WIDESPREAD TAXA, SYMPATRY, DISPERSAL, AND AN ALGORITHM FOR RESOLVED AREA CLADOGRAMS

Abstract — It is argued that in area biogeographical studies, the information content of widespread taxa is comparable to that of endemic taxa; widespread taxa should therefore be treated under Assumption 0. For areas of sympatry (redundant distributions) on the other hand, Assumption 2 is warranted because dispersal must always be invoked to explain sympatry. It is argued that all occurrences in an area of sympatry should be treated equally, regardless of whether the taxa are widespread or endemic, and regardless of whether the taxa occupy terminal or basal positions on the cladogram. An algorithm for translation of taxon-area cladograms into resolved area cladograms under these conditions is given. As an example, this algorithm is applied to inocelliid snakeflies and gerrine pondskaters.     

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed.     

Marine Area Relationships from Twenty Sponge Phylogenies. A Comparison of Methods and Coding Strategies

Published phylogenies of 20 marine sponge groups are used to build general area cladograms of marine areas of endemism under three different methods for which algorithms adapted for personal computers are available, viz. COMPONENT, BPA and TAS, and two different coding strategies, Assumption 0 (A0) and "no assumption" (NA). The latter is a recently proposed procedure for handling the distributions of widespread taxa by treating these as separate areas of endemism, rather than as suites of smaller constituent areas. The 20 phylogenies contained large numbers of problem data which prevented an exhaustive search for all possible equally "best" general area cladograms. The Nelson consensus trees and their equivalents in parsimony analysis for all six attempts (viz. three different methodologies under two different coding strategies) were compared using their fit with the 20 sponge phylogenies as a measure of quality. Fit was determined using the number of "cospeciations" between a general area cladogram and a taxon area cladogram computed with TreeMap 1.0. No single method or coding strategy yielded a clearly better fit, each cladogram fitting variously better or worse with various phylogenies. In general, fit with NA coding was higher than with A0 coding, but random tree tests failed to generate statistically significant support for the conclusion that NA coding improves fit. Assuming that available sponge phylogenies are representative of marine benthic groups, software and hardware limitations are serious obstacles to a successful development of marine general area cladograms under any method or coding strategy.     

Phylogeny of the subfamilies of Chironomidae (Diptera)

Summary The phylogeny of the subfamilies of Chironomidae are cladistically analysed using parsimony. A data matrix is presented and some characters discussed. Different outgroup taxa, constraints and options are used, characters unordered or ordered, weighted or unweighted, the results reweighted or not and the results discussed. Telmatogetoninae in all cladograms forms the sister group of the remaining subfamilies. Aphroteniinae in some cladograms forms the sister group of all subfamilies except Telmatogetoninae, whereas in other cladograms, including the preferred cladogram, it is part of Tanypodoinae, which otherwise includes Podonominae, Usumbaromyiinae and Tanypodinae. Chilenomyiinae is basal in Tanypodoinae in some cladograms. In most cladograms, including the preferred cladogram, it is basal in Chironomoinae, which also includes Buchonomyiinae, Diamesinae, Prodiamesinae, Orthocladiinae and Chironominae. The preferred cladogram is compared with the relationships between different subfamilies suggested by previous authors.     

黄耆属簇毛黄耆亚属系统学研究

簇毛黄耆亚属以其柱头上具簇毛等形态特征与黄耆属其它类群相区别,约含49种（变种）。主要分布在青藏高原及其邻近地区,绝大多数种类分布于横断山区。本文基于形态特征和分支系统学方法分析亚属内种系发生关系。结果表明,49种（变种）可分为9组。其中双小苞组Sect.Bibracteolati含种类最多,是一个并系类群。借助于分支图,分析了6个较重要的鉴定特征的演化,习性,茎的着生方式,小苞片,果实形态,柱头具簇毛,果实膨胀状况等。最后作出了这个亚属的一个分类纲要。     

Cladistic analysis of Enkianthus with notes on the early diversification of the Ericaceae

The genus Enkianthus (Ericaceae) has been subject to a cladistic analysis of morphological, anatomical, embryological, and cytological data, using two species of Clethra as outgroup. In order to evaluate the monophyly of Enkianthus , the genera Epigaea and Phyllodoce from the subfamily Rhododendroideae, and the genus Andromeda from the subfamily Vaccinioideae were also included in an initial analysis which yielded 20 equally parsimonious cladograms. The results indicated that Enkianthus is monophyletic, and a subsequent analysis with only the outgroup taxa and 14 species of Enkianthus yielded two equally parsimonious cladograms with a more resolved topology. In order to obtain strictly monophyletic taxa, the current subgeneric classification of Enkianthus is revised, recognizing four sections: Enkianthus (9 spp.), Andromedina (2 spp.), Meisteria (2 spp.), and Enkiantella (4 spp.). The paper provides a key, illustrations of representative taxa, a cladogram, and strict consensus trees.     

Towards simultaneous analysis of morphological and molecular data in Hymenoptera

Principles and methods of simultaneous analysis in cladistics are reviewed, and the first, preliminary, analysis of combined molecular and morphological data on higher level relationships in Hymenoptera is presented to exemplify these principles. The morphological data from Ronquist et al . (1999) matrix, derived from the character diagnoses of the phylogenetic tree of Rasnitsyn (1988) , are combined with new molecular data for representatives of 10 superfamilies of Hymenoptera by means of optimization alignment. The resulting cladogram supports Apocrita and Aculeata as groups, and the superfamly Chrysidoidea, but not Chalcidoidea, Evanioidea, Vespoidea and Apoidea.     

Molecular phylogenetics of the tribeInuleae s. str.(Asteraceae), based on ITS sequences of nuclear ribosomal DNA

The sequences of the internal transcribed spacer (ITS) region of 18S–26S nrDNA for a sample of 16 taxa from theInuleae s. str. and two outgroup taxa are analysed cladistically with PAUP. A consensus tree of the four most parsimonious cladograms is presented. Three different tests of cladogram stability are conducted (Bremer support, parsimony jackknifing and bootstrapping); all tests indicate a high degree of support for the basal nodes of the tree. The ITS phylogeny of the tribe is compared with previous hypotheses based on morphological data. The position ofAnisopappus as sister group to the rest of the tribe is supported by the molecular data, but the proposed subdivision ofInuleae s. str. into a paleate grade group and an epaleate clade is not. The interpretation of the character evolution of, e.g. receptacular paleae and pappus features within the tribe is discussed.     

Phylogeny of the Baldratiina (Diptera: Cecidomyiidae) inferred from morphological, ecological and molecular data sources, and evolutionary patterns in plant-galler relationships

The phylogeny of the gall-midge subtribe Baldratiina (Diptera: Cecidomyiidae) was reconstructed from molecular (partial sequence of the mitochondrial 12S rDNA), morphological and ecological data sets, using 16 representative species of most of the genera. The morphological and ecological data were combined in a single character matrix and analyzed separately from the molecular data, resulting in an eco-morphological cladogram and a molecular cladogram. Attributes of galls and host associations were superimposed on the molecular cladogram in order to detect possible trends in the evolution of these traits. The cladograms resulting from the two independent analyses were statistically incongruent, although both provide evidence for the monophyly of the genera Baldratia and Careopalpis and the paraphyly of the genera Stefaniola and Izeniola. The results suggest a minor impact of the morphological characters traditionally used in the classification of the Baldratiina, whereas ecological data had a major impact on the phylogenetic inference. Mapping of gall and host attributes on the molecular cladogram suggests that multi-chambered stem galls constitute the ancestral state in the subtribe, with several subsequent shifts to leaf galls. It is concluded that in contrast to other studied groups of gall insects, related baldratiine species induce different types of galls, attesting to speciation driven by gall-type shifts at least as often as host shifts.     

Parsimony analysis of endemicity (PAE) of Mexican terrestrial mammals at different area units: when size matters

Abstract Aim Parsimony analysis of endemicity (PAE) is a biogeographical method that uses a parsimony algorithm to obtain an area cladogram, based on taxa inhabiting the study areas. We compare its performance at different geographical units (½° and 1° quadrats, ecoregions and biogeographical provinces) to analyse distributional patterns of Mexican terrestrial mammals, in order to assess the importance of the size of area units. Location The area analysed corresponds to Mexico. Methods Parsimony analyses were based on 56,859 collection records, corresponding to 703 genera, species and subspecies. Four data matrices were constructed for: (1) 716 quadrats of ½° latitude × ½° longitude, (2) 230 quadrats of 1° latitude × 1° longitude, (3) forty‐five ecoregions and (4) fourteen biogeographical provinces. Results For the ½° quadrat matrix, we obtained six cladograms of 17,138 steps. For the 1° quadrat matrix, we obtained five cladograms (strict consensus with 9394 steps). For the matrix of ecoregions, we obtained twelve cladograms (strict consensus cladogram with 3009 steps). For the provinces, we obtained a single cladogram with 1603 steps. Main conclusions The best results were obtained with natural areas instead of quadrats. There seems to exist a trend to decrease the absolute number of steps and an increase in the absolute and relative number of synapomorphies as the size of the area units decreases, although this does not necessarily occur for the number of cladograms.     

POLYMORPHIC TAXA, MISSING VALUES AND CLADISTIC ANALYSIS

Abstract Missing values have been used in cladistic analyses when data are unavailable, inapplicable or sometimes when character states are variable within terminal taxa. The practice of scoring taxa as having "missing values" for polymorphic characters introduces errors into the calculation of cladogram lengths and consistency indices because some character change is hidden within terminals. Because these hidden character steps are not counted, the set of most parsimonious cladograms may differ from those that would be found if polymorphic taxa had been broken into monomorphic subunits. In some cases, the trees found when polymorphisms are scored as missing values may not include any of the most parsimonious trees found when the data are scored properly. Additionally, in some cases, polymorphic taxa may be found to be polyphyletic when broken into monomorphic subunits; this is undetected when polymorphisms are treated as missing. Because of these problems, terminal units in cladistic analysis should be based on unique, fixed combinations of characters. Polymorphic taxa should be subdivided into subunits that are monomorphic for each character used in the analysis. Disregarding errors in topology, the additional hidden steps in a cladogram in which polymorphisms are scored as missing can be calculated by a simple formula, based on the observation that if it is assumed that polymorphic terminals include all combinations of character states, 2 ^p − 1 additional steps are required for each taxon in which p polymorphic binary characters are scored as missing values. Thus, when several polymorphisms are scored as missing in the same taxon, very large errors can be introduced into the calculation of tree length.     

Parsimony analysis of the distribution pattern of Japanese primary freshwater fishes, and its application to the distribution of the bagrid catfishes

The geographic distribution of Japanese primary and some secondary freshwater fishes was analyzed using parsimony analysis of endemicity (PAE). Analysis of 73 taxa (species and intraspecific forms) on the four main islands of Japan (divided into 25 geographic areas), produced 44 most parsimonious cladograms. In all of the latter, a total of eight single and compound areas were recognized as endemic areas in nested relationships. The area cladograms showed Japan as comprising a middle-eastern Hokkaido area plus southern areas, the latter containing mainly a northeastern-Honshu endemic area and more heterogeneous southwestern areas, including four endemic areas (western Kyushu, southeastern Chugoku, middle Kinki and Tokai around Ise Bay) and several peripheral areas. Some patterns, e.g., the distinction in fauna across Fossa Magna, noted by previous studies, were supported by these results. Even though the analysis had some problems (e.g., not all geographic ranges of taxa could be included), it provided evidence for the detection of general distribution patterns, because the relationships or similarities among areas were clearly defined by shared taxa. To demonstrate the historical implications of the analysis, the allopatric distribution of, four bagrid catfishes was reconsidered in the area cladogram. The general pattern implied secondary extinction ofPseudobagrus nudiceps around lse Bay, which was in keeping with the fossil record.     

Phylogenetic revision of Agapophytinae subf.n. (Diptera: Therevidae) based on molecular and morphological evidence

Agapophytinae subf.n. is a highly diverse lineage of Australasian Therevidae, comprising eight described and two new genera: Agapophytus Guérin‐Méneville, Acupalpa Kröber, Acraspisa Kröber, Belonalys Kröber, Bonjeania Irwin & Lyneborg, Parapsilocephala Kröber, Acatopygia Kröber, Laxotela Winterton & Irwin, Pipinnipons gen.n. and Patanothrix gen.n. A genus‐level cladistic analysis of the subfamily was undertaken using sixty‐eight adult morphological characters and c. 1000 base pairs of the elongation factor‐1α (EF‐1α) protein coding gene. The morphological data partition produced three most parsimonious cladograms, whereas the molecular data partition gave a single most parsimonious cladogram, which did not match any of the cladograms found in the morphological analysis. The level of congruence between the data partitions was determined using the partition homogeneity test (HT_F) and Wilcoxon signed ranks test. Despite being significantly incongruent in at least one of the incongruence tests, the partitions were combined in a simultaneous analysis. The combined data yielded a single cladogram that was better supported than that of the individual partitions analysed separately. The relative contributions of the data partitions to support for individual nodes on the combined cladogram were investigated using Partitioned Bremer Support. The level of support for many nodes on the combined cladogram was non‐additive and often greater than the sum of support for the respective nodes on individual partitions. This synergistic interaction between incongruent data partitions indicates a common phylogenetic signal in both partitions. It also suggests that criteria for partition combination based solely on incongruence may be misleading. The phylogenetic relationships of the genera are discussed using the combined data. A key to genera of Agapophytinae is presented, with genera diagnosed and figured. Two new genera are described: Patanothrix with a new species (Pat. skevingtoni) and Pat. wilsoni (Mann) transferred from Parapsilocephala, and Pipinnipons with a new species (Pip. kroeberi). Pipinnipons fascipennis (Kröber) is transferred from Squamopygia Kröber and Pip. imitans (Mann) is transferred from Agapophytus. Agapophytus bicolor (Kröber) is transferred from Parapsilocephala. Agapophytus varipennis Mann is synonymised with Aga. queenslandi Kröber and Aga. flavicornis Mann is synonymised with Aga. pallidicornis (Kröber).     

Tests of the accuracy of cladograms in Gilia (Polemoniaceae) and some other angiosperm genera

 This paper deals with the use of cladistic methods and cladograms in phylogeny reconstruction in plant groups containing numerous taxa. How accurate are the cladograms as to details? Accuracy tests at the level of details require an independently known phylogeny, which excludes most plant groups, but such tests can be carried out in domesticated and experimental plant groups which have documented pedigrees. Four such tests are known and are presented here: a new case in Gilia and three previously published cases in Avena, Hordeum, and Helianthus. The four cases include domesticated and experimental plants, use of morphological and molecular evidence, and presence of dichotomous as well as reticulate phylogenies. The cladograms of the four plant groups all differ in significant details from the known pedigrees. These results are discussed in relation to problems of interpretation of cladograms. Received March 21, 2000 Accepted August 16, 2001     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Phylogeny of the vipers of the Caucasus (Reptilia, Viperidae)

Phylogenetic relationships for five taxa of Palearctic vipers (genus Vipera ) from the Caucasian region were revealed by cladistic analyses of separate and combined morphological and biochemical characters. The different data sets yielded largely congruent cladograms. Vipera berus from Sweden was included as an ingroup and V. aspis was used for outgroup comparison. For V. kaznakovi and V. dinniki , three and four different sub-populations, respectively, were treated as independent terminal taxa in the analyses. The most parsimonious cladograms confirmed the systematic positions of these populations, discussed in a recent study, and support the hypothesis that the montane populations of the western main Caucasus comprise one polymorphie species: V. dinniki.
Analyses of combined biochemical and morphological data generated two equally parsimonious cladograms (for all ingroups compared), but yielded only one fully resolved topology when ingroups were condensed to the species level: ( berus ((renardi ('ursinii'-eriwanensis )))( dinnikikaznakovi )).     

Cladistic analysis, phylogeny and biogeography of the Hawaiian Platynini (Coleoptera: Carabidae)

The 128 known native Hawaiian species of the tribe Platynini are analysed cladistically. Cladistic analysis is based on 206 unit-coded morphological characters, and also includes forty-one outgroup taxa from around the Pacific Rim. Strict consensus of the multiple equally parsimonious cladograms supports the monophyly of the entire species swarm. The closest outgroup appears to be the south-east Asian-Pacific genus Lorostema Motschulsky, whose species are distributed from India and Sri Lanka to Tahiti, supporting derivation of the Hawaiian platynines from a source in the western or south-western Pacific. The biogeographic relationships of the Hawaiian taxa are analysed using tree mapping, wherein items of error are minimized. The area cladogram found to be most congruent with the phylogenetic relationships, and most defensible based on underlying character data is {Kauai[Oahu(Hawaii{Lanai[East Maui(West Maui + Molokai)]})]}. This progressive vicariant pattern incorporates progressive colonization from Kauai, and vicariance of the former Maui Nui into the present islands of Molokai, Lanai, West Maui and East Maui. The evolution of flightlessness, tarsal structure, pronotal setation and bursal asymmetry are evaluated in the context of the cladogram. Brachyptery is a derived condition for which reversal is not mandated by the cladogram, although repeated evolution of reduced flight wings is required. Tarsal structure supports Sharp's (1903) recognition of Division 1 as a monophyletic assemblage, but exposes his Division 2 as a paraphyletic group requiring removal of the genus Colpocaccus Sharp. Pronotal setation is exceedingly homoplastic, and is not useful for delimiting natural groups. Left-right asymmetry of the bursa copulatrix reversed twice independently, resulting in mirror-image bursal configurations in B. rupicola and Prodisenochus terebratus of East Maui. The amount of character divergence is greater among species comprising Division 1 than among species of its sister group, the redefined Division 2. Based on superior fit of Division 1 relationships to the general biogeographic pattern, a greater speciation rate coupled with more extensive extinction is rejected as the cause for this greater divergence. Intrinsic differentiation in the processes underlying cuticular evolution appears to be more consistent with the observed biogeographic and morphological patterns.     

Anthropocentricisms in cladograms

Both written and graphic accounts of history can be biased by the perspective of the historian. O’Hara (Biol Philos 7:135–160, 1992) has demonstrated that this also applies to evolutionary history and its historians, and identified four narrative devices that introduce anthropocentricisms into accounts of phylogeny. In the current paper, I identify a fifth such narrative device, viz. the left–right ordering of the taxa at the tips of cladograms. I define two measures that make it possible to quantify the degree of anthropocentricism of cladograms, the human attention score and human rightness score. I then carry out an analysis of the presence of the different distorting mechanisms in phylogenetic textbooks. I deliberately chose two textbooks that adopted a cladistic perspective, since their authors can be assumed to be more conscious about the aim of avoiding anthropocentricisms. Three of the narrative devices are thus absent from cladistic works. However, there is a weak tendency that the resolution of cladogram branches is biased in favour of Homo sapiens. Furthermore, the human perspective is clear and highly significant in the positioning of taxa along the left–right axis of cladograms. I discuss the reasons for and implications of these biased presentations.

Age rank/clade rank metrics--sampling,taxonomy, and the meaning of "stratigraphic consistency"

Paleontologists frequently contrast clade rank (i.e., nodal or patristic distance from the base of a cladogram) with age rank (i.e., relative first known appearances of the analyzed taxa) to measure the degree of congruence between the estimated phylogeny and the fossil record. Although some potential biases of these methods have been examined (e.g., the effect of tree imbalance), other properties of age rank/clade rank (ARCR) comparisons have not been studied in detail. A basic premise of ARCR metrics is that outgroup taxa diverged earlier than ingroups and thus should first appear in older strata. For example, given phylogeny (A,(B,C)), then taxon A should be sampled before either taxon B or taxon C. We examine this premise in the context of (1) phylogenetic theory, (2) taxonomic practice, (3) sampling intensity (R), and (4) factors other than sampling intensity (including cladogram accuracy). Simulations combining clade evolution and sampling over time indicate a poor relationship between ARCR metrics and R when all taxa are apomorphy-based monophyletic groups. However, a good relationship exists when taxa are either stem-based monophyletic groups or if workers include taxa without a priori decisions about monophyly or paraphyly. These results are not surprising because cladograms predict the order in which lineages diverged (which applies to stem-based monophyletic taxa) and the order in which morphologic grades appeared (which applies to paraphyletic taxa relative to derived monophyletic groups). Other factors that increase ARCR metrics when the average R stays the same include high temporal variation in R, budding instead of bifurcating speciation patterns, low extinction rates, cladogram inaccuracy, and (to a much lesser extent) large clade size. These results suggest several plausible explanations for patterned differences in ARCR metrics among clades, thereby compromising their validity as measures of the quality of the fossil record.     

鹅观草属的系统发育分析

根据分支系统学的原理和方法, 对禾本科鹅观草属进行了系统发育分析。鹅观草属传统分类上的18 个系被确定为终端类群, 来自形态学、解剖学、细胞学和孢粉学的23 个性状被选作建立矩阵的依据;雀麦族中的短柄草属作为外类群被用于外部性状的极性识别, 过去分析过的性状资料被用于微观特征的极性判断;采用PAUP 程序对矩阵进行运算, 共获得6 个同等简约的谱系分支图, 其中具最低f-比值的图被选作分支分析的基础。结果表明, 分支图上显示的组、系划分与传统分类的基本一致, 各类群间的演化关系与过去凭借单一证据所作的零散推断也基本吻合。所不同的是半颖组各支类群不是共祖起源, 可能具有复杂的内部组成;在个别系间, 分支图展现的类群位置与宏观分析的存在差异。