Phylogenetic inference using non‐redundant coding of dependent characters versus alternative approaches for protein‐coding genes

Contemporary molecular phylogenetic analyses often encompass a broad range of taxonomic diversity while maintaining high levels of sampling within each major taxon. To help maximize phylogenetic signal in such studies, one may analyse multiple levels of characters simultaneously. We test the performance of both the original and the modified versions of non‐redundant coding of dependent characters (NRCDC) relative to commonly applied alternative character‐sampling strategies using codon‐based simulations under a range of conditions. Both original and modified NRCDC generally outperformed other character‐sampling strategies that only sampled characters at one level (nucleotides or amino acids) over a broader range of simulation parameters than any of the alternative character‐sampling strategies with respect to both overall success of resolution and averaged overall success of resolution in the parsimony‐based analyses. Based on theoretical considerations and the results of our simulations, we encourage application and further testing of modified NRCDC in parsimony‐based molecular phylogenetic analyses that sample exons of protein‐coding genes. We expect that modified NRCDC will generally increase both accuracy and branch‐support over commonly applied alternative character‐sampling strategies when analysed using the same phylogenetic inference method, particularly in studies that sample both closely and distantly related taxa with clades representing both ancient and recent divergences. © The Willi Hennig Society 2010.     

How does sampling strategy influence detection of morphological variation in orchids? A case-study of the epiphyte Oberonia hosseusii

Effects of sampling strategy on detection of morphological variation were studied in the epiphytic orchid Oberonia hosseusii in Thailand. We compared the different effects of local versus regional sampling on the one hand and the size of local samples on the other. A local data set was collected by sampling a natural population on Doi Inthanon, during which process a preservation experiment was made. A regional data set was established by measurement of 18 preserved specimens from 12 different localities. Based on the preservation experiment, data from the regional sampling were calibrated (whenever needed) to make the two data sets more directly comparable. Heat drying and spirit preservation significantly influenced measurements for two mutually exclusive sets of characters. Increasing the local sample size from 18 to 52 individuals had no statistically significant effect on the mean value of any character. In contrast, local versus regional sampling significantly influenced the mean value of every character, virtually irrespective of local sample size. In the regional data set only, a difference was found in overall variability in vegetative versus floral characters. Three cluster analyses with equal representation of individuals from the local and regional samples were performed using different clustering techniques. Only in the analysis using neighbour-joining did pure “local clusters” prove to be significantly larger than pure “regional clusters”, suggesting that this clustering technique is particularly sensitive to effects from sampling strategy.     

拟南芥花粉活力的测定及其在花粉发育研究中的应用

花粉发育是植物生活周期中一个重要且复杂的过程, 需要多种基因的参与。花粉发育是否完善可以根据花粉形态特征, 并通过检测花粉的生活力、萌发力、可育性和受精能力等生理特征来判断。以拟南芥候选基因突变体为材料, 通过对花粉的这些生理特征的检测, 可以初步推测候选基因参与花粉发育的功能和作用机制。本文介绍了用于花粉活力测定的几种技术的原理和方法, 以及应用这些方法进行花粉发育研究的进展。     

拟南芥花粉活力的测定及其在花粉发育研究中的应用

花粉发育是植物生活周期中一个重要且复杂的过程,需要多种基因的参与。花粉发育是否完善可以根据花粉形态特征,并通过检测花粉的生活力、萌发力、可育性和受精能力等生理特征来判断。以拟南芥候选基因突变体为材料,通过对花粉的这些生理特征的检测,可以初步推测候选基因参与花粉发育的功能和作用机制。本文介绍了用于花粉活力测定的几种技术的原理和方法,以及应用这些方法进行花粉发育研究的进展。     

A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases

Current phylogenetic methods attempt to account for evolutionary rate variation across characters in a matrix. This is generally achieved by the use of sophisticated evolutionary models, combined with dense sampling of large numbers of characters. However, systematic biases and superimposed substitutions make this task very difficult. Model adequacy can sometimes be achieved at the cost of adding large numbers of free parameters, with each parameter being optimized according to some criterion, resulting in increased computation times and large variances in the model estimates. In this study, we develop a simple approach that estimates the relative evolutionary rate of each homologous character. The method that we describe uses the similarity between characters as a proxy for evolutionary rate. In this article, we work on the premise that if the character-state distribution of a homologous character is similar to many other characters, then this character is likely to be relatively slowly evolving. If the character-state distribution of a homologous character is not similar to many or any of the rest of the characters in a data set, then it is likely to be the result of rapid evolution. We show that in some test cases, at least, the premise can hold and the inferences are robust. Importantly, the method does not use a "starting tree" to make the inference and therefore is tree independent. We demonstrate that this approach can work as well as a maximum likelihood (ML) approach, though the ML method needs to have a known phylogeny, or at least a very good estimate of that phylogeny. We then demonstrate some uses for this method of analysis, including the improvement in phylogeny reconstruction for both deep-level and recent relationships and overcoming systematic biases such as base composition bias. Furthermore, we compare this approach to two well-established methods for reweighting or removing characters. These other methods are tree-based and we show that they can be systematically biased. We feel this method can be useful for phylogeny reconstruction, understanding evolutionary rate variation, and for understanding selection variation on different characters.     

Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae.

We report the potential phylogenetic utility of DNA sequence data from the last 700 bp of a ca. 1-kb intron of the MADS-box gene pistillata from a sampling of Sphaerocardamum species and other Brassicaceae. These results are compared with nrDNA ITS and the chloroplast trnL intron for the same taxa to demonstrate the potential phylogenetic utility of this pistillata intron and to identify potential historically independent sequences for an ongoing study of relationships within Sphaerocardamum. Analyses of the DNA sequence data for Brassicaceae indicated that pairwise divergences and potentially informative characters were higher in the pistillata intron (0.6-30.8%, 284 characters) and ITS (0-24%, 94 characters) than in the chloroplast trnL intron (0-4.2%, 17 characters). A comparison of Sphaerocardamum sequences identified low divergences and numbers of informative characters for trnL intron (0-2.4%, 1 character) and nrDNA ITS (0-2.5%, 2 characters) and substantially more variation among the pistillata sequences (0.15-3.7%, 19 characters). Phylogenetic analyses of these pistillata sequences fully resolve ingroup relationships without character conflict. Results of pistillata PCR amplifications from a broader dicot sample showed that some primers may be useful in amplifying orthologous pistillata sequences. Ultimately this pistillata intron may be a valuable source of phylogenetic characters at lower taxonomic levels.     

Taxon sampling, character sampling and systematics: how gradist presuppositions created additional ganglia in gastropod euthyneuran taxa

In gastropods, the pentaganglionate condition of the nervous visceral loop has been accepted as a general character and one of the most important synapomorphies of the Euthyneura. The review of published data on 50 generic taxa shows an extreme confusion in both terminology and application of the homology concept to the two parietal ganglia observed in some Euthyneura, in addition to the three observed in most gastropods. A parsimonious re-interpretation of the data leads to the conclusion that the occurrence of five visceral ganglia is ascertained in only six genus-group taxa, and therefore cannot be accepted as a general character of Euthyneura. We propose that in phylogenetic analysis, taxonomic sampling should be determined according to the variability of characters and independently of the rank of the taxa taken into account, until every taxon in the data matrix is monomorphic for every character, and until all the taxa in which the characters occur are represented in the data matrix. We propose to use the term 'domain of definition' of a character for such a taxonomic sample. Implementing the domain of definition of characters in construction of data matrices would avoid the abuse of generalities leading to circularity in evolutionary interpretations of classification, which in the case of Euthyneura result from an a priori gradist interpretation of the evolution of the nervous system.     

The disparity of priapulid, archaeopriapulid and palaeoscolecid worms in the light of new data

Priapulids and their extinct relatives, the archaeopriapulids and palaeoscolecids, are vermiform, carnivorous ecdysozoans with an armoured, extensible proboscis. These worms were an important component of marine communities during the Palaeozoic, but were especially abundant and diverse in the Cambrian. Today, they comprise just seven genera in four families. Priapulids were among the first groups used to test hypotheses concerning the morphological disparity of Cambrian fossils relative to the extant fauna. A previous study sampled at the generic level, concluding that Cambrian genera embodied marginally less morphological diversity than their extant counterparts. Here, we sample predominantly at the species level and include numerous fossils and some extant forms described in the last fifteen years. Empirical morphospaces for priapulids, archaeopriapulids and palaeoscolecids are relatively insensitive to changes in the taxon or character sample: their overall form has altered little, despite the markedly improved sampling. Cambrian and post-Cambrian genera occupy adjacent rather than broadly overlapping regions of these spaces, and Cambrian species still show lower morphological disparity than their post-Cambrian counterparts. Crucially, the significance of this difference has increased with improved taxon sampling over research time. In contrast with empirical morphospaces, the phylogeny of priapulids, archaeopriapulids and palaeoscolecids derived from morphological characters is extremely sensitive to details of taxon sampling and the manner in which characters are weighted. However, the extant Priapulidae and Halicryptidae invariably resolve as sister families, with this entire clade subsequently being sister group to the Maccabeidae. In our most inclusive trees, the extant Tubiluchidae are separated from these other living taxa by a number of small, intervening fossil clades.     

Sampling volume in root studies: the pitfalls of under‐sampling exposed using accumulation curves

Root systems are important for global models of below‐ground carbon and nutrient cycling. Notoriously difficult sampling methods and the fractal distribution of root diameters in the soil make data being used in these models especially susceptible to error resulting from under‐sampling. We applied the concept of species accumulation curves to root data to quantify the extent of under‐sampling inherent to minirhizotron and soil coring sampling for both root uptake and carbon content studies. Based on differences in sample size alone, minirhizotron sampling missed approximately one third of the root diameters observed by soil core sampling. Sample volumes needed to encounter 90% of root diameters averaged 2481 cm³ for uptake studies and 5878 cm³ for root carbon content studies. These results show that small sample volumes encounter a non‐representative sample of the overall root pool, and provide future guidelines for determining optimal sample volumes in root studies.     

Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for "basal" clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to "correctly" resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of "incorrect" resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate "incorrect" resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, "incorrectly" resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method.     

ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH

Abstract— A new method for weighting characters according to their homoplasy is proposed; the method is non-iterative and does not require independent estimations of weights. It is based on searching trees with maximum total fit, with character fits defined as a concave function of homoplasy. Then, when comparing trees, differences in steps occurring in characters which show more homoplasy on the trees are less influential. The reliability of the characters is estimated, during the analysis, as a logical implication of the trees being compared. The "fittest" trees imply that the characters are maximally reliable and, given character conflict, have fewer steps for the characters which fit the tree better. If other trees save steps in some characters, it will be at the expense of gaining them in characters with less homoplasy.     

疏花水柏枝结构性状多样性研究

以疏花水柏枝(Myricaria laxiflora)茎的11个解剖结构参数作为表型性状,对覆盖整个分布区域的居群进行部分抽样取样,研究了该物种表型性状的多样性及其格局、表型性状的分化及其与环境的关系。结果表明,各性状在居群间以及不同居群总体性状之间都存在显著或极显著的差异,63％的表型分化属居群内分化,37％为居群间地理差异引起的分化,居群内性状的变异程度与立地环境条件的分化程度一致,奉节以上居群相似程度较大,而以下居群相似程度则较小,并有独立分化的居群出现,这表明表型性状的多样性中心是在三峡河谷区域内,而不是在三峡以上的河谷区段。     

A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems

Character coding entails assumptions that may be problematic within the context of parsimony analysis using current computer algorithms. The example discussed here involves a character-variable (e.g., tail color) that is inapplicable in some taxa in the analysis because the part (e.g., tail) with which it is associated is lacking in those taxa. The part and character-variable can be coded as separate characters, or they can be fused into a single character. If the part and character-variable are coded as separate characters there is transformational independence between the part and the character-variable, but the logical dependence inherent to the hierarchical relationship between the part and its character-variable is only partly accounted for. Fusing the part and character-variable into one multistate character fully accounts for the logical dependence, but it is equivocal regarding the transformational independence. Separate coding is consistent with the primary homology statement that the part is homologous in all taxa possessing it, whereas fused coding is equivocal regarding this hypothesis of primary homology. As a result fused coding involves a loss of phylogenetic information. Use of a stepmatrix or other mechanisms associated with fused coding that preserve this phylogenetic information involves weighting schemes or ordered characters that have other assumptions that may also be difficult to justify.     

Comparison of spatula and nonspatula methods for cervical sampling

A comparison between nonspatula (cotton swab and Cytobrush) cervical sampling methods and spatula (wooden Ayre spatula and plastic extended-tip Szalay Cyto-Spatula) sampling methods was made in 109 cases. Based on the presence of endocervical cells, there were statistically significant qualitative differences between the non-spatula methods as well as between the spatula methods, but not between the Cytobrush and Cyto-Spatula smears or the cotton swab and Ayre spatula smears. In all kinds of inflammatory lesions, the spatula samples were more accurate and diagnostic than the nonspatula ones. In all cases of cervical intraepithelial neoplasia and in most cases of squamous metaplasia, the Cyto-Spatula sample was the most accurate. It is concluded that the Szalay Cyto-Spatula method is superior to the other cervical sampling methods because it provides well-preserved cells from both the endocervix and the ectocervix in one smear. The Cytobrush should be used in conjunction with spatula sampling (combination method) for effective sampling of the cervix. The Cytobrush alone is effective mainly for endocervical sampling while the Ayre spatula alone is effective mainly for ectocervical sampling; the cotton swab is ineffective for both endocervical and ectocervical sampling.     

Jaw musculature during the dawn of turtle evolution

Using a new approach to study muscle anatomy in vertebrates, the fully differentiated jaw musculature of 42 turtle species was studied and character mappings were performed. Soft tissue arrangements were correlated to the temporal openings (emarginations) of the skull and the trochlearis system of the jaw apparatus among turtle taxa. When compared to the cranial anatomy of stem Testudines, most characters detected as diagnostic of particular extant groups have to be considered as being evolved first within Testudines. Hence, jaw muscle anatomy of extant turtles is difficult to compare to that of other reptilian taxa. Moreover, the high number of apomorphic character changes speaks for a divergating turtle and saurian morphotype of jaw musculature, which could indicate either a position of turtles outside of Sauria or a highly derived, undetectable origin within that group. In general, a low direct correlation of most soft and hard tissue characters was detected. This finding could imply that both character complexes are more integrated to each other driven by functional morphology; i.e., the composition of muscle fibre types. That condition highlights the difficulty in using gross anatomy of jaw muscle characters to interpret temporal bone arrangements among amniotes in general.     

Adaptation and functional integration in primate phylogenetics

In two areas of phylogenetics, contrary predictions have been developed and maintained for character analysis and weighting. With regard to adaptation, many have argued that adaptive characters are poorly suited to phylogenetic analysis because of a propensity for homoplasy, while others have argued that complex adaptive characters should be given high weight because homoplasy in complex characters is unlikely. Similarly, with regard to correlated sets of characters, one point of view is that such sets should be collapsed into a single character-a single piece of phylogenetic evidence. Another point of view is that a suite of correlated characters should be emphasized in phylogenetics, again because recurrence of detailed similarity in the same suite of features is unlikely. In this paper, I discuss the theoretical background of adaptation and functional integration with respect to phylogenetic systematics of primates. Several character examples are reviewed with regard to their functional morphology and phylogenetic signal: postorbital structures, tympanic morphology, fusion of the mandibular symphysis, the tooth comb, strepsirrhine talar morphology, and the prehensile tail. It is clear when considering characters such as these that some characters are synapomorphic of major clades and at the same time functionally important. This appears particularly to be the case when characters are integrated into a complex and maintained as stable configurations. Rather than being simply a problem in character analysis, processes of integration may help to explain the utility of phylogenetically informative characters. On the other hand, the character examples also highlight the difficulty in forming a priori predictions about a character's phylogenetic signal. Explanations of patterns of character evolution are often clade-specific, which does not allow for a simple framework of character selection and/or weighting.     

Morphological character evolution in hepialid moths (Lepidoptera: Hepialidae) from New Zealand

Mapping morphological characters on a molecular-based phytogeny enabled examination of character evolution and an historical perspective into evolutionary processes, both of which are important aspects of systematic research and comparative biology. In this study, 63 morphological characters from hepialid moths in New Zealand were mapped on a phylogenetic tree reconstructed from mitochondrial DNA COI & II sequence data. Morphological characters hypothesized to be synapomorphies for the New Zealand 'Oxycanus' lineages and 'Oxycanus' lineage s.s. were confirmed to be homologous when mapped on the COI & II phytogeny. The direction of character state transformation was determined for five characters, with members of the Aenetus and Aoraia lineages exhibiting hypothesized ancestral states. Male genitalic characters were less homoplasious than other character partitions and covaried significandy with phytogeny.     

The peristomatic structures of Lithobiomorpha (Myriapoda, Chilopoda): comparative morphology and phylogenetic significance

A comparative survey of the epipharynx and hypopharynx of lithobiomorph centipedes by light and scanning electron microscopy examines 18 species that sample the major groups of both families, the Lithobiidae and Henicopidae. Cladistic analysis of 11 characters of the peristomatic structures together with 29 additional morphological characters serves as a basis for interpreting the evolution of the lithobiomorph peristomatic structures. Scutigeromorpha is used for outgroup comparison in the framework of a homology scheme for the basic components of the epi- and hypopharynx. Compared to other chilopods, the monophyly of Lithobiomorpha is supported by a row of distinctive bottle-shaped gland openings at the border between the labral and clypeal parts of the epipharynx, as well as by a distinctive shape of the hypopharynx. Paired rows of elongate spines on the clypeal part of the epipharynx are an apomorphic character of Lithobiidae. The transformation of these spine rows into a few groups of branching spines is characteristic for the Monotarsobius group sensu Verhoeff. Similar groups of branching clypeal spines characterize the Anopsobiinae within Henicopidae, whereas Henicopinae possess a dense cluster of short, simple spines instead. The recently described genus Dzhungaria is resolved closer to Henicopinae than to Anopsobiinae, a hypothesis supported by a field of grooves on the medial labral part of the epipharynx. Monophyly of Henicopidae does not receive unique support from the peristomatic structures although two homoplastic characters contribute to this node; among these, the reduction of a median spine field between clypeal and labral parts of the epipharynx to a narrow transverse band also supports a close relationship between the Ezembius group and Hessebius within Lithobiidae. An Ezembius+Hessebius clade is additionally supported by the absence of a transverse bulge between the clypeal and labral parts of the epipharynx, a character otherwise present in all lithobiomorph species studied so far. Lithobius is resolved as polyphyletic, with different species being most closely related to such genera as Australobius, Hessebius and Pleurolithobius.     

Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling

Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a data set compiled from published sources and data original to this study supports monophyly of Amniota, Synapsida, Reptilia, Parareptilia, Eureptilia, Eosuchia, Diapsida, Neodiapsida, Sauria, Lepidosauria, and Archosauriformes, as well as several more highly nested divisions within the latter two clades. Turtles are here resolved as the sister taxon to a monophyletic Lepidosauria (squamates + Sphenodon), a novel phylogenetic position that nevertheless is consistent with recent molecular and morphological studies that have hypothesized diapsid affinities for this clade.     

Avian higher-level phylogeny: well-supported clades and what we can learn from a phylogenetic analysis of 2954 morphological characters

It has been shown that increased character sampling betters the accuracy of phylogenetic reconstructions in the case of molecular data. A recently published analysis of avian higher-level phylogenetics based on 2954 morphological characters now provides an empirical example to test whether this is also true in the case of morphological characters. Several clades are discussed which are supported by multiple analyses of mutually independent molecular data (sequences of nuclear genes on different chromosomes and mitochondrial genes) as well as morphological apomorphies, but did not result from parsimony analysis of the large morphological data set. Incorrect character scorings in that analysis notwithstanding, it is concluded that in the case of morphological data, increased character sampling does not necessarily better the accuracy of a phylogenetic reconstruction. Because morphological characters usually have a strongly varying complexity, many simple and homoplastic characters may overrule fewer ones of greater phylogenetic significance in large data sets, thus producing a low ratio of phylogenetic signal to 'noise' in the data.