x). This index was improved here to handle the incomplete taxonomic overlap among datasets. The results lead to the identification of new reliable clades within the ‘acanthomorph bush’. Within a clade containing the Atherinomorpha, the Mugiloidei, the Plesiopidae, the Blennioidei, the Gobiesocoidei, the Cichlidae and the Pomacentridae, the Plesiopidae is the sister-group of the Mugiloidei. The Apogonidae are closely related to the Gobioidei. A clade named ‘H’ grouping a number of families close to stromateids and scombrids (Stromateidae, Scombridae, Trichiuridae, Chiasmodontidae, Nomeidae, Bramidae, Centrolophidae) is related to another clade named ‘E’ (Aulostomidae, Macrorhamphosidae, Dactylopteridae). The Sciaenidae is closely related to the Haemulidae. Within clade ‘X’ (Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71–85. URL http://dx.doi.org/10.1017/S0954102004), the Cottoidei, the Zoarcoidei, the Gasterosteidae, the Triglidae, the Scorpaenidae, the Sebastidae, the Synanceiidae, and the Congiopodidae form a clade. Within clade ‘L’ (Chen, W.-J., Bonillo, C., Lecointre, G., 2003. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol. Phylogenet. Evol. 26, 262–288; Dettaï, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarct. Sci. 16 (1), 71–85. URL http://dx.doi.org/10.1017/S0954102004) grouping carangoids with flatfishes and other families (Centropomidae, Menidae, Sphyraenidae, Polynemidae, Echeneidae, Toxotidae, Xiphiidae), carangids are the stem-group of echeneids and coryphaenids, and sphyraenids are the sister-group to the Carangoidei. The Howellidae, the Epigonidae and the Lateolabracidae are closely related. We propose names for most of the clades repeatedly found in acanthomorph phylogenetic studies of various teams of the past decade.

The influence of spatial scale on the congruence of classifications circumscribing morphological units of biodiversity

AbstractAim The ‘taxonomic impediment’ has led to a growing trend in ecology and conservation biology to use operational surrogates for species within the context of a particular research project. Because such ‘parataxonomic’ classifications are typically spatially limited in scope, we examined the influence of increasing spatial scale on the congruence of two such approaches with a more traditional taxonomic classification.Location Sturt National Park, north‐western New South Wales, Australia.Methods Specimens of two ant genera, Camponotus and Rhytidoponera, were classified by three independent methods. The ‘parataxonomic’ classification assigned specimens to morphospecies without specialist taxonomic expertise; the ‘taxonomic’ classification assigned specimens to either described species or, where this was not possible, to operational taxonomic units (OTUs) using specialist taxonomic expertise; the ‘phenetic’ classification assigned specimens to putative species using a K‐means partitioning algorithm on basic morphometric data. Specimens of each genus were pooled into ‘assemblages’, which were defined at multiple spatial scales using a nested sampling design. Congruence in the interspecimen relationships of the different classifications was tested for each assemblage using pair‐wise Mantel correlations.Results Classification congruence tended to decrease with increasing spatial scale. There were, however, clear differences between the genera. Parataxonomic–taxonomic congruence was consistently greater for Camponotus, while phenetic–taxonomic congruence showed the opposite pattern.Conclusions Observed patterns in classification congruence are attributed to two principal causes: (i) within‐species morphological variation, including ecotypic variation in Rhytidoponera and caste polymorphism in Camponotus; and (ii) a limit to the morphological similarity of potentially competing species at small spatial scales. Regardless of cause, the decline in agreement as the spatial scale of observation is increased has important implications for the measurement of biodiversity, particularly when comparing samples over regional, continental, and global scales.

A protocol for large-scale rRNA sequence analysis: Towards a detailed phylogeny of Coleoptera

Large-scale phylogenetic analyses involving thousands of rRNA sequences are complicated due to length variability which compounds the already complex problem of large tree searches. Here, we generated a large data matrix and test phylogenetic procedures for large-scale analysis in the Coleoptera (beetles), as a resource for evolutionary biology and identification of this hugely diverse group. The analysis included nearly 1200 species, including representatives of 126 (75%) families, all 18 superfamilies of Polyphaga, and the four suborders. Alignments were obtained by a fragment-extension method derived from the BLAST algorithm using the BlastAlign script [Belshaw, R., Katzourakis, A., 2005. BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21, 122–123], followed by fast parsimony and maximum likelihood searches. Trees were assessed against the existing classification, using a formal procedure for coding the hierarchical position of taxa and establishing taxonomic congruence. We found that the BlastAlign procedure greatly exceeded the performance of standard progressive alignment methods such as Clustal. The resulting trees, when used as guide tree, also greatly improved the Clustal-based alignments. Long-branch attraction potentially affecting the quality of the tree was reduced by the systematic removal of all branches longer than a 95% interval of the distribution of branch lengths. We applied this protocol to the test for monophyly of major proposed lineages of Coleoptera, including Crowson’s 18 superfamilies in the hyperdiverse suborder Polyphaga. While searches for very large trees remained challenging and details of the tree topology were not always satisfactory, the strategy for alignment and tree searches used here makes large-scale phylogenetics of super-diverse groups such as Coleoptera amenable to desktop computing.

Towards reconstructing a metabolic tree of life.

Using information from several metabolic databases, we have built our own metabolic database containing 434 pathways and 1157 different enzymes. We have used this information to construct a dendrogram that demonstrates the metabolic similarities between 282 species. The resulting species distribution and the clusters defined in the tree show a certain taxonomic congruence, especially in recent relationships between species. This dendrogram is another representation of the tree of life, based on metabolism that may complement the trees constructed by other methods. For example, the metabolic dissimilarity we demonstrate between Symbiobacterium thermophilum (previously defined as Actinobacteria) and the other Actinobacteria species, and the metabolic similarity between S. thermophilum and Clostridia, combined with other evidence, suggest that S. thermophilum may be re-classified as Firmicutes, Clostridia.

Phylogenetic and taxonomic incongruence involving nuclear and mitochondrial markers in Korean populations of the freshwater snail genus Semisulcospira (Cerithioidea: Pleuroceridae)

We investigated the population genetic structure and phylogenetic relationships of four morphospecies of Semisulcospira sampled from multiple South Korean drainages. One, S. extensa, displayed modest levels of genetic diversity and formed a species-specific clade for both mitochondrial (mt) and nuclear markers. In contrast, the other three, S. coreana, S. gottschei, and S. libertina, were polyphyletic for both mt and nuclear markers. They formed, together with other nominal congeners ( S. forticosta, S. multicincta, S. nodiperda, and S. tegulata), a taxonomically heterogeneous species complex containing population-level admixtures of genotypes from numerically predominant modal clades in addition to rare, phylogenetically divergent, mt and nuclear genotypes. The modal mt haplotypes exhibited far more geographic than taxonomic congruence and typically co-clustered into drainage-specific tip clades, irrespective of nominal taxonomic status. The evolutionary origins of the observed non- extensa phylogenetic heterogeneity are unclear at present although the available data do not support paralogous mt marker phenomena or the presence of cryptic species. We cannot distinguish among retention of ancestral polymorphisms or recticulate evolutionary origins as explanatory mechanisms and it may require the genetic characterization of Semisulcospira lineages throughout much of their collective east Asian range to address this issue. Based on the available data, we consider it best to view all of our non- extensa Korean study taxa as a single polymorphic species complex of the type species S. libertina. There is considerable evidence that similarly complex genetic structuring, at least for mt, may be typical of many other freshwater cerithioidean snail taxa. In light of our Semisulcospira results, we suggest that meaningful molecular phylogenetic characterization of freshwater cerithioidean lineages may require the use of both mt and nuclear markers together with population level sampling of all nominal taxa within regional drainages.