Giant taxon‐character matrices: quality of character constructions remains critical regardless of size

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one‐third of the almost 1000 characters analysed were classified within at least one of our categories of “types” of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re‐analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.     

Combining taxon‐by‐trait and taxon‐by‐site matrices for analysing trait patterns of macroinvertebrate communities: a rejoinder to Monaghan & Soares ()

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Molecular systematics and morphological character evolution of the Condamineeae (Rubiaceae)

? Premise of the study: The Condamineeae have in previous molecular studies been shown to be part of an early-divergent clade within the subfamily Ixoroideae, together with the tribes Calycophylleae, and Hippotideae, and genera of the former Cinchoneae and Rondeletieae. Generic relationships within this clade have, however, remained largely unresolved. ? Methods: In this study, the systematics of the Condamineeae was further examined by phylogenetic reconstruction of six cpDNA regions and one nrDNA region using parsimony and Bayesian Markov chain Monte Carlo inference. Morphological character evolution within the tribe was assessed by ancestral state reconstruction using likelihood optimization of characters onto Bayesian trees. ? Key results: Calycophylleae appears polyphyletic. "Hippotideae" is monophyletic but nested within the Condamineeae. The phylogenetic hypotheses presented support a resurrection of the genera Holtonia, Schizocalyx, and Semaphyllanthe. Furthermore, Bathysa is found to be polyphyletic, Tresanthera is found nested within Rustia, and the taxonomically disputed genus Dialypetalanthus is here shown to be sister to a Bothriospora-Wittmackanthus clade. Morphological ancestral state reconstructions indicate that protogyny have evolved at least two times within the tribe and that indehiscent fruits, loculicidal fruit dehiscence, and intrapetiolar stipules have evolved independently several times. The occurrence of calycophylls (leaf-like calyx lobes), poricidal anthers, and winged seeds also appear homoplastic within the tribe. ? Conclusions: A diagnosis and delimitation of the tribe Condamineeae is presented, with taxonomic proposals to synonymize Tresanthera and to transfer several species of Bathysa as well as Phitopis to a resurrected Schizocalyx.     

Development of taxon‐specific markers for high‐throughput screening of microbial‐feeding nematodes

In an effort to assess the taxonomic identity of large‐scale samplings of nematodes from the Konza Tallgrass Prairie, we sequenced a portion of the 18S rRNA gene and its associated internally transcribed spacer (ITS1) from 74 nematodes encompassing four taxonomic families. From these sequences, we have developed a series of molecular probes to distinguish 16 distinct microbivorous nematode taxa. Using a combination of low power microscopy and taxon‐specific real‐time probes, the 74 nematodes were correctly assigned to their respective taxonomic groups. This optimized method provides a high‐throughput assay to determine nematode identities across larger data sets.     

Back to the future: A synthesis of strepsirrhine systematics

The stepsirrhine primates, defined here as living tooth-combed primates, their immediate ancestor, and all of its descendants, are a diverse assemblage of mammals, viewed by some as exemplars of the richness of evolutionary innovation and by others as uninteresting “primitive” primates. Fortunately, the former view has taken precedence in recent years. The Strepsirrhini have been central to numerous debates touching on key issues such as the congruence of phylogeny to biogeography, the reliability of morphological characters for phylogeny reconstruction, and the relationship of living lineages to fossil lineages. Thanks to important theoretical and methodological advances, particularly within the arena of genetics, a robust picture of strepsirrhine phylogeny is emerging that casts light on these and numerous other evolutionary questions. © 1997 Wiley-Liss, Inc.     

Phylogenetics and the future of helminth systematics

Phylogenetic systematics is a relatively new formal technique that increases the precision with which one can make direct estimates of the history of phylogenetic descent. These estimates are made in the form of phylogenetic trees, or cladograms. Cladograms may be converted directly into classifications or they may be used to test various hypotheses about the evolutionary process. More than 20 phylogenetic analyses of helminth groups have been published already, and these have been used to investigate evolutionary questions in developmental biology, biogeography, speciation, coevolution, and evolutionary ecology.     

Can taxon‐sampling effects be minimized by using branch supports?

Rydin and Källersjö (2002 ) found that taxon‐sampling effects were a strongly disturbing factor in a high‐level phylogenetic analysis. I have reanalyzed some of their data to assess whether bootstrap frequencies can be used to predict the stability of clades to taxon sampling, and to compare it with the performance of a stability measure based on taxon resampling (“taxon jackknifing”). High bootstrap frequencies correctly identify a small number of stable clades, but miss many other equally stable clades. When the total error rate is considered, no cut‐off level based on bootstrap frequencies performs better than using all clades in the strict consensus, whereas a slight improvement was observed when cut‐off levels based on taxon jackknifing frequencies are used. © The Willi Hennig Society 2006.     

Strong but taxon‐specific responses of termites and wood‐nesting ants to forest regeneration in Borneo

Land use change is accelerating globally at the expense of biodiversity and ecosystem functioning. Invertebrates are numerically dominant and functionally important in old growth tropical rain forests but highly susceptible to the adverse effects of forest degradation and fragmentation. Ants (Formicidae) and termites (Blattodea: Termitoidae) perform crucial ecosystem services. Here, the potential effects of anthropogenic disturbance on ant and termite communities in dead wood are investigated. Community composition, generic richness, and occupancy rates of ants and termites were compared among two old growth sites (Danum Valley and Maliau Basin) and one twice‐logged site (the Stability of Altered Forest Ecosystems’ (SAFE) Project), in Sabah, Malaysian Borneo. Occupancy was measured as the number of ant or termite encounters (1) per deadwood items, and (2) per deadwood volume, and acts as surrogates for relative abundance (or generic richness). Termites had a lower wood‐occupancy per volume in logged forest. In contrast, there were more ant encounters, and more ant genera, in logged sites and there was a community shift (especially, there were more Crematogaster encounters). The disruption of soil and canopy structure in logged forest may reduce both termite and fungal decay rates, inducing increased deadwood residence times and therefore favoring ants that nest in dead wood. There is an anthropogenic‐induced shift of dead wood in ants and termites in response to disturbance in tropical rain forests and the nature of that shift is taxon‐specific.     

Micro‐spatial separation and associated morphological adaptations in the original case of avian character displacement

Divergent evolution between Western Rock Nuthatch Sitta neumayer and Eastern Rock Nuthatch Sitta tephronota is widely recognized as the original case study of character displacement. However, in their contact zone in the Zagros Mountains, Iran, the morphological differences important for niche segregation between the two species remain unknown. We investigated microhabitat use and morphological adaptations of the two species, predicting that morphological adaptations to different habitats in these two nuthatches have led to spatial segregation. Seventy‐seven birds were captured and measured in the contact zone and allopatric zone in Iran. Twenty‐two primary variables related to flight apparatus, functional foot apparatus and feeding apparatus were measured and 11 ratios of primary variables were calculated as secondary variables due to their importance in habitat use. We also measured environmental variables related to geological features, mineral substrates and vegetation cover at a random sample of 100 of the locations where a nuthatch was observed. Results of morphometric and habitat analyses indicated that, in addition to trophic niche segregation, the two nuthatch species also differ in their microhabitat use and show differences in morphological features accordingly. In many case studies of character displacement, much more interest has been focused on the morphological differences in feeding apparatus than on those relating to habitat use. We suggest that future studies of character displacement should pay more attention to spatial niche segregation between sympatric species rather than trophic niche segregation.     

The systematics of Porphyra: character evolution in closely related species

Isozymes, vegetative and reproductive morphology, seasonality, vertical and geographic distributions and chromosomes were compared for six pairs of putative sibling species of Porphyra (P. abbottae/P. torta, P. fallax subsp. fallax/P. fallax subsp. conwayae, P. amplissima/P. cuneiformis, P. fucicola/P. leucostica, P. miniata/P. variegata, P. umbilicalis/P. umbilicalis) and among five species in a complex (P. brumalis, P. kurogii, P. linearis, P. pseudolinearis, and P. purpurea.) Geographic distribution and zymograms for certain proteins showed the greatest change between species pairs: only one pair of species had identical distributions, and most species pairs were disjunct; every species had a different allozyme for GOT-1, whereas all species had apparently identical proteins for phycoerythrin. Seasonality and habitat exhibited moderate differentiation: Northeast Pacific sibling species were characterized by a high intertidal winter species pairing with a mid intertidal spring species, whereas all but one of the other species pairs exhibited nearly identical vertical distributions and seasonalities. There were few changes in morphology: most species pairs had essentially identical morphologies and coloration and the same arrangement of reproductive cells. Chromosome numbers and karyotypes were identical for species pairs and in the species complex. These results provide evidence for different rates of evolution of different characters in the genus Porphyra.     

Status‐dependence and morphological trade‐offs in the expression of a sexually selected character in the mite,Sancassania berlesei

Abstract In the male dimorphic mite Sancassania berlesei, fighter males kill rivals with a pair of armoured legs whereas scrambler males are benign with unmodified legs. In an adaptive response mediated by colony pheromones, fighter expression increases at low colony density. Under the status‐dependent evolutionarily stable strategy (ESS) model we expected heavier final instar nymphs to become fighters. This was supported in group reared nymphs. In individually reared nymphs fighter expression was experimentally suppressed using two concentrations of colony pheromone. Here, male morph expression again depended on tritonymphal body mass and contact is therefore unnecessary for individuals to judge their status. Fighter suppression was greater in the higher pheromone treatment, but morph determination remained status dependent. The weight and length of fighters was lower than scramblers of same‐weight final instar nymphs, indicating a developmental trade‐off, and a cost not recouped at the adult stage.     

Phylogenetic systematics and character evolution in the angiosperm family Haloragaceae

The poorly known Haloragaceae R. Br. (Saxifragales) are highly diverse in habit (small trees to submerged aquatics) and labile in floral merosity (2-4), both uncommon among the core eudicots. This family has a cosmopolitan distribution, but taxonomic diversity is concentrated in Australia. An explicit phylogenetic approach has not previously been utilized to examine relationships or character evolution in this family. We used molecular evidence from nrDNA ITS and cpDNA trnK and matK regions under both Bayesian and parsimony analyses to address phylogenetic relationships. Combined molecular analyses defined a monophyletic Haloragaceae with the woody genera (Haloragodendron, Glischrocaryon) sister to the rest. Relationships among many genera were well resolved, with genera as currently delimited generally well supported, although there were notable exceptions; a new genus (Trihaloragis) is recognized, and the aquatic genus Meionectes is again distinct from Haloragis. Three new species combinations are also recognized. There are multiple (two or three) origins of the submerged aquatic habit in the family and potentially an intermediate reversal to the terrestrial habit, neither previously demonstrated in a core eudicot family using an explicit phylogenetic hypothesis. Ancestral character analyses suggest two origins of trimerous flowers and multiple reductions to dimerous flowers throughout Haloragaceae.     

Platyrrhine systematics: A simultaneous analysis of molecular and morphological data

Platyrrhine phylogeny has been investigated repeatedly with morphological characters and DNA nuclear gene sequences, with partially inconsistent results. Given the finding in the past decade that the mitochondrial genome is a potentially valuable source of phylogenetic information, we gathered DNA sequence data of a fragment of the 16S and the entire 12S mitochondrial genes. The objectives were to generate a cladistic phylogeny based on these data and to combine them in a simultaneous analysis with morphological characters and preexisting nuclear DNA sequences. Mitochondrial data analyzed on its own yielded a cladogram that was different from those generated with other data sets. The simultaneous analysis of mitochondrial, nuclear, and morphological data yielded a tree most congruent with that generated with nuclear data and to a lesser degree with the morphological one. It depicted a basal dichotomy that led to two major clades: one of them comprised [Atelinae (Callicebus + Pitheciini)] and the other major clade comprised [Aotus ((Cebus, Saimiri) (Callitrichinae))]. The weakest point of the phylogeny was the position of Aotus as basal within their clade as opposed to more closely linked with either the callitrichines or Cebus-Saimiri. Relationships within callitrichines and atelines were unstable as well. The simultaneous phylogenetic analysis of all data sets revealed congruent signal in all of them that was partially obscured in the separate analyses. Am J Phys Anthropol 106:261–281, 1998. © 1998 Wiley-Liss, Inc.     

The phylogeography of the Placozoa suggests a taxon‐rich phylum in tropical and subtropical waters

Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.     

Prediction of taxon occurrence: a test on taxon‐specific change point values of stream benthic invertebrates

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我国放线菌系统学研究历史、现状及未来发展趋势

放线菌系统学是以实现对放线菌进行分类、鉴定、命名为目标的基础学科, 因此它是放线菌资源研究和开发利用的重要理论基础。自20世纪50年代起, 我国放线菌系统学的奠基人阎逊初院士及同事们就开创了我国放线菌系统学的研究, 经过近六十年、几代人的艰苦努力, 我国放线菌系统学工作者在国际微生物系统学权威杂志(International Journal of Systematics and Evolutionary of Microbiology, IJSEM)发表的有关放线菌新分类单元的论文数量连续十年排名稳居前列, 部分学者在国际上发表的某些改良的分类技术和新修订的分类系统等为国际同行所广泛采用, 这些均标志着我国放线菌系统学研究在国际上已成为微生物系统学界的一支重要力量。本文全面介绍了我国放线菌系统学研究的发展历程, 同时对其发展现状给予理性分析, 并就未来发展方向进行了展望。     

Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses

For a nearly complete set of species of Erythronium (Liliaceae), we examined two plastid loci (the rps16 intron and the 5′ trnK intron, excluding the matK exon), one nuclear locus (nrITS) and morphology to evaluate species relationships and that of Erythronium to Amana, the putatively most closely allied genus. A matrix of morphological characters was developed through observation of around 900 living and herbarium specimens; evolution of these was examined using character optimization on the combined (total‐evidence) tree. Parsimony methods were used to examine the morphological and molecular data sets produced, both separately and in combination, with Bayesian methods also used on the molecular data sets. These established that the genus is probably sister to Amana (although most analyses placed Amana inside Erythronium) and that Tulipa is sister to the pair of Erythronium and Amana. Within Erythronium, there are three strongly supported geographically distinct clades: (1) Eurasian and (2) eastern and (3) western North American. Separation of species in these three clades is less clear, particularly among the western North American taxa. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.     

A framework for developing and validating taxon‐specific primers for specimen identification from environmental DNA

Taxon‐specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates noninvasive ecological studies but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon‐specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity and utility. Our framework makes possible a rigorous evaluation of likely sources of error. The first five steps can be conducted relatively rapidly and (where reference DNA sequences are available) require minimal laboratory resources, enabling assessment of primer suitability before investing in further work. Steps six to eight require more costly laboratory analyses but are essential to evaluate risks of false‐positive and false‐negative results, while step 9 relates to field implementation. As an example, we have developed and evaluated primers to specifically amplify part of the mitochondrial ND2 gene from Australian bandicoots. If adopted during the early stages of primer development, our framework will facilitate large‐scale implementation of well‐designed DNA tests to detect specific wildlife from eDNA samples. This will provide researchers and managers with an understanding of the strengths and limitations of their data and the conclusions that can be drawn from them.