外群选择对隧蜂科（膜翅目：蜜蜂总科）系统重建的影响

外群用于给树附根和推断祖先性状状态。通常,来自内群的姐妹群中的多个分类单元被共同选择作为外群。为了在经验上验证这一方法, 我们采用了3种外群选择策略： 姐妹群中的单一分类单元, 姐妹群中的多个分类单元和连续姐妹群中的多个分类单元。以隧蜂科（膜翅目： 蜜蜂总科）的系统发育重建为例, 我们评估了这3种策略对树拓扑结构的影响, 包括最大似然树、 最大简约树和贝叶斯树。初步结果表明： 相比其他两种策略, 采用姐妹群中的多个分类单元作为外群更有利于系统发育重建得到现已被广泛认可的隧蜂科系统发育关系; 相比最大似然法和贝叶斯法, 虽然隧蜂科系统发育关系没有被很好地解决, 但最大简约法在不同外群选择策略下得到了较为一致的拓扑结构     

NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS

Abstract— When divergent taxa are used to root networks, it is assumed that the character stales in the outgroup have historical similarity to those in the ingroup. Yet, if the data are nucleic acid sequences, the character stales shared by a divergent outgroup may be based not on history but on random similarity. A simple procedure is proposed to test this possibility. In the absence of an appropriate outgroup, root position can be estimated with the use of an asymmetrical character transformation matrix. If the matrix is sufficiently biased, it can supply the polarity information usually derived from an outgroup. This outgroup test and rooting procedure are demonstrated with ADH sequences from the genus Drosophila .     

Phyletic patterns of early development in gastropod molluscs

Cell lineage data for 30 exemplar gastropod taxa representing all major subclades and the outgroup Polyplacophora were examined for phylogenetic signal using cladistic analysis. Most cell lineages show phyletic trends of acceleration or retardation relative to the outgroup and more basal ingroup taxa, and when coded this variation is phylo-genetically informative. PAUP analyses of a cell lineage data set under three sets of character ordering assumptions produced similar tree topologies. The topologies of the strict consensus trees for both ordered and Dollo (near irreversibility of character transformations) character assumptions were similar, whereas the unordered character assumption recovers the least phyletic information. The cell lineage cladograms are also in agreement with the fossil record of the timing and sequence of gastropod subclade origination. A long branch lies between the Patellogastropoda+Vetigastropoda grade and the Neritopsina+Apogastropoda clade. The geological timing of this long branch is correlated with the first large-scale terrestrially derived eutrophication of the near-shore marine habitat, and one possible explanation for this branch may be a developmental shift associated with the evolution of feeding larvae in response to the more productive conditions in the near-shore water column. Although character transformations are highly ordered in this data set, developmental rate characters (like all other morphological and molecular characters) are also subject to homoplasy. Finally, this study further supports the hypothesis that early development of gastropod molluscs has conserved a strong phyletic signal for about half a billion years.     

Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal.

In this paper we use hypothetical and empirical data matrices to evaluate the ability of relative apparent synapomorphy analysis (RASA) to measure phylogenetic signal, select outgroups, and identify terminals subject to long-branch attraction. In all cases, except for equal character-state frequencies, RASA indicated extraordinarily high levels of phylogenetic information for hypothetical data matrices that are uninformative regarding relationships among the terminals. Yet, regardless of the number of characters or character-state frequencies, RASA failed to detect phylogenetic signal for hypothetical matrices with strong phylogenetic signal. In our empirical example, RASA indicated increasing phylogenetic signal for matrices for which the strict consensus of the most parsimonious trees is increasingly poorly resolved, clades are increasingly poorly supported, and for which many relationships are in conflict with more widely sampled analyses. RASA is an ineffective approach to identify outgroup terminal(s) with the most plesiomorphic character states for the ingroup. Our hypothetical example demonstrated that RASA preferred outgroup terminals with increasing numbers of convergent character states with ingroup terminals, and rejected the outgroup terminal with all plesiomorphic character states. Our empirical example demonstrated that RASA, in all three cases examined, selected an ingroup terminal, rather than an outgroup terminal, as the best outgroup. In no case was one of the two outgroup terminals even close to being considered the optimal outgroup by RASA. RASA is an ineffective means of identifying problematic long-branch terminals. In our hypothetical example, RASA indicated a terminal as being a problematic long-branch terminal in spite of the terminal being on a zero-length branch and having no possibility of undergoing long-branch attraction with another terminal. RASA also failed to identify actual problematic long-branch terminals that did undergo long-branch attraction, but only after following Lyons-Weiler and Hoelzer's (1997) three-step process to identify and remove terminals subject to long-branch attraction. We conclude that RASA should not be used for any of these purposes.     

Finding Optimal Ingroup Topologies and Convexities When the Choice of Outgroups Is Not Obvious

Considerable confusion remains among theoreticians and practicioners of phylogenetic science on the use of outgroup taxa. Here, we show that, despite claims to the contrary, details of the optimal ingroup topology can be changed by switching outgroup taxa. This has serious implications for phylogenetic accuracy. We delineate between the process of outgroup selection and the various possible processes involved in using an outgroup taxon after one has been selected. Criteria are needed for the determination that particular outgroup taxa do not reduce the accuracy of evolutionary tree topologies and inferred character state transformations. We compare previous results from a sensitivity bootstrap analysis of the mitochondrial cytochromebphylogenetic relationships among whales to the results of a Bremer support sensitivity analysis and of a recently developed application of RASA theory to the question of putative outgroup taxon plesiomorphy content.     

Optimal outgroup analysis

We present and critically examine a statistical criterion for the selection of outgroup taxa for rooting evolutionary trees. The criterion is the amount of phylogenetic signal for the ingroup when the states of the candidate outgroup taxa are assumed to be plesiomorphic relative to the ingroup for the purpose of measuring plesiomorphy content of the outgroup taxon. A statistical measure of rooted, ingroup signal was subjected to a suite of critical tests which indicate that it provides a proxy measure of plesiomorphy content. As the evolutionary distance between the ingroup ancestral node and outgroup taxa increases, the tree-independent measure of signal decreases, tracking the decay in plesiomorphy content and the increase in convergence to the ingroup states. We show that a priori generalizations about optimal outgroup taxon sampling strategies are likely to be misleading, and that testing for the suitability of available outgroup taxon sampling in specific instances is warranted. Software for optimal outgroup analysis is available.     

Fifty years of character compatibility concepts at work

In the mid 19th century,systematic biologists realized that observable similarities and differences among a group of related species could be the basis for hypotheses about the evolutionary relationships among the species and their ancestors.Such hypotheses Can be expressed as characters.A character is comprised of two or more character states of species considered to be similar with respect to a basis for comparison.The states of a character may also be arranged into a character state tree to hypothesize speciation events associated with changes from one character state to another.In the mid 20th century.some systematists realized that sometimes paxrs of characters(or character state trees)could be incompatible as hypotheses,i.e.,they could not both be true.Through the 1950s,'60s and'70s,tests for,and ways to resolve,incompatibilities were used to estimate an ancestor relation based on mutually compatible characters.An estimate was often shown as a diagram connecting ancestors to their immediate descendants(not quite correctly)called a phylogenetic tree.More recently,other applications of compatibility concepts have been developed,including:identify characters that appear to be random in the context of their data set;combine estimates of ancestor relations for subsets of taxa in a larger collection into a single estimate(a so-called supertree)for the whole collection;and interpret geographic patterns in an evolutionary context.     

The threefold parallelism of Agassiz and Haeckel,and polarity determination in phylogenetic systematics

A parallel exists between the threefold parallelism of Agassiz and Haeckel and the three valid methods of polarity determination in phylogenetic systematics. The structural gradation among taxa within a linear hierarchy, ontogenetic recapitulation, and geological succession of the threefold parallelism resemble outgroup comparison, the ontogenetic method, and the paleontological method, respectively, which are methods of polarity determination in phylogenetic systematics. The parallel involves expected congruence among similar components of the distribution of character states among organisms. The threefold parallelism is a manifestation of a world view based on linear hierarchies, whereas polarity determination is part of the methodology of phylogenetic systematics which assumes that organisms are grouped into a nested hierarchy. The threefold parallelism facilitated the ranking of previously established taxa into linear hierarchies consisting mostly of paraphyletic groups. In contrast, methods of polarity determination identify apomorphies that determine and diagnose monophyletic taxa (clades) in the nested genealogical hierarchy. Taxa in linear hierarchies are defined by sets of character states, whereas clades are defined by common ancestry. Although the threefold parallelism was ostensibly abandoned with the rejection of Haeckel's biogenetic law, some of its components continue to facilitate the progressive scenarios that are common in evolutionary thought. Although a general view of progression in organismal history may be invalid, the progressive or directional sequence of character state changes that results in the characterization of a particular clade has considerable heuristic value. Agassiz's ostensibly nested hierarchy and other pre-Darwinian classifications do not provide support for the view that the natural system can be discovered without recourse to the principle of common descent.     

A phylogenetic analysis of the monogenomic Triticeae (Poaceae) based on morphology

A cladistic analysis, primarily based on morphology, is presented from 40 diploid taxa representing the 24 monogenomic genera of the Triticeae. General problems related to the treatment of hybrids and supposedly allopolyploid heterogenomic taxa are highlighted. Special emphasis is given to taxa not traditionally included in Aegilops s.J. Most of the 33 characters used in the analysis are coded as binary. The only four multistate characters in the matrix are treated as unordered. Three diploid species of Bromus are used as outgroup. The number of equally parsimonious trees found is very large (approx. 170000; length = 107, ci = 0.36, ri = 0.75) and the strict consensus tree has an expectedly low level of resolution. However, most of the equally parsimonious trees owe their existence to an unresolved Aegilops clade. If this clade is replaced by its hypothetical ancestor, the number of equally parsimonious trees drops dramatically (48; length = 78, ci = 0.45, ri = 0.76). When trees for which more highly resolved compatible trees exist are excluded, only two trees remain. Bremer support is used as a measure of branch support. The trees based on morphology and on molecular data are largely incongruent.     

Phylogeny of Dicranophoridae (Rotifera: Monogononta) – a maximum parsimony analysis based on morphological characters

This study presents the first phylogenetic analysis of Dicranophoridae (Rotifera: Monogononta), a species rich rotifer family of about 230 species currently recognized. It is based on a maximum parsimony analysis including 77 selected ingroup and three outgroup taxa and a total of 59 phylogenetically informative morphological characters. Character coding is based on personal investigation of material collected by the authors and an extensive survey of the literature. Apart from covering general body organization, character coding primarily relies on scanning electron microscopic preparations of the mastax jaw elements. Our study suggests monophyly of Dicranophoridae with a clade of Dicranophorus and Dorria as the sister taxon of all other dicranophorid species. Monophyly of Encentrum , the most species rich genus within Dicranophoridae, cannot be demonstrated. Within Dicranophoridae our study identifies the monophyletic taxa Caudosubbasifenestrata, Intramalleata, Praeuncinata and Proventriculata, each based on unambiguous character transformations evolved in their stem lineages. However, resolution within Praeuncinata and Proventriculata is very limited. Although some terminal clades within Praeuncinata and Proventriculata are recognized, basal splits remain obscure. Probably, other characters such as DNA sequence data are needed to further our understanding of phylogenetic relationships within these poorly resolved taxa.     

Is there a direct ontogenetic criterion in systematics?

Much recent literature focuses on whether ontogenetic information can be used as a direct criterion for determining the polarity of character trasformations in systematic analysis. This paper reviews the relevant literature and concludes that the ontogenetic criterion is dependent on parsimony rather than the sequence observed during ontogeny. It is not, therefore, based on the discredited arguments of recapitulation. From the perspective of phyologenetic systematics the ontogenetic criterion is a valid means of polarizing character transformations that represents a special case of a broader methodology involving parsimony. The alternative perspective perspective of patttern cladistics holds that polarity should be contained within the data and not imposed upon it. Thus, ontogeny is not required to polarize characters, but ontogenetic information can generate unequivocal character interpretations in terms of the relative generality of related attributes, and in the sense that absence precedes presence. Furthermore, ontogeny is central to systematics, providing empirical evidence of character transformation, information on the whole life cycle and an escape from systematics being teleologically related to phylogenetic inference and the theory of evolution.     

Mapping characters on a tree with or without the outgroups

A character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non‐exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest. © The Willi Hennig Society 2004.     

Phylogenetics of Chondrichthyes and the problem of rooting phylogenies with distant outgroups

Erroneous estimates of ingroup relationships can be caused by attributes in the outgroup chosen to root the tree. Phylogenetic analyses of DNA sequences frequently yield incorrect estimates of ingroup relationships when the outgroup used to "root" the tree is highly divergent from the ingroup. This is especially the case when the outgroup has a different base composition than the ingroup. Unfortunately, in many instances, alternative less divergent outgroups are not available. In such cases, investigators must either target genes with attributes that minimize the problem (slowly evolving genes with stationary base compositions--which are often not ideal for estimating relationships among the more closely related ingroup taxa) or use inference models that are explicitly tailored to deal with an attenuated historical signal with a superimposed non-stationary base composition. In this paper we explore the problem both empirically and through simulation. For the empirical component we looked at the phylogenetic relationships among elasmobranch fishes (sharks and rays), a group whose closest living outgroup, the holocephalan Ghost fishes, are separated from the elasmobranchs by more than 100 million years of evolution. We compiled a data set for analysis comprising 10 single-copy nuclear protein-coding genes (12,096 bp) for representatives of the major lineages within elasmobranchs and holocephalans. For the simulation, we used an evolutionary model on a fixed tree topology to generate DNA sequence data sets which varied both in their distance to the outgroup, and in their base compositional difference between ingroup and outgroup. Results from both the empirical data set and the simulation, support the idea that deviation from base compositional stationarity, in conjunction with distance from the root can act in concert to compromise accuracy of estimated relationships within the ingroup. We tested several approaches to mitigate such problems. We found, that excluding genes with overall faster rates and heterogeneous base compositions, while the least sophisticated of the methods evaluated, seemed to be the most effective.     

PHYLOGENY OF THE NEMERTEAN SUBCLASS PALAEONEMERTEA (ANOPLA, NEMERTEA)

Abstract— A cladistic analysis based on 50 morphological characters was performed for 49 of the 98 species currently assigned to the subclass Palaeonemertea (phylum Nemertea), and six additional undescribed species. Thirty-five species were excluded from the parsimony analysis because of the high number of unknowns in the character matrix, and one species since it was considered a nomen nudum . An initial analysis suggested that the subclass Hoplonemertea is the sistergroup to the clade Palaeo- and Heteronemertea and the ingroup cladograms are rooted using a paraphyletic outgroup based on this information. Seventy-two equally most parsimonious cladograms were found; the consistency index was low but tree-length distribution for the character set is skewed to the left, and the cladograms are invariably shorter than trees based on random data. These cladograms suggested a character transformation series for the cerebral organ where this complex character reappeared several times after being absent. We considered this biologically implausible and the final discussion is based on three cladograms, one step longer than the most parsimonious, where the evolution of this character appears to be more realistic. The cladistic analysis indicates that many previously recognized genera (e.g. Cephalothrix, Procephalothrix and Cephalotrichella ), and higher taxa, are paraphyletic. It furthermore indicates that the previously suggested hypothesis of the Archinemertea as a monophyletic sistertaxon to Palaeonemertea is unsupported.     

Cladistic analysis of self‐grooming indicates a single origin of eusociality in corbiculate bees (Hymenoptera: Apidae)

Behavioural traits have been used extensively in recent years as an important character source for making phylogenetic inferences. The phylogenetic positions of the members of the Apini subtribe are increasingly being debated, and new characters must be examined. We analysed the presence and absence of certain behavioural patterns, as well as the sequences of some of these patterns, to generate 79 characters. Eleven species comprised the ingroup, and Xylocopini comprised the outgroup. Parsimony analysis showed that the most parsimonious tree was (Euglossina(Bombina(Apina+Meliponina))). This topology is consistent with most studies that use morphological data and the few that use behavioural data, which suggests that advanced eusociality arose only once in a common ancestor of the clade Apina plus Meliponina; however, this hypothesis is inconsistent with our molecular data. Thus we considered behavioural, molecular, and morphological data and recovered the same topology, in which eusociality has a single origin in corbiculate bees.     

An empirical test of the midpoint rooting method

The outgroup method is widely used to root phylogenetic trees. An accurate root indication, however, strongly depends on the availability of a proper outgroup. An alternate rooting method is the midpoint rooting (MPR). In this case, the root is set at the midpoint between the two most divergent operational taxonomic units. Although the midpoint rooting algorithm has been extensively used, the efficiency of this method in retrieving the correct root remains untested. In the present study, we empirically tested the success rate of the MPR in obtaining the outgroup root for a given phylogenetic tree. This was carried out by eliminating outgroups in 50 selected data sets from 33 papers and rooting the trees with the midpoint method. We were thus able to compare the root position retrieved by each method. Data sets were separated into three categories with different root consistencies: data sets with a single outgroup taxon (54% success rate for MPR), data sets with multiple outgroup taxa that showed inconsistency in root position (82% success rate), and data sets with multiple outgroup taxa in which root position was consistent (94% success rate). Interestingly, the more consistent the outgroup root is, the more successful MPR appears to be. This is a strong indication that the MPR method is valuable, particularly for cases where a proper outgroup is unavailable.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 669–674.     

中鲤亚属的分支系统学分析

基于外部形态特征和内部骨骼特征对鲤科鲤属中鲤亚属进行了分支系统学分析,内群包括中鲤亚属的全部5种和鲤亚属的2种鱼类,外群采用乌原鲤。在鲤属鱼类和外群间共有48个性状存在变化。系统发育分析采用PAUP^*软件的Parsimony和Bootstrap两种方式的Branch-and-Bound算法,排除不能极化的特征和特有离征之后,还有28个特征可用,由这28个特征可得到唯一的系统树,树长69,一致性系数0.7246,排除无用特征的一致性系数0.6122,保留系数0.6346。由5种中鲤组成的中鲤亚属明显不构成一个单系群。结果表明：中鲤亚属是一个复系群,该类元应该被撤销。     

The problem of rooting rapid radiations

There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult problem. In this simulation study, we tested the performances of different phylogenetic methods at estimating a tree that models a rapid radiation. We found that maximum likelihood, corrected and uncorrected neighbor-joining, and corrected and uncorrected parsimony, all suffer from biases toward specific tree topologies. In addition, we found that using a single-taxon outgroup to root a tree frequently disrupts an otherwise correct ingroup phylogeny. Moreover, for uncorrected parsimony, we found cases where several individual trees (in which the outgroup was placed incorrectly) were selected more frequently than the correct tree. Even for parameter settings where the correct tree was selected most frequently when using extremely long sequences, for sequences of up to 60,000 nucleotides the incorrectly rooted trees were each selected more frequently than the correct tree. For all the cases tested here, tree estimation using a two taxon outgroup was more accurate than when using a single-taxon outgroup. However, the ingroup was most accurately recovered when no outgroup was used.     

木兰科的分支分析

主要以形态学、解剖学、细胞学为依据,以德坚木属为外类群,用分支分析的方法探讨了木兰科属间的系统发育关系。有２３个分支单位,选取３２个性状,根据外类群比较原则和化石地层学资料,确定了性状的祖征和衍征。对数据矩阵的分支分析使用ＰＡＵＰ３．１．１和Ｈｅｎｎｉｇ ８６ ｖ．１．５分别在Ｍａｃｉｎｔｏｓｈ和ＩＢＭ机上运行,前者以启发法,后者以ＢＢ命令运算,经严格一致化处理,得到一致化分支图。结果表明：１）木     

Phylogeny and systematics of the subfamily Bryocorinae based on morphology with emphasis on the tribe Dicyphini sensu Schuh,

The classification of the hyperdiverse true bug family Miridae is far from settled, and is particularly contentious for the cosmopolitan subfamily Bryocorinae. The morphological diversity within the subfamily is pronounced, and a lack of explicit character formulation hampers stability in the classification. Molecular partitions are few and only a handful of taxa have been sequenced. In this study the phylogeny of the subfamily Bryocorinae has been analysed based on morphological data alone, with an emphasis on evaluating the tribe Dicyphina sensu Schuh, 1976, within which distinct groups of taxa exist. A broad sample of taxa was examined from each of the bryocorine tribes. A broad range of outgroup taxa from most of the other mirid subfamilies was also examined to test for bryocorine monophyly, ingroup relationships and to determine character polarity. In total a matrix comprising 44 ingroup, 15 outgroup taxa and 111 morphological characters was constructed. The phylogenetic analysis resulted in a monophyletic subfamily Bryocorinae sensu Schuh (1976, 1995), except for the genus Palaucoris, which is nested within Cylapinae. The tribe Dicyphini sensu Schuh (1976, 1995) has been rejected. The subtribe Odoniellina is synonymized with the subtribe Monaloniina and the subtribes Dicyphina, Monaloniina and Eccritotarsina are now elevated to tribal level, with the Dicyphini now restricted in composition and definition. The genus Felisacus is highly autapomorphic and a new tribe – the Felisacini – is erected for the included taxa. This phylogeny of the tribes of the Bryocorinae comprises the following sister‐group relationships: Dicyphini ((Bryocorini + Eccritotarsini)(Felisicini + Monaloniini)).