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Arbitrary Resolutions, Missing Entries, and the Problem of Zero-Length Branches in Parsimony Analysis
... Analysis of our morphological dataset (including molecular backbone constraints: Supplementary Fig. S7) produced both poor ingroup resolution and node support for the placement of fossil taxa ( Supplementary Figs S8 and S9). We attribute this to missing data and pervasive homoplasy, which was detected during construction of our matrix (see Methods) and subsequently examined via serial pruning of redundant fossils 40 and wildcards 41 (Supplementary Figs S10-S12). These procedures returned Lemdubuoryctes, together with Bulungu palara, Yarala burchfieldi and species of Galadi as labile stem peramelemorphians. ...
... (2) Excessively incomplete DNA characters were removed in morphology-only analyses to examine the effects of extinct taxa with numerous missing entries 71 . A manual screen for redundant taxa (safe taxonomic reduction 40 ) identified all OTUs that degraded strict consensus resolution and pinpointed instability caused by missing data versus character conflict 72 . (3) The 'amb-' option was implemented during all PAUP* v4.0b10 73 parsimony searches to eliminate ambiguous zero length branches 74 . ...
... (3) The 'amb-' option was implemented during all PAUP* v4.0b10 73 parsimony searches to eliminate ambiguous zero length branches 74 . (4) A posteriori screening of wildcard taxa produced a strict reduced consensus profile based on the semi-strict Adams consensus (where wildcards do not obscure adequately supported nodes 40,41 ) and assessments of relative character support at affected nodes 74 . (5) Bootstrapping and branch (Bremer) decay indices were alternately employed with and without wildcard exclusion to test the impact of mobile OTUs upon support measures. ...
Bandicoots (Peramelemorphia) are a unique order of Australasian marsupials whose sparse fossil record has been used as prima facie evidence for climate change coincident faunal turnover. In particular, the hypothesized replacement of ancient rainforest-dwelling extinct lineages by antecedents of xeric-tolerant extant taxa during the late Miocene (~10 Ma) has been advocated as a broader pattern evident amongst other marsupial clades. Problematically, however, this is in persistent conflict with DNA phylogenies. We therefore determine the pattern and timing of bandicoot evolution using the first combined morphological + DNA sequence dataset of Peramelemorphia. In addition, we document a remarkably archaic new fossil peramelemorphian taxon that inhabited a latest Quaternary mosaic savannah-riparian forest ecosystem on the Aru Islands of Eastern Indonesia. Our phylogenetic analyses reveal that unsuspected dental homoplasy and the detrimental effects of missing data collectively obscure stem bandicoot relationships. Nevertheless, recalibrated molecular clocks and multiple ancestral area optimizations unanimously infer an early diversification of modern xeric-adapted forms. These probably originated during the late Palaeogene (30–40 Ma) alongside progenitors of other desert marsupials, and thus occupied seasonally dry heterogenous habitats long before the onset of late Neogene aridity.
... The consequences of including missing data in phylogenetic analysis have long been discussed (Dunn, McEachran, & Honeycutt, 2003;Fulton & Strobeck, 2006;Huelsenbeck, 1991;Jiang, Chen, Wang, Li, & Wiens, 2014;Novacek, 1992;Wiens, 1998;Wilkinson, 1995aWilkinson, , 1995bWilkinson, , 1995aWilkinson, , 1995bWilkinson, , 2003Wilkinson & Benton, 1995). This discussion has continued in the age of reduced representation genome methods (Hosner, Faircloth, Glenn, Braun, & Kimball, 2016;Rubin et al., 2012;Streicher, Schulte, & Wiens, 2016b). ...
... The consequences of including missing data in phylogenetic analysis have long been discussed (Dunn, McEachran, & Honeycutt, 2003;Fulton & Strobeck, 2006;Huelsenbeck, 1991;Jiang, Chen, Wang, Li, & Wiens, 2014;Novacek, 1992;Wiens, 1998;Wilkinson, 1995aWilkinson, , 1995bWilkinson, , 1995aWilkinson, , 1995bWilkinson, , 2003Wilkinson & Benton, 1995). This discussion has continued in the age of reduced representation genome methods (Hosner, Faircloth, Glenn, Braun, & Kimball, 2016;Rubin et al., 2012;Streicher, Schulte, & Wiens, 2016b). ...
Restriction site‐associated DNA sequencing (RADseq) has emerged as a useful tool in systematics and population genomics. A common feature of RADseq data sets is that they contain missing data that arise from multiple sources including genealogical sampling bias, assembly methodology and sequencing error. Many RADseq studies have demonstrated that allowing sites (single nucleotide polymorphisms, SNPs) with missing data can increase support for phylogenetic hypotheses. Two non‐mutually exclusive explanations for this observation are that (a) larger data sets contain more phylogenetic information; and (b) excluding missing data disproportionally removes sites with the highest mutation rates, causing the exclusion of characters that are likely variable and informative. Using a RADseq data set derived from the East African banana frog, Afrixalus fornasini (up to 1.1 million SNPs), we found that missing data thresholds were positively correlated with the proportion of parsimony‐informative sites and mean branch support. Using three proxies for estimating site‐specific rate, we found that the most conservative missing data strategies excluded rapidly evolving sites, with four‐state sites present only when allowing ≥60% missing data per SNP. Topological similarity among estimated phylogenies was highest for the data sets with ≥60% missing data per SNP. Our results suggest that several desirable phylogenetic qualities were observed when allowing ≥60% missing data per SNP. However, at the highest missing data thresholds (80% and 90% missing data per SNP), we observed differences in performance between high‐ and mixed‐weight DNA extraction samples, which may indicate there are trade‐offs to consider when using degraded genomic template with RADseq protocols.
... Because only one sex is known for 31 of the 65 Hortipes species described here, the complete data matrix for all species has a large number of missing entries, a situation known to cause problems when searching for most parsimonious trees (Platnick et al., 1991a;Wilkinson, 1995a). For example, when a preliminary tree search was performed using PeeWee 2.6 on a matrix for all 65 species under implied weighting, excessively long run times were needed and very large numbers of trees were generated, causing memory overflow even when the tree buffer was set to contain 40000 trees. ...
... These trees differ by the optimization of four multistate characters (54, 76, 83 and 90) and one binary character (88). There are no zerolength branches (Coddington and Scharff, 1994;Wilkinson, 1995b): by careful manipulation of the optimization of characters 54, 76, 83, 88, and 90 in Clados 1.9.1 it is possible to obtain full support for all nodes on all six trees. However, there is no justification for preferring one optimization of the multistate characters over another. ...
Hortipes Bosselaers and Ledoux (type species Hortipes luytenae Bosselaers and Ledoux from South Africa) is a genus of small (1.5-4 mm), pale, mainly soil-dwelling spiders from sub-Saharan Africa. The genus, which is tentatively placed in the Liocranidae, is characterized by the presence of a peculiar ellipsoidal array of setae on the dorsal side of metatarsi I and II and by the large anterior median eyes with a dark retina restricted to the median portion. Ledoux and Emerit (1998) described five more species from Ivory Coast and Gabon. Sixty-three additional Hortipes species are described here as new: H. platnicki (♀), H. castor (♂ ♀), H. pollux (♂ ♀), H. fastigiensis (♂ ♀), H. ostiovolutus (♂ ♀), H. salticola (♂ ♀), H. exoptans (♂ ♀), H. scharffi (♂ ♀), H. cucurbita (♂ ♀), H. hesperoecius (♀), H. klumpkeae (♀), H. aurora (♂ ♀), H. echo (♀), H. stoltzei (♂), H. creber (♂ ♀), H. orchatocnemis (♂ ♀), H. contubernalis (♂ ♀)', H. mesembrinus (♀), H. coccinatus (♂ ♀), H. wimmertensi (♂ ♀), H. irimus (♀), H. licnophorus (♀), H. schoemanae (♂ ♀), H. aelurisiepae (♀), H. hyakutake (♂), H. rothorum (♂) H. griswoldi (♂), H. oronesiotes (♂ ♀), H. penthesileia (♀), H. zombaensis (♂ ♀), H. atalante (♀), H. merwei (♂ ♀), H. leno (♂ ♀), H. mulciber (♀), H. libidinosus (♂ ♀), H. delphinus (♂ ♀), H. bjorni (♂), H. amphibolus (♀), H. hastatus (♂ ♀), H. horta (♀), H. angariopsis (♀), H. falcatus (♂ ♀), H. lejeunei (♂ ♀), H. narcissus (♂ ♀), H. auriga (♂), H. puylaerti (♀), H. chrysothemis (♀), H. machaeropolion (♂ ♀), H. centralis (♀), H. tarachodes (♂ ♀), H. terminator (♂), H. baerti (♂), H. robertus (♂ ♀), H. abucoletus ♀, H. alderweireldti (♂), H. architelones (♂ ♀), H. calliblepharus (♂), H. fortipes (♂), H. bosmansi (♂ ♀), H. sceptrum (♂ ♀), H. anansiodatus ♀, H. hormigricola (♂ ♀), and H. depravator (♂). The genus has a vast Afrotropical distribution, occurring from as far south as East London in South Africa to Sierra Leone in western Africa. So far, no specimens are available from northeastern tropical Africa. Apart from H. merwei, which seems to prefer grassland, all species are found in leaf litter or the canopy of different kinds of forests and dense thickets. In captivity, H. contubernalis readily fed on Collembola. Specimens raised from cocoons obtained in the laboratory reached adulthood after three molts. A cladistic analysis of the 34 species for which both sexes are known, largely based on secondary genitalic characters, is proposed.
... This artifact has been identified in the case of matrices with missing values , or without (Lorenzen and Sieg, 1991). This deficiency of current microcomputer programs was addressed in NONA (and PIWE, Goloboff, 1993a, b; these programs were overlooked by Wilkinson, 1995, in his discussion of zero-length branches. Wilkinson also overlooked PHYSYS). ...
... Optimization on multifurcations can accomplish this. Wilkinson (1995) lamented the lack of an option for suppressing semistrictly supported cladograms with PAUP, but Total Collapsibility can easily be implemented with several other available microcomputer programs: ...
Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.
... Thus, coding absence in a multistate character may render It has also been suggested that partial ordering of Sankoff (composite) characters will cause reductive inapplicable data informative in determining the phylogenetic relationships when it should not. and composite characters to be analytically equivalent (Wilkinson, 1995b). In this case, partial ordering by Composite coding may succeed in recovering the expected tree, but only when absence is primitive and the method of intermediates (Mabee and Humphries, 1993) yields a character state tree with each state sepa-there are no secondary losses. ...
... Because this absence has only one Riggins, 1997). biological cause, this violates the requirement of bio- Wilkinson (1995b) distinguished between biological logical independence of characters. Further, if absence and logical independence of characters. ...
Inapplicable character states occur when character complexes are absent or reduced in some of the taxa. Several approaches have been proposed for representing such states in a character matrix so that the inapplicable condition has no effect on the placement of taxa and/or the applicable states are independent and not redundant. Here we examine each of these approaches and demonstrate that all have shortcomings. Coding inapplicables as '?' (reductive coding), although flawed, is currently the best way to analyze data sets that contain inapplicable character states.
... Super-matrix trees have been criticized for ignoring the effects of large sections of missing character data, although simulation studies have been successful in investigating the effect of missing data under a variety of circumstances (reviewed in Sanderson & Driskell 2003). The effects of missing character data on cladistic analyses have been examined at various times in the history of phyloge-netic tree building as characters not applicable to certain taxa become prominent for phylogenetic reconstruction (Dunn et al. 2003, Nixon 1996, Nixon & Davis 1991, Platnick et al. 1991Wilkinson 1995aWilkinson , 1995b; see Wiens 2006 for review) and such issues are not insurmountable. ...
... Super-matrix trees have been criticized for ignoring the effects of large sections of missing character data, although simulation studies have been successful in investigating the effect of missing data under a variety of circumstances (reviewed in Sanderson & Driskell 2003). The effects of missing character data on cladistic analyses have been examined at various times in the history of phyloge-netic tree building as characters not applicable to certain taxa become prominent for phylogenetic reconstruction (Dunn et al. 2003, Nixon 1996, Nixon & Davis 1991, Platnick et al. 1991Wilkinson 1995aWilkinson , 1995b; see Wiens 2006 for review) and such issues are not insurmountable. ...
Assembling phylogenetic trees for groups of organisms with thousands of taxa is problematic because of the large amount of data and trees that must be generated and analyzed. Several attempts have been made to develop a better way to handle the problems of large trees. Meta-trees (Meta Supertrees) are suggested as a way to generate a phylogeny for groups where you have many different data sets of overlapping but not identical sets of taxa and without a common set of markers. Meta-trees graft phylogenies onto a fixed base tree and avoid the problems of missing or redundant data and misplaced taxa that plague other types of supertrees. Supertrees are constructed from novel analyses of multiple independently de-rived tree topologies or data matrices with overlapping but not identical taxa. They can provide an excellent summary of past work and a useful framework for exam-ining character evolution in a broader historic and phylogenetic framework. For all types of supertrees, the major concern is how reliable they are at providing an estimate of phylogenetic relationships, or how much confidence can be placed in each of the nodes and the taxonomic associations they indicate. As with all types of analyses, the worth of the product is based on the quality of the data used and the reliability of the method. It seems that the term was first used by Gordon (1986) but then languished until it was made popular by Sanderson et al. (1998) in conjunction with developing taxonomically broad ''trees of life.'' In the last five years, with the advent of large-scale phylogenetic programs, using
... This note focuses on practical implications of the "soft" interpretation of polytomies in primary, as opposed to consensus, cladograms (Maddison, 1989), and especially the implications of that assumption for tree choice under parsimony. Several other criteria for tree choice within the philosophical framework of parsimony exist (Carpenter, 1988;Coddington and Scharff, 1995;Farris, 1969;Michevich, 1982;Maddison, 1993;Platnick et al. 1991;Wilkinson, 1995aWilkinson, , 1995b. For example, character optimization (Lipscomb, 1992;Swofford and Maddison, 1992), is often a more compelling criterion for choice than topological resolution. ...
... exhaustive or exact solution sets); and "legitimate" or "valid" cladograms by definition have support at all nodes simultaneously. In other words, topologies that must contain unsupportable (zero-length) branches are discarded because they cannot be completely justified with the available data (Wilkinson, 1995a;Coddington and Scharff, 1995). Tree 6 in Fig. 1 contains a zero-length branch (either HI or HICGF) due to the behaviour of the third character. ...
The “soft” assumption attributes polytomies to lack of data, not simultaneous cladogenesis (the “hard” assumption). Most systematists prefer the first interpretation, but most parsimony programs implicitly use the second. Results can thus be inconsistent with initial assumptions. Under certain circumstances that seem especially typical for large data sets treating higher taxa, it may be valid to eliminate both compatible and incompatible polytomous trees from consideration. Consistent treatment of soft polytomies can reduce the ambiguity of cladistic solutions and improve the resolution, and testability, of phylogenetic hypotheses.
... Thus, coding absence in a multistate character may render It has also been suggested that partial ordering of Sankoff (composite) characters will cause reductive inapplicable data informative in determining the phylogenetic relationships when it should not. and composite characters to be analytically equivalent (Wilkinson, 1995b). In this case, partial ordering by Composite coding may succeed in recovering the expected tree, but only when absence is primitive and the method of intermediates (Mabee and Humphries, 1993) yields a character state tree with each state sepa-there are no secondary losses. ...
... Because this absence has only one Riggins, 1997). biological cause, this violates the requirement of bio- Wilkinson (1995b) distinguished between biological logical independence of characters. Further, if absence and logical independence of characters. ...
Inapplicable character states occur when character complexes are absent or reduced in some of the taxa. Several approaches have been proposed for representing such states in a character matrix so that the inapplicable condition has no effect on the placement of taxa and/or the applicable states are independent and not redundant. Here we examine each of these approaches and demonstrate that all have shortcomings. Coding inapplicables as “?” (reductive coding), although flawed, is currently the best way to analyze data sets that contain inapplicable character states.
... This note focuses on practical implications of the "soft" interpretation of polytomies in primary, as opposed to consensus, cladograms (Maddison, 1989), and especially the implications of that assumption for tree choice under parsimony. Several other criteria for tree choice within the philosophical framework of parsimony exist (Carpenter, 1988;Coddington and Scharff, 1995;Farris, 1969;Michevich, 1982;Maddison, 1993;Platnick et al. 1991;Wilkinson, 1995aWilkinson, , 1995b. For example, character optimization (Lipscomb, 1992;Swofford and Maddison, 1992), is often a more compelling criterion for choice than topological resolution. ...
... exhaustive or exact solution sets); and "legitimate" or "valid" cladograms by definition have support at all nodes simultaneously. In other words, topologies that must contain unsupportable (zero-length) branches are discarded because they cannot be completely justified with the available data (Wilkinson, 1995a;Coddington and Scharff, 1995). Tree 6 in Fig. 1 contains a zero-length branch (either HI or HICGF) due to the behaviour of the third character. ...
posed the problem abstractly, a single character on one tree, addressed only one horn of the dilemma,(branches ambiguously,of zero or greater length were always assigned zero length), considered solutions only within the philosophical frame- work offered by PAUP, and offered no advice regarding what practicing system- atists could do to detect the problem. In addition, the treatment of the zero-length branch problem by programmers is already more diverse than reported by Wilkinson (1995), and users of the most common packages should be aware of the different interpretations adopted by programmers. Wilkinson (1995) offered some algorithmic suggestions for a solution, but his solution, although helpful, strikes us as less than ideal. We also focus here on what practicing systemadsts can do now to detect and avoid the problem. Finally, the solution is not necessarily as simple as eliminadng "arbitrary resolutions". Most importandy, Wilkinson (1995) did not consider what happens if branches of ambiguous,length are permitted to be non-zero rather than zero-length. A more fundamental issue is the meaning,of "acceptable support" for phylogenedc,hypoth- eses, and therefore which hypotheses are worth considering, as Platnick et al. (1991) discussed. That debate is just beginning, but should involve the user com- munity in addidon to programmers and methodologists. Table 1 conveys the problem of zero-length branches more concretely than the
... This note focuses on practical implications of the "soft" interpretation of polytomies in primary, as opposed to consensus, cladograms (Maddison, 1989), and especially the implications of that assumption for tree choice under parsimony. Several other criteria for tree choice within the philosophical framework of parsimony exist (Carpenter, 1988;Coddington and Scharff, 1995;Farris, 1969;Michevich, 1982;Maddison, 1993;Platnick et al. 1991;Wilkinson, 1995aWilkinson, , 1995b. For example, character optimization (Lipscomb, 1992;Swofford and Maddison, 1992), is often a more compelling criterion for choice than topological resolution. ...
... exhaustive or exact solution sets); and "legitimate" or "valid" cladograms by definition have support at all nodes simultaneously. In other words, topologies that must contain unsupportable (zero-length) branches are discarded because they cannot be completely justified with the available data (Wilkinson, 1995a;Coddington and Scharff, 1995). Tree 6 in Fig. 1 contains a zero-length branch (either HI or HICGF) due to the behaviour of the third character. ...
Abstract— The “soft” assumption attributes polytomies to lack of data, not simultaneous cladogenesis (the “hard” assumption). Most systematists prefer the first interpretation, but most parsimony programs implicitly use the second. Results can thus be inconsistent with initial assumptions. Under certain circumstances that seem especially typical for large data sets treating higher taxa, it may be valid to eliminate both compatible and incompatible polytomous trees from consideration. Consistent treatment of soft polytomies can reduce the ambiguity of cladistic solutions and improve the resolution, and testability, of phylogenetic hypotheses.
... Of those, six corresponds to features of the upper lips and philtrum and the remainder 17 describes specifically the rhinarium (Appendix B). Reductive coding (Wilkinson, 1995) was favored when constructing characters but multistate one can be produced easily from the presented data. The obtained matrix, 23 characters scored for 61 genera (Aepeomys, Chibchanomys, Kunsia, Lundomys, Phaenomys, and Rheomys have been excluded because the poorly-quality material available to score characters; Appendix C), was phylogenetically evaluated through optimization on the most complete to date multilocus topology resolving sigmodontine relationships. ...
This study presents a comprehensive analysis of the rhinarium morphology and associated features in sigmodontine rodents, a highly diverse group within the Cricetidae family. The research encompassed 483 specimens representing 145 species, accounting for 75% of genera in the clade, including all 13 recognized tribes, three incertae sedis genera, and representatives from the murid Mus and Rattus. The inconsistent use of terminology in describing rhinarium traits across literature presented a challenge for comparative analyses. To address this issue, a standardized terminology was proposed to characterize the rhinarium, upper lip, and philtrum. Notably, a paired complex protuberance with epidermal ridges, termed here the Tubercle of Hill, was identified as a distinctive feature in muroid rhinaria. Comparative assessments among tribes revealed unique sets of features defining each major clade, encompassing variations in hairiness, dorsal nasal complexity, size and positioning of the Tubercles of Hill, and other key attributes. Two primary rhinarium configurations were discerned: one shared by Oryzomyalia and Sigmodontini and another specific to Ichthyomyini. The former groups display a ventrally positioned rhinarium prominently featuring the Tubercle of Hill and sculptured areolae circularis. In contrast, Ichthyomyini exhibit frontally directed rhinaria characterized by an enlarged dorsum nasi, resulting in a distinctive “cherry” appearance. These distinct morphological patterns are postulated to be associated with functional adaptations. Convergent rhinarium structures observed in fossorial species, characterized by well-developed plicae alaris and hair fringes, are presumed to mitigate potential damage during excavatory behaviors. Conversely, semiaquatic carnivorous sigmodontines showcase an integrated apical structure in their rhinarium, facilitating enhanced somatosensory capabilities crucial for predation activities during diving expeditions.
... An equally weighted analysis of the data matrix was performed in PAUP with hsearch addseq=random nreps=1000 (heuristic search with tree bisection and reconnection swapping and 1000 random addition sequences). In order to avoid spurious resolution due to unsupported (Coddington & Scharff 1994;Wilkinson 1995) or ambiguously supported (Nixon & Carpenter 1996) branches, those with a minimum length of zero were collapsed with condense collapse=minbrlen. Eighteen shortest trees (length = 676) were found in 517 out of 1000 random addition sequences, involving 2223800000 rearrangements. ...
The endemic South African spider genus Austrachelas Lawrence, 1938 is revised. The type species, A. incertus Lawrence, 1938, and A. natalensis Lawrence, 1942, are redescribed, and their males described for the first time. Seven new species are described: A. bergi n. sp. (female only), A. kalaharinus n. sp. (male only), A. merwei n. sp. (both sexes), A. pondoensis n. sp. (both sexes), A. reavelli n. sp. (both sexes), A. sexoculata n. sp. (male only), and A. wassenaari n. sp. (both sexes). A cladistic analysis performed including Austrachelas and various species of the corinnid subfamilies Trachelinae, Castianeirinae, Corinninae and Phrurolithinae, and species from the Liocranidae, Gallieniellidae, Gnaphosidae and Lamponidae, suggests that Austrachelas is currently misplaced. Its transfer to the Gallieniellidae is proposed.
... Missing data were first accommodated by a priori screening for safe taxonomic reduction (Wilkinson, 1995) using TAXEQ3 (Wilkinson, 2001). This identified Ekaltadeta ima/ E. jamiemulvaneyi and Macropus fuliginosus/M. ...
SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: den Boer, W., and B. P. Kear. 2018. Is the fossil rat-kangaroo Palaeopotorous priscus the most basally branching stem macropodiform? Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2017.1428196. 2018
... An equally weighted analysis of the data matrix was performed in PAUP with hsearch addseq = random nreps = 5000 (heuristic search with tree bisection and reconnection swapping and 5000 random addition sequences). In order to avoid spurious resolution due to unsupported (Coddington and Scharff, 1994;Wilkinson, 1995) or ambiguously supported (Nixon and Carpenter, 1996) branches, those with a minimum length of zero were collapsed with pset collapse = minbrlen. Multistate character states were coded as polymorphic with pset mstaxa = polymorph. ...
2013. X-ray micro-CT reconstruction reveals eight antennomeres in a new fossil taxon that constitutes a sister clade to Dundoxenos and Triozocera (Strepsiptera: ABSTRACT Eocenoxenos palintropos gen. nov. et sp.nov., a new fossil strepsipteran taxon from Baltic amber is described. The position of the new genus is based on cladistic analyses of morphological data sets. Most data of the fossil where retrieved with 3D micro-CT scan reconstructions. The new taxon is unambiguously situated as a sister group of the Dundoxenos-Triozocera clade within the Corioxenidae. The eocene taxon combines derived characteristics typical of Corioxenidae with the posession of eight antennomeres with five long flabella, a regained ancestral characteristic.
... Second, the branch supporting the monophyly of Linyphiini plus the rest of the linyphiids (excluding the Micronetini) (Figure 37B) is an artifact due to the way programs treat missing entries (Platnick et al., 1991;Coddington and Scharff, 1996;NUMBER 609 13 Wilkinson, 1995). This branch either is supported by character 34 under Farris optimization or is of zero length. ...
... First, those trees supported with ambiguous branches were avoided. Recently, Wilkinson (1995), and Coddington and ScharfF (1 994) have addressed the problem of zero-length branches. Coddington and ScharfF (1994:417) stated: "All monophyletic groups must have synapomorphies; all branches must have support simultaneously." ...
The genus Cidaria Treitschke is revised. Eight species of the genus which occur widely in the Palaearctic and northern India, are recognized, of which one, Cidaria luteata sp. nov., is described as new while two subspecies of C. fulvata (Forster) are elevated to species, C. nugata Felder stat. rev., and C. distinctata Staudinger stat. nov. C. ochripennis Prout is proposed as a junior synonym of C. ochreata Staudinger. C. deletaria Hampson is excluded from the genus. All species of Cidaria and their genitalia are described and illustrated. The cladistic analysis of these eight species of Cidaria is carried out using two data matrices, the first comprising morphological characters alone and the second morphological and distributional characters. The most parsimonious cladogram of Cidaria is selected, and its monophyly defined. The character analysis shows that some distribution characters contribute to resolving the in group node. The choice of multiple trees is discussed.
... One step is optimized on two of the three branches in all three possible optimizations, but where those two steps are optimized is ambiguous. In the context of parsimony, ''All monophyletic groups must have synapomorphies; all branches must have support simultaneously'' (Coddington and Scharff, 1994, p. 417; see also Platnick et al. (1991) and Wilkinson (1995)). Because each of the three branches is unsupported by one of the most parsimonious optimizations, all three branches are collapsed in the strict consensus. ...
The greater power of parametric methods over parsimony is frequently observed in empirical phylogenetic analyses by providing greater resolution and higher branch support. This greater power is provided by several different factors, including some that are generally regarded as disadvantageous. In this study we used both empirical and (modified) simulated matrices to examine how Bayesian MCMC, maximum likelihood, and parsimony methods interpret ambiguous optimization of character states. We describe the information content in "redundant" terminals as well as a novel approach to help identify clades that cannot be unequivocally supported by synapomorphies in empirical matrices. Four of our main conclusions are as follows. First, the SH-like approximate likelihood ratio test is a more reliable indicator than the bootstrap of branches that are only ambiguously supported in likelihood analyses wherein only a single fully resolved optimal tree is presented. Second, bootstrap values generated by methods that only ever present a single fully resolved optimal tree are less robust to differences in taxon sampling than are those generated by more conservative methods. Third, PAUP∗ likelihood is more resilient to producing apparently unambiguous resolution and high support from ambiguous characters than is GARLI collapse 1 and MrBayes, which in turn are more resilient than PhyML. GARLI collapse 0, IQ-TREE, and RAxML are the least resilient bootstrapping methods examined. Fourth, frequent discrepancies with respect to resolution and/or branch support may be obtained by methods that only ever present a single fully resolved optimal tree in different contexts that are apparently unique to the specific program and/or method of quantifying branch support.
... according to the second rule (SET AMBIGUOUS=), a branch is supported when at least one character has at least one MPR that assigns non-zero length to the branch (cf. Scharff 1994 andWilkinson 1995 for a general discussion of the problem of zero-length branches). ...
[Introduction, pp. xiii-xv]
The central theme of this thesis is cladistics. This approach to phylogenetic analysis has its roots in Willi Hennig’s theoretical work of the fifties (see chapter 1), and after a modest take-off in the sixties and a period of exponential growth in the seventies and the eighties, cladistics has now become a basic tool in systematic research. Its merits are that it has stimulated the development of a conceptual framework that enables us to think and talk in a clear way about phylogenetic relationships, and that it provides a set of powerful methods to analyze systematic data in order to discover the underlying phylogenetic relationships. In the first chapter, a basic survey of the main concepts and terms of cladistics is given. It is presented in Dutch because to date no general introductions to cladistics exist in Dutch.
At present, there is a set of generally accepted methods in cladistics. However, this does not mean that the theoretical work has come to an end. To the contrary, old ideas are constantly being refined and new ideas keep popping up. Two of those are treated in the second and the third chapter.
The first one is three-item analysis, a method that was introduced some years ago as a novel approach to parsimony analysis in both biogeography (Nelson & Ladiges 1991a, b) and systematics (Nelson & Platnick 1991). The name three-item analysis refers to the fact that each statement about relationships between more than three items (areas in biogeography, homologous features in systematics) is decomposed into a series of basic statements, each of which involves only three items. Such a basic statement simply says which two of the three items are thought to be related more closely to each other than either is related to the third. Following its introduction, three-item analysis has been severely criticized because of three basic defects: (1) it is flawed because it presupposes that character evolution is irreversible; (2) it is flawed because basic statements that are not logically independent are treated as if they are; (3) it is flawed because some of the three-item statements that are considered as independent support for a given tree may be mutually exclusive on that tree. In the second chapter it is shown that these criticisms only relate to the particular way that the approach was implemented by Nelson & Platnick (1991), and an alternative implementation that solves each of the three basic problems is derived. However, the resulting method is not an improvement over standard parsimony analysis: it is identical to the standard approach but for one small constraint, which is a highly unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. As this restriction follows directly from the decomposition of character state distributions into basic statements, it is concluded that any approach that is based on such decompositions will be defective.
The second one is about character weighting. Some years ago, Goloboff (1993a) proposed a non-iterative homoplasy-based weighting method in which the weight or fit of a character on a cladogram is defined as a hyperbolic decreasing function of its homoplasy. The best trees are those that have the highest total fit over all characters of a data set. Goloboff considered his approach to be in direct agreement with cladistic ideas, but most parsimonious trees are those trees that imply the lowest amount of weighted homoplasy (Farris 1983), and these are not necessarily the trees that imply that the characters have the highest total fit, as is shown in chapter three. Several implications of this observation are discussed, and an alternative way of weighting characters is proposed. A computer program in which this approach is available is discussed in appendix A, and the approach is illustrated by using an indecisive data set (see chapter six) and the morphological Gentianaceae data set that is presented in chapter five.
Several cladistic analyses based on various types of data indicate that the Gentianaceae, a cosmoplolitan family of medium size, is one of the principal families of a monophyletic order Gentianales. Recent developments concerning the order Gentianales are reviewed against a historical background in chapter four. While a consensus is emerging about the monophyly of the Gentianales, much work remains to be done concerning the interfamilial and intrafamilial relationships within the order.
The most recent worldwide monograph of the Gentianaceae is over a century old (Gilg 1895). The 21 genera that are selected for the current analysis represent all Gilg’s tribes and subtribes except Leiphaimeae, Rusbyantheae and Voyrieae. Standard parsimony analyses and analyses using Goloboff’s approach of maximum fit give congruent results as far as the global relationships are concerned. The best supported clade contains Eustoma (Tachiinae) and all included Gentianinae, Erythraeinae and Chironiinae. The basal parts of the cladograms, involving the woody tropical representatives and Exacum, are poorly resolved.
This thesis is concluded with a short chapter on indecisive data sets. Goloboff (1991a, b) defined the cladistic decisiveness of a data set as the degree to which all possible resolved trees for the data set differ in length. He proposed a measure of the decisiveness of data sets, the DD statistic, and discussed some properties of indecisive data sets, a special type of data set for which every possible cladogram has the same length. His discussion of indecisive data sets was restricted to characters that have no missing entries. In this chapter I will first show how indecisive data sets can be constructed when missing entries are present. Without missing entries, there is essentially only a single indecisive data set for a given number of taxa, but by allowing missing entries a wide variety of different indecisive data sets with a wide range of ensemble consistency and retention indices can be constructed (easy-to-calculate formulas for the length of an indecisive data set on a dichotomous tree and on an unresolved bush are derived in Appendix C). Such data sets are useful in the construction of hypothetical examples that illustrate the elusive nature of data decisiveness. It is concluded that simple measures such as Goloboff’s DD statistic are unable to capture the various aspects of the concept.
... An equally weighted analysis of the data matrix was performed in PAUP with hsearch addseq=random nreps=20000 (heuristic search with tree bisection and reconnection swapping and 20000 random addition sequences). In order to avoid spurious resolution due to unsupported (Coddington & Scharff 1994; Wilkinson 1995) or ambiguously supported (Nixon & Carpenter 1996) branches, those with a minimum length of zero were collapsed with condense collapse=minbrlen. Two shortest trees (length = 95) were found, the strict consensus of which can be found inFig. ...
A new Paratrachelas Kovblyuk & Nadolny, 2009 species, P. atlantis sp. n., is described from Algeria. As a result of a cladistic analysis involving ten Palaearctic Trachelas L. Koch, 1872 and Paratrachelas species, T. validus Simon, 1884,
and T. ibericus Bosselaers et al., 2009 are transferred to Paratrachelas as P. validus new combination and P. ibericus new
combination, and a new genus, Metatrachelas gen. n., is erected, to which T. rayi Simon, 1878, T. macrochelis
Wunderlich, 1992, and T. amabilis Simon, 1878 are transferred as M. rayi new combination, M. macrochelis new
combination and M. amabilis new combination.
... This method of handling inapplicables has been termed 'reductive coding' (Strong and Lipscomb 1999) and is considered by many investigators who have dealt with inapplicables in phylogenetic inference, including us, to be the best solution to handling such characters (Strong and Lipscomb 1999). Readers interested in the issue of how to handle inapplicable characters are directed to the following additional papers on this topic: Nixon and Davis (1991), Platnick et al. (1991), Maddison (1993), Wilkinson (1995a) (1995b) and Hawkins et al. (1997). The issue of how to code inapplicables in morphological data is almost identical to the issue of how to treat indels (insertion/deletion events, gaps) in molecular data, particularly whether to code each site of an indel as a fifth state or as missing data. ...
Carrion beetles of the genus Nicrophorus Fabricius, 1775 (Silphidae) are well known for their biparental brood care and monopolisation of small vertebrate carcasses in subterranean crypts. Although the taxonomy of New World species has received modern attention, the fauna of Asia, primarily of the nepalensis-group of species, has not. Herein we revise this species-group and describe as new the following seven species: Nicrophorus charon Sikes & Madge (Sulawesi), Nicrophorus herscheli Sikes & Madge (Sumatra), Nicrophorus insignis Sikes & Madge (Flores Island), Nicrophorus melissae Sikes & Madge (Nepal, Bhutan), Nicrophorus reticulatus Sikes & Madge (Guadalcanal), Nicrophorus schawalleri Sikes & Madge (Gansu, Shaanxi, Sichuan Province) and Nicrophorus trumboi Sikes & Madge (Nepal, Bhutan). We obtained a preliminary phylogeny using morphology and mtDNA (COII). This was inferred using maximum likelihood and Bayesian methods with the Mkv and GTR+I+G models (parsimony was rejected by the Akaike information criterion for being excessively parameter-rich). The phylogenetic signal in the morphological dataset was not strong and results were confounded by a ‘long-branch’ species, N. reticulatus. The signal was stronger in the combined dataset and the COII-only dataset. The molecular phylogeny supported the new status of species N. trumboi and N. melissae. Support was found for a mainland origin of the group with subsequent radiations into the Malay Archipelago.
... Nodes are present because of mutually exclusive optimisations of the same character and optimisations at internal nodes of unobserved conditions. Wilkinson (1995) considered that some of these trees contained linked sets of interior branches that simultaneously have zero and nonzero lengths, a problem that current computer algorithms have difficulty dealing with. Investigation of the trees that cannot be supported by any conceivable assignment of the possible states indicates that taxa are separated without information. ...
This major systematic revision of fireflies (Coleoptera: Lampyridae) concentrates on the genera related to Atyphella
Olliff in the Luciolinae. Seven new genera and 19 new species are described, which with two exceptions occur in the area
encompassed by Australia, the Republic of Palau, Federated States of Micronesia, Papua New Guinea, Indonesia (West
Irian), Solomon Islands, New Caledonia, Vanuatu and Fiji. Keys to the genera and subgenera of the Luciolinae are
included. The revision is based upon a phylogenetic analysis of 343 morphological characters of males, females and larvae
of 112 Luciolinae species, including the type species of the six genera and four subgenera of the Luciolinae sensu
McDermott (1966). The genus Atyphella Olliff is redefined and redescribed from 23 species including 14 endemic Australian
species, and nine species from the wider study area. A. leucura Olivier, A. scabra Olivier and A. testaceolineata
Pic are redescribed. A. palauensis Wittmer is elevated to species level from A. carolinae palauensis Wittmer and redescribed.
Aquilonia gen. n. is described for Aq. costata (Lea), transferred from Atyphella Olliff. Convexa gen. n. is
described for C. wolfi (Olivier), transferred from Atyphella. Gilvainsula gen. n. includes the new species, G. similismessoria
sp. n., and G. messoria (Olivier), transferred from Atyphella Olliff. Lloydiella gen. n. includes four species; Ll.
majuscula (Lea) transferred from Atyphella, and three new species, Ll. japenensis sp. n., Ll. uberia sp. n., and Ll. wareo
sp. n. Pygatyphella (Ballantyne) is elevated to generic status from Luciola (Pygatyphella) Ballantyne and redescribed
from 22 species including ten new species Pygat. japenensis sp. n., Pygat. karimui sp. n., Pygat. kiunga sp. n., Pygat.
limbatifusca sp. n., Pygat. nabiria sp. n., Pygat. okapa sp. n., Pygat. russellia sp. n., Pygat. tomba sp. n., Pygat. uberia
sp. n., and Pygat. wisselmerenia sp. n., with uberia representing specimens known in previous analyses as ‘Sisiak’.
Pygat. eliptaminensis (Ballantyne), Pygat. marginata (Ballantyne), Pygat. peculiaris (Olivier) and Pygat. pulcherrima
(Ballantyne) are transferred from Luciola (Pygatyphella) Ballantyne. Pygat. tagensis (Ballantyne), Pygat. hounensis
(Ballantyne), Pygat. obsoleta (Olivier), and Pygat. undulata (Pic) are transferred from Atyphella Olliff; Pygat. obsoleta
is reassessed, geographic varieties are suggested, and the species redescribed from a greatly expanded number of specimens.
Pygat. ignota (Olivier), Pygat. plagiata (Blanchard) and Pygat. salomonis (Olivier) are transferred from Luciola
Laporte and redescribed. Pygat. limbatipennis (Pic) is transferred from Atyphella salomonis var limbatipennis Pic, and
redescribed. Magnalata gen. n. is described for three species, M. rennellia sp. n., M. limbata (Blanchard) transferred
from Luciola, and M. carolinae (Olivier) transferred from Atyphella. Missimia gen. n. is erected for a single species M.
flavida sp. n. based on four specimens dealt with in previous phylogenetic analyses as ‘Mt Missim’. Photuroluciola Pic
is elevated to generic status from Luciola (Photuroluciola) Pic and redescribed from its single species Photuro. deplanata
Pic. Asymmetricata gen. n. is erected for two SE Asian species As. ovalis (Hope) and As. circumdata (Motsch.),
both transferred from Luciola and redescribed. Where available, females are associated and are characterised briefly. A.
testaceolineata, M. limbata, Pygat. huonensis, Pygat. limbatipennis, Pygat. peculiaris, and Pygat. uberia sp. n. are identified
by light patterns. Discussion addresses: the interpretation of female aptery, the extent of the labrum, numbering of
abdominal segments using actual segment number, and use of the term ventrite to reflect visible abdominal sternites.
Functional morphology of many terminal abdomen modifications is addressed as is the range and nature of colour patterns.
Determination of polarity in various states of bipartite light organs is overviewed, as are problems with the homology
of characters, and difficulties in interpretation of characters in soft bodied insects especially those preserved in
ethanol.
... Columbiformes was represented by one species. For extant modern birds, individual species rather than supraspecific terminals were preferred while composite terminals were used for the fossil taxa (Enantiornithes, Ichthyornis and Lithornis) in light of unavoidable issues of missing data (Wilkinson, 1995). ...
A new bird from the Late Cretaceous of Patagonia (Argentina), known from associated wing elements, is described and its phylogenetic position evaluated. Fossil taxa as well as representatives of species of extant birds sampled from lineages considered to be basal within the crown clade were included in a cladistic analysis of 72 characters primarily from the thoracic limb. Based on the results of the phylogenetic analysis and identification of autapomorphies in the specimen, we name a new taxon Limenavis patagonica. Limenavis patagonica is identified as closer to the crown clade than Enantiornithes by the presence of three unambiguous synapomorphies: a fossa (sometimes with two distinguishable subparts) on the dorsal, distalmost extremity of the humerus; distal fusion of metacarpals II and III; and an extensor process on metacarpal I. It is placed closer to the crown clade than Ichthyornis, and, thus, unambiguously as a carinate (see Methods for terminology), by two further synapomorphies: the abruptly truncate contact of the dorsal trochlear surface of the ulna with the ulnar shaft and the loss of a tubercle adjacent to the tendinal groove on the distal ulna. Finally, Limenavis patagonica is diagnosed by three autapomorphies: the attachment of the pars ulnaris of the trochlea humeroulnaris on the proximal ulna developed as a pit-shaped fossa; the location of the pisiform process with its proximal surface at approximately the same level as the proximal surface of metacarpal I; and a scar of the ligamentum collaterale ventrale of the ulna proximodistally elongate and extending down the caudal margin of the brachial impression. Limenavis patagonica is placed just outside the avian crown clade. The shortest tree with the new taxon as part of the crown clade is five steps longer than the most parsimonious topology.
... Each heuristic search employed 1000 replicates of randomtaxon addition with TBR branch swapping. Only clades with at least one unambiguous synapomorphy (i.e., present in both AC-CTRAN and DELTRAN character reconstructions; Wilkinson, 1995) were retained (commands PSET COLLAPSE 5 MIN; FILTER BEST in PAUP*). This option avoids some of the undesirable analytical artifacts of missing data reported by Platnick et al. (1991), and it reduces the number of fundamental trees to a minimal conservative set. 1 Characters were equally weighted in all analyses. ...
In this study I provide a phylogenetic hypothesis for the tribe Oryzomyini that can be used to understand the diversification and evolution of this group of rodents and to revise the current generic-level classification. Morphological and molecular data were used for these purposes in combined and separate analyses. Molecular data consisted of partial sequences (1266 bp) from the first exon of the nuclear gene encoding the interphotoreceptor retinoid binding protein (IRBP); the morphological matrix comprised 99 characters, including 16 integumental characters, 32 skull characters, 29 dental characters, 7 postcranial characters, and 10 characters from the phallus and soft-anatomy systems. I present anatomical descriptions for each character, including delineation of different states observed among oryzomyines. Results of the combined analysis were congruent with the IRBP-only dataset for oryzomyine higher-level relationships. Morphological analyses, although showing discrepancies from the combined or IRBP consensus cladograms and with low nodal support values, recovered several clades similar to the combined and IRBP analyses. Systematics of the tribe and the evolution of a few pivotal characters are discussed in light of the proposed phylogeny. Different taxonomic arrangements for species currently included in the genus Oryzomys are suggested. Finally, I evaluate evolutionary and biogeographic hypotheses that are compatible with our current knowledge on oryzomyine relationships.
... First, those trees supported with ambiguous branches were avoided. Recently, Wilkinson (1995), and Coddington and ScharfF (1 994) have addressed the problem of zero-length branches. Coddington and ScharfF (1994:417) stated: "All monophyletic groups must have synapomorphies; all branches must have support simultaneously." ...
The genus Cidaria Treitschke is revised. Eight species of the genus which occur widely in the Palaearctic and northern India, are recognized, of which one, Cidaria luteata sp. nov., is described as new while two subspecies of C. fulvata (Forster) are elevated to species, C. nugata Felder stat. rev., and C. distinctata Staudinger stat. nov.C. ochripennis Prout is proposed as a junior synonym of C. ochreata Staudinger. C. deletaria Hampson is excluded from the genus. All species of Cidaria and their genitalia are described and illustrated. The cladistic analysis of these eight species of Cidaria is carried out using two data matrices, the first comprising morphological characters alone and the second morphological and distributional characters. The most parsimonious cladogram of Cidaria is selected, and its monophyly defined. The character analysis shows that some distribution characters contribute to resolving the in group node. The choice of multiple trees is discussed.
... Second, the results of the significance test of heterogeneity and comparison of the unreversed synapomorphies in the two data sets indicate that both characters from adult and immatures propose the same phylogeny (Tables 1-3). Third, as pointed out by Wilkinson (1995), a consensus tree will be affected if the consensus tree is based on all most parsimonious trees, including those that contain zero-length branches. The strict consensus tree from the four uncollapsed trees was the same as the consensus tree from all eight trees. ...
A cladistic analysis of forty-one species, belonging to ten genera, of the Cidariini sensu Herbulot from the Holarctic and the Indo-Australian areas, was performed using seventy-seven characters including larval and pupal data. Eight most parsimonious cladograms were found (length 398, CI 0.30, RI 0.70). The monophyly of the Cidariini is demonstrated, using selected species of Xanthorhoini sensu Herbulot as the outgroup. The relationships among the genera are as follows: (Ecliptopera (Eulithis (Cidaria ((Plemyria (Chloroclysta, Dysstroma))((Thera, Pennithera) (Heterothera))))). This result suggests some taxonomic changes: Dysstroma Hübner, stat. rev. and Chloroclysta Hübner stat. rev. are sister taxa;Heterothera Inoue stat. rev. includes Viidaleppia Inoue, syn.n., Heterothera firmata (Hübner) comb.n. is transferred from Pennithera Viidalepp to Heterothera sensu lato. The results of confirmation and incongruence tests suggest that the characters from adult and immature stages exhibit the same evolutionary pattern. Thus the phylogeny derived from the combined data matrix does not give a misleading conclusion, even though there are many missing states in the larval data set.
... If not discarded, such illegitimate topologies help to obscure valid topologies, and bias operations involving sets of trees, such as consensus procedures or successive weighting procedures. Missing data (Platnick et al., 1991) exacerbate the problem of zero-length branches, but zero-length branches can occur even when matrices have no missing entries (Coddington & Scharff, 1995;Wilkinson, 1995). Character optimizations must be carefully checked to ensure that data do in fact support each node on a diagnosed tree. ...
We present the first cladistic analysis focused at the tribal and subfamily level of the orb-weaving spider family Araneidae. The data matrix of 82 characters scored for 57 arancid genera of 6 subfamilies and 19 tribes (and 13 genera from 8 outgroup families) resulted in 16 slightly different, most parsimonious trees. Successive weighting corroborated 62 of the 66 informative nodes on these cladograms; one is recommended as the ‘working’ araneid phylogcny. The sister group of Araneidae is all other Araneoidea. Araneidae comprises two major clades: the subfamily Araneinae, and the ‘argiopoid’ clade, which includes all other subfamilies and most tribes (((Gasteracanthinae, Caerostreae), (((Micratheninae, Xylcthreae), Eruyosaccus), (Eurycorminae, Arciinae)), Cyrlarachninae), ((Argiopinae, Cyrtophorinae), Arachnureae)). Cyrtarachneae and Mastophoreae are united in a new subfamily, Cyr-tarachninae. The spiny orb-weavers alone (Gasteracanthinae and Micratheninae) are not monophyletic. The mimetid subfamily Arciinae and the ‘tetragnathid’ genus Zygiella are araneids, but .Nephila (and other tetragnathids) are not. On the preferred tree, web decorations (stabilimenta) evolved 9 times within 15 genera, and were lost once. The use of silk to subdue prey evolved once in cribellate and four times in ecribillate orb weavers. Sexual size dimorphism evolved once in nephilines, twice in araneids, and reverted to monomorphism five times. Evolution in other genitalic and somatic characters is also assessed; behavioral and spinneret features arc most consistent (male genitalia, leg and prosomal features least consistent) on the phylogeny.
... In the example worked in this paper the data matrix was chosen deliberately as it contains missing values and results in some cladograms with zero-length branches. Both these issues (missing values and zero-length branches) have been discussed recently in the literature (Platnick et al., 1991;Scotland and Williams, 1993;Maddison, 1993;Coddington and Scharff, 1995;Wilkinson, 1995b). We chose to explore Maddison's (1993) example here because we believe that primary homology assessment is directly relevant; those pursuing solutions to the inapplicable data problem need to consider the theoretical basis of primary homology assessment. ...
We discuss contrasting approaches to cladistic character definition and thus to cladistic data matrix compilation. The conventional approach considers character states as alternate forms of the “same thing” (the character). A review of the challenges to this convention is presented, and their implications evaluated. We argue that the recognition of structures which are alternate forms is a vital stage of primary homology assessment and is equivalent to the conceptualization of a transformational homology. Such a view complies with the demand that characters are independent and that character states are hierarchically related. We identify one justifiable solution to the inapplicable data coding problem (coding for organisms which have red tails, blue tails or no tails), and show that alternative approaches to character definition support spurious solutions which deny the relation of structures which are “the same but different”. We propose that the term character can be defined, in a cladistic context, as the descriptive label referring to a transformational homology evidenced by the similarity criterion.
... The computer program TAXEQ3 (Wilkinson 2001) is designed to flag fragmentary taxa in a matrix that have no unique character combinations (their character coding has no conflict with some other, more complete, taxon). These 'redundant taxonomic equivalents' are potential wildcard taxa (see Wilkinson 1995; Kearny 2002; Kearny & Clark 2003) and can thus be 'safely' removed, without sacrificing character information. Here, A. sumisolena is the taxonomic equivalent of A. nigrescens; removing A. sumisolena results in a fully resolved ethicus group, and support for the group and clades within it increases (seeFig. ...
Two species groups of the social spider genus Anelosimus are revised. The ethicus group contains six species found in South America, in an area ranging from the Guianas to southern Brazil and Argentina. Of these, A. rabus Levi, 1963, A. ethicus (Keyserling, 1884), and A. nigrescens (Keyserling, 1884) are redescribed, while A. nigrescens is removed from synonymy with A. ethicus. Three new species are described: A. misiones sp. nov., A. sumisolena sp. nov. and A. inhandava sp. nov. Anelosimus ethicus is reportedly either subsocial or solitary, while the behaviour of the other species in the group is unknown. The rupununi group contains two quasisocial species, A. rupununi Levi, 1956 and A. lorenzo Fowler & Levi, 1979, from the Caribbean and tropical South America. Both are redescribed here. A parsimony analysis of morphological characters provides support for the monophyly of both groups. In the phylogeny, subsociality optimizes to the base of Anelosimus, indicating that the common ancestor of the ethicus group was subsocial. Its members can thus be predicted to be subsocial, or secondarily solitary. Quasisociality arose de novo in the rupununi group, representing one of 6−7 independent origins in theridiids. Study of the biology of Anelosimus is important to advance our understanding of the evolution of sociality in spiders.
We present the first cladistic analysis focused at the tribal and subfamily level of the orb-weaving spider family Araneidae. The data matrix of 82 characters scored for 57 araneid genera of 6 subfamilies and 19 tribes (and 13 genera from 8 outgroup families) resulted in 16 slightly different, most parsimonious trees. Successive weighting corroborated 62 of the 66 informative nodes on these cladograms; one is recommended as the ‘working’ araneid phylogeny. The sister group of Araneidae is all other Araneoidea. Araneidae comprises two major clades: the subfamily Araneinae, and the ‘argiopoid’ clade, which includes all other subfamilies and most tribes (((Gasteracanthinae, Caerostreae), (((Micratheninae, Xylethreae),Encyosaccus), (Eurycorminae, Arciinae)), Cyrtarachninae), ((Argiopinae, Cyrtophorinae), Arachnureae)). Cyrtarachneae and Mastophoreae are united in a new subfamily, Cyrtarachninae. The spiny orb-weavers alone (Gasteracanthinae and Micratheninae) are not monophyletic. The mimetid subfamily Arciinae and the ‘tetragnathid’ genusZygiellaare araneids, butNephila(and other tetragnathids) are not. On the preferred tree, web decorations (stabilimenta) evolved 9 times within 15 genera, and were lost once. The use of silk to subdue prey evolved once in cribellate and four times in ecribillate orb weavers. Sexual size dimorphism evolved once in nephilines, twice in araneids, and reverted to monomorphism five times. Evolution in other genitalic and somatic characters is also assessed; behavioral and spinneret features are most consistent (male genitalia, leg and prosomal features least consistent) on the phylogeny.
The Early Devonian (Lochkovian) sarcopterygian fish Styloichthys has been interpreted as the immediate sister taxon of the clade comprising both the dipnoan and the tetrapod total groups, but support for this placement is weak. Many derived characters of the lower jaw, braincase and dermal skull align Styloichthys with coelacanths and their bearing on the affinities of this genus is set against the evidence in support of earlier interpretations. A revised cladistic analysis places Styloichthys as the most basal coelacanth, which, if correct, fills conspicuous stratigraphic and morphological gaps in the fossil record of this clade. This analysis also raises questions about the phylogenetic placement of onychodonts and the Early Devonian ‘actinopterygians’ Ligulalepis and Dialipina, indicating that these taxa should be the specific targets of future systematic study.
The order Gruiformes, for which even familial composition remains controversial, is perhaps the least well understood avia order from a phylogenetic perspective. The history of the systematics of the order is presented, and the ecological and biogeographi characteristics of its members are summarized. Using cladistic techniques, phylogenetic relationships among fossil and moder genera of the Gruiformes were estimated based on 381 primarily osteological characters; relationships among modern specie of Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae) were assessed based on these characters augmented b 189 characters of the definitive integument. A strict consensus tree for 20,000 shortest trees compiled for the matrix o gruiform genera (length = 967, CI = 0.517) revealed a number of nodes common to the solution set, many of which were robus to bootstrapping and had substantial support (Bremer) indices. Robust nodes included those supporting: a sister relationshi between the Pedionomidae and Turnicidae; monophyly of the Gruiformes exclusive of the Pedionomidae and Turnicidae; a siste relationship between the Cariamidae and Phorusrhacoidea; a sister relationship between a clade comprising Eurypyga and Messelornis and one comprising Rhynochetos and Aptornis; monophyly of the Grues (Psophiidae, Aramidae, Gruidae, Heliornithidae and Rallidae); monophyly of a clade (Gruoidea) comprisin (in order of increasingly close relationship) Psophia, Aramus, Balearica and other Gruidae, with monophyly of each member in this series confirmed; a sister relationship between the Heliornithida and Rallidae; and monophyly of the Rallidae exclusive of Himantornis. Autapomorphic divergence was comparatively high for Pedionomus, Eurypyga, Psophia, Himantornis and Fulica; extreme autapomorphy, much of which is unique for the order, characterized the extinct, flightless Aptornis.
In the species–level analysis of modern Grues, special efforts were made to limit the analytical impacts of homoplasy relate to flightlessness in a number of rallid lineages. A strict consensus tree of 20,000 shortest trees compiled (length = 1232 CI = 0.463) confirmed the interfamilial relationships resolved in the ordinal analysis and established a number of other variably supported groups within the Rallidae. Groupings within the Rallidae included: monophyly of Rallidae exclusive o Himantornis and a clade comprising Porphyrio (including Notornis) and Porphyrula; a poorly resolved, basal group of genera including Gymnocrex, Habroptila, Eulabeornis, Aramides, Canirallus and Mentocrex; an intermediate grade comprising Anurolimnas, Amaurolimnas, and Rougetius; monophyly of two major subdivisions of remaining rallids, one comprising Rallina (paraphyletic), Rallicula, and Sarothrura, and the other comprising the apparently paraphyletic ‘long–billed’ rails (e.g. Pardirallus, Cyanolimnas, Rallus, Gallirallus and Cabalus and a variably resolved clade comprising ‘crakes’ (e.g. Atlantisia, Laterallus and Porzana, waterhens (Amaurornis), moorhens (Gallinula and allied genera) and coots (Fulica). Relationships among ‘crakes’ remain poorly resolved; Laterallus may be paraphyletic, and Porzana is evidently polyphyletic and poses substantial challenges for reconciliation with current taxonomy. Relationships amon the species of waterhens, moorhens and coots, however, were comparatively well resolved, and exhaustive, fine–scale analyse of several genera (Grus, Porphyrio, Aramides, Rallus, Laterallus and Fulica) and species complexes (Porphyrio porphyrio –group,Gallirallus philippensis –group and Fulica americana –group) revealed additional topological likelihoods. Many nodes shared by a majority of the shortest trees under equal weightin were common to all shortest trees found following one or two iterations of successive weighting of characters. Provisiona placements of selected subfossil rallids (e.g. Diaphorapteryx, Aphanapteryx and Capellirallus ) were based on separate heuristic searches using the strict consensus tree for modern rallids as a backbone constraint.
These analyses were considered with respect to assessments of robustness, homoplasy related to flightlessness, challenge and importance of fossils in cladistic analysis, previously published studies and biogeography, and an annotated phylogeneti classification of the Gruiformes is proposed.
The endemic South African spider genus Austrachelas Lawrence, 1938 is revised. The type species, A. incertus Lawrence, 1938, and A. natalensis Lawrence, 1942, are redescribed, and their males described for the first time. Seven new species are described: A. bergi n. sp. (female only), A. kalaharinus n. sp. (male only), A. merwei n. sp. (both sexes), A. pondoensis n. sp. (both sexes), A. reavelli n. sp. (both sexes), A. sexoculata n. sp. (male only), and A. wassenaari n. sp. (both sexes). A cladistic analysis performed including Austrachelas and various species of the corinnid subfamilies Trachelinae, Castianeirinae, Corinninae and Phrurolithinae, and species from the Liocranidae, Gallieniellidae, Gnaphosidae and Lamponidae, suggests that Austrachelas is currently misplaced. Its transfer to the Gallieniellidae is proposed.
The genus PseudocorinnaSimon, 1910 is revised. The type species Pseudocorinna rutilaSimon, 1910 from Guinea-Bissau and Pseudocorinna septemaculeataSimon, 1910 from Bioko are redescribed. No material could be found of Pseudocorinna graciliorSimon, 1910 from Bioko which is to be considered nomen dubium. The genus further contains 27 species which are described as new: Pseudocorinna alligator, Pseudocorinna amicorum, Pseudocorinna amphibia, Pseudocorinna banco, Pseudocorinna bilobata, Pseudocorinna brianeno, Pseudocorinna celisi, Pseudocorinna christae, Pseudocorinna cymarum, Pseudocorinna doutreleponti, Pseudocorinna eruca, Pseudocorinna evertsi, Pseudocorinna febe, Pseudocorinna felix, Pseudocorinna gevaertsi, Pseudocorinna incisa, Pseudocorinna juakalyi, Pseudocorinna lanius, Pseudocorinna lobelia, Pseudocorinna natalis, Pseudocorinna naufraga, Pseudocorinna okupe, Pseudocorinna orientalis, Pseudocorinna perplexa, Pseudocorinna personata, Pseudocorinna ubicki, and Pseudocorinna victoria. The genus is characterized by the wide carapace and sternum and the dense network of dark warts on all sclerites of the prosoma. These structures are apparently outlets of underlying glands producing a gel-like substance. The genus is restricted to the West and Central African forest area, ranging from Guinea-Bissau to the eastern Democratic Republic of Congo. The species are mainly found in very wet, temporarily inundated forests. A cladistic analysis strongly supported the erection of a new, closely related genus, Crinopseudoa gen. nov., with very similar habitus but with poorly developed warts that have kept their original hair-socket function. This genus contains 11 species, all of which are new, and has a distribution restricted to the West-African refuge areas around Liberia and Cameroon. The type species is Crinopseudoa bong from Liberia. It further contains Crinopseudoa billeni, Crinopseudoa bongella, Crinopseudoa caligula, Crinopseudoa catharinae, Crinopseudoa ephialtes, Crinopseudoa flomoi, Crinopseudoa leiothorax, Crinopseudoa otus, Crinopseudoa paucigranulata, and Crinopseudoa titan. Both genera can be regarded as examples of successful somatic templates with a large range of morphologically different genitalia corroborating the ‘mate check’ hypothesis. Illustrated keys to the species of both genera are provided.
© 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162, 271–350.
Evolutionary interpretation of paleontological patterns requires a hypothesis of phylogeny, but our phylogenetic hypotheses may not perfectly mirror organismal phylogeny. Tree summary methods less conservative than strict consensus may increase resolution, but these methods may present a biased summary of the full set of most parsimonious trees. When we fail to acknowledge all equally optimal topologies, we risk disregarding trees that are closer to the correct phylogeny. We discuss a case where two subsets of trees were recovered in the set of most parsimonious trees, each with a profoundly different interpretation of character evolution near the root of Echinodermata. This was caused by the presence of a bimodally labile taxon in the matrix with two different topological subsets, each equally parsimonious but differing in the number of consistent trees. Majority-rule consensus favors the subset with the largest number of trees consistent with the placement of the rogue taxon. This bias favors clusters not because of the biological implications of the tree, but on the basis of great inequality in the sizes of the islands of parsimony. We thus recommend that majority-rule consensus trees not be used to summarize the results of a phylogenetic analysis.
This study presents a new phylogeny of erigonine spiders with emphasis on genera from the Neotropics. Thirty-nine exemplar taxa representing mostly Neotropical genera were added to a global sample of 31 erigonine and 12 outgroup exemplar taxa analyzed in a previous study. These 82 taxa were coded for 176 (172 informative) mostly morphological characters. Eighty-one characters were identical to or modified from the 73 (67 informative) characters included in a previous study; the remaining 95 characters are new. The complete data set includes 70 erigonine exemplars representing 65 genera, seven nonerigonine linyphiid exemplars, and five exemplars representing four araneoid families in the outgroup. Cladistic analysis resulted in a single most parsimonious tree (L =904, CI = 0.23, RI = 0.58; uninformative characters excluded: L = 900, CI = 0.23). This paper explores the implications of the new topology for the evolution of several characters of interest in erigonine evolution. The phylogeny implies that the desmitracheate condition is a synapomorphy of erigonines, with a reversal to the haplotracheate condition in one large clade within Erigoninae. We infer that the loss of the paracymbium in Neotropical erigonines occurred twice and may have progressed by different evolutionary pathways. Our phylogeny differs markedly from the previous cladistic hypothesis of erigonine relationships. We investigate how the addition of characters and taxa (alone and together) have altered the earlier hypothesis of erigonine phylogeny. We conclude that topological changes from the previous study to the current one are largely the result of adding and modifying characters, not adding taxa. Continuous Jackknife Function (CJF) analysis predicts that the inclusion of additional character data will continue to imply changes in the relationships among taxa in our analysis.
We review the widespread notion that the inclusion of taxa scored for relatively few characters is problematic in phylogenetic analyses. Taxa scored for few characters may lead to lack of resolution, but need not. Lack of resolution may be unrelated to missing data when characters conflict. Missing data cannot produce groupings for which there is no evidence. A common approach to avoid the “missing data problem” is to exclude incomplete taxa, but excluding such taxa is inadvisable because the information content of taxa is not necessarily correlated with degree of completeness. Another prevalent strategy—excluding characters with a high proportion of missing data—may actually contribute to the low resolution problem rather than ameliorate it because removing any character data removes potentially informative synapomorphies. Other approaches, including the use of less-than-strict consensus techniques, have the potential to obscure evidence for alternative relationships or, at best, provide incomplete summaries of the primary trees. Missing data simply represent the unknown and should not be viewed as an impediment to considering all available evidence in phylogenetic analyses, nor used as justification for excluding specific taxa or characters.
Cladistic phylogenies of the archosaur ingroup are reviewed in light of recent concerns regarding an over-dependence on characters relating to tarsal and pedal morphology. The use of simple statistical techniques shows that the exclusion of ankle characters from recent cladistic phylogenies has no significant effect on the relative support of relationships proposed. Contrary to current opinion, ankle characters should be considered unimportant when attempting to reconstruct the broad shape of archosaur phylogeny.
The diatom genus Tetracyclus Ralfs (Bacillariophyta) is composed largely of extinct, freshwater species many of which have been used as stratigraphic markers across several continents under the assumption that they are relatively widespread and confined to precise geological epochs. Until recently the taxonomy of the genus relied almost exclusively on the shape and dimensions of the preserved siliceous valves. This study forms part of a revision of the entire genus. In this paper the morphology of fossils from the `ellipticus' species group is discussed. Significant to this study is the relative usefulness of diatom valve dimensions and overall shape, seen here in the context of siliceous morphogenesis and the appearance of particular valve `shapes' at particular stages in their life cycles. In addition, alternative ways of representing character data have been applied to establish whether the `ellipticus' species group is monophyletic with respect to the genus. Results suggest that the `ellipticus' species group is not monophyletic and that the elliptical shape of valves is better viewed as a variable property of ontogeny.
The reduced cladistic consensus method offers a means of avoiding the lack of resolution frequently observed when large numbers of equally parsimonious trees are summarized in a strict component consensus tree. It does so by identifying relationships (in the form of n‐taxon statements) that are unambiguously supported by the parsimonious interpretation of the data. We apply the method to qualitative morphological character data for 70 genera from the clade containing the cassiduloid echinoids. A sample of 31,000 most parsimonious trees contains 21 basic reduced cladistic consensus trees. As these cannot be combined into any single highly resolved consensus for the majority of the taxa, the multiple most parsimonious trees do not differ solely in the placement of a small number of taxa. The homoplasy present in the morphological data prevents the determination of a robust cassiduloid phylogeny.
Hortipes Bosselaers and Ledoux (type species Hortipes luytenae Bosselaers and Ledoux from South Africa) is a genus of small (1.5–4 mm), pale, mainly soil-dwelling spiders from sub-Saharan Africa. The genus, which is tentatively placed in the Liocranidae, is characterized by the presence of a peculiar ellipsoidal array of setae on the dorsal side of metatarsi I and II and by the large anterior median eyes with a dark retina restricted to the median portion. Ledoux and Emerit (1998) described five more species from Ivory Coast and Gabon. Sixty-three additional Hortipes species are described here as new: H. platnicki (♀), H. castor (♂♀), H. pollux (♂♀), H. fastigiensis (♂♀), H. ostiovolutus (♂♀), H. salticola (♂♀), H. exoptans (♂♀), H. scharffi (♂♀), H. cucurbita (♂♀), H. hesperoecius (♀), H. klumpkeae (♀), H. aurora (♂♀), H. echo (♀), H. stoltzei (♂), H. creber (♂♀), H. orchatocnemis (♂♀), H. contubernalis (♂♀), H. mesembrinus (♀), H. coccinatus (♂♀), H. wimmertensi (♂♀), H. irimus (♀), H. licnophorus (♀), H. schoemanae (♂♀), H. aelurisiepae (♀), H. hyakutake (♂), H. rothorum (♂), H. griswoldi (♂), H. oronesiotes (♂♀), H. penthesileia (♀),H. zombaensis (♂♀), H. atalante ♀), H. merwei (♂♀), H. leno (♂♀), H. mulciber (♀), H. libidinosus (♂♀), H. delphinus (♂♀), H. bjorni (♂), H. amphibolus (♀), H. hastatus (♂♀), H. horta (♀), H. angariopsis (♀), H. falcatus (♂♀), H. lejeunei (♂♀), H. narcissus (♂♀), H. auriga (♂), H. puylaerti (♀), H. chrysothemis (♀), H. machaeropolion (♂♀), H. centralis (♀), H. tarachodes (♂♀), H. terminator (♂), H. baerti (♂), H. robertus (♂♀), H. abucoletus ♀, H. alderweireldti (♂), H. architelones (♂♀), H. calliblepharus (♂), H. fortipes (♂), H. bosmansi (♂♀), H. sceptrum (♂♀), H. anansiodatus ♀, H. hormigricola (♂♀), and H. depravator (♂). The genus has a vast Afrotropical distribution, occurring from as far south as East London in South Africa to Sierra Leone in western Africa. So far, no specimens are available from northeastern tropical Africa. Apart from H. merwei, which seems to prefer grassland, all species are found in leaf litter or the canopy of different kinds of forests and dense thickets. In captivity, H. contubernalis readily fed on Collembola. Specimens raised from cocoons obtained in the laboratory reached adulthood after three molts. A cladistic analysis of the 34 species for which both sexes are known, largely based on secondary genitalic characters, is proposed.
This paper studies the phylogeny of the spider families Liocranidae and Corinnidae as they have been delimited to date, using an exemplar approach. In the analysis, 40 species belonging to 24 liocranid and 14 corinnid genera are scored for 157 morphological characters. The genera Clubiona (Clubionidae) and Gnaphosa (Gnaphosidae) are used as outgroups. Under implied weighting, a single fittest tree is found. This hypothesis seriously challenges the presently prevailing classification of the former Clubionidae sensu lato. The subfamily Phrurolithinae (Liocranidae) turns out to be the sister group of Trachelinae and is transferred to Corinnidae. In the interest of taxonomic stability, no radical rearrangement of the families constituting Clubionidae sensu lato is proposed, as it is felt that the present results should first be further corroborated by additional, more elaborate analyses on an even larger data set.
Jan Bosselaers, ‘Dochterland’, R. novarumlaan 2, B-2340 Beerse, Belgium. E-mail: hortipes@dochterland.org
Rudy Jocqué, Musée Royal de l’Afrique Centrale, B-3080 Tervuren, Belgium. E-mail: jocque@africamuseum.be
This study presents a general cladistic analysis of pisaurid genera, with emphasis on the Neotropical genera Architis Simon and Staberius Simon. The analysis was based on a matrix with 21 terminal taxa: eight species of Architis, Staberius spinipes (Taczanowski), seven exemplars of other pisaurid genera and five outgroup taxa. These terminals were scored for 59 morphological and three behavioural characters. An analysis with all characters equally weighted resulted in two most parsimonious trees, differing only in the position of Architis colombo Santos. In both trees Pisauridae arouse as a monophyletic group, and the exemplars of Architis composed a clade with S. spinipes. Contrary to hypotheses from the literature, Thalassius Simon emerged as sister-group of all remaining pisaurids, not as a close relative of Dolomedes Latreille. The genera Tinus F.O.P. -Cambridge and Thaumasia Perty appeared in the trees as the closest relatives of Architis and Staberius Simon. The analysis strongly supported S. spinipes as the sister-group of A. helveola (Simon), indicating that Architis as currently delimited is paraphyletic. Based on these results, Staberius is considered a subjective junior synonym of Architis. Additionally, the genus Mimicosa Petrunkevitch, originally described in Tetragnathidae, is transferred to Pisauridae and considered a junior synonym of Architis. Two species are proposed as junior synonyms of A. spinipes comb.n. Mimicosa spinosa Petrunkevitch and Staberius lemoulti Caporiacco.
It has been proposed in recent years that the phyla Pogonophora and Vestimentifera are a derived clade of polychaete annelids. It has also been proposed that if this clade belongs among polychaetes, then the taxon name Pogonophora is misleading and should revert to a name first formulated for the group, Siboglinidae Caullery, 1914. This recommendation is adopted in this paper, and a cladistic study using terminals of ‘generic’ rank in the former Pogonophora (including Vestimentifera) is undertaken. The purpose of this is to assess which taxon names should now be used for clades within Siboglinidae, and to provide a revised taxonomy, based on phylogenetic principles. Another major aim is to assess the position of the vestimentiferan clade within Siboglinidae. The results show that Vestimentifera is the sister group to Sclerolinum, and this clade is then sister group to Frenulata, i.e. the remaining Siboglinidae. The results suggest that all taxa within Siboglinidae that are not genera or species are redundant, except for the following: Siboglinidae is defined as the first polychaete, and all its descendants, to have an gut occluded by expanded endoderm filled with chemoautotrophic bacteria, as seen in the holotype of Riftia pachyptila Jones, 1981. Monilifera can be defined based on apomorphy-based system such that it is the first siboglinid, and all its descendants, to have rings of chaetae (uncini) in the opisthosoma, as seen in the holotype of Sclerolinum magdalenae Southward, 1972. Vestimentifera can be denned as the first siboglinid and all its descendants to have a vestimentum as seen in the holotype of Riftia pachyptia. Frenulata is defined as the siboglinid, and all its descendants, to have a mid-trunk girdle, as seen in the holotype of Siboglinum weberi Caullery, 1914. The taxa of generic rank are not defined here since their monophyly was not investigated.
We report on and name two new taxa of basal crocodylomorph archosaurs from the Lower Jurassic, Litargosuchus leptorhynchus gen. et sp. nov., from the upper Elliot Formation (Stormberg Group) of South Africa, and Kayentasuchus walkeri gen. et sp. nov., from the Kayenta Formation (Glen Canyon Group) of Arizona, USA. Examination of this material led to a reconsideration of basal crocodylomorph interrelationships. A phylogenetic analysis found no support for the monophyly of Sphenosuchia. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society, 2002, 136, 77–95.
SYNOPSIS Ornithischia is a familiar and diverse clade of dinosaurs whose global phylogeny has remained largely unaltered since early cladistic analyses in the mid 1980s. Current understanding of ornithischian evolution is hampered by a paucity of explicitly numerical phylogenetic analyses that consider the entire clade. As a result, it is difficult to assess the robustness of current phylogenetic hypotheses for Ornithischia and the effect that the addition of new taxa or characters is likely to have on the overall topology of the clade. The new phylogenetic analysis presented here incorporates a range of new basal taxa and charac-ters in an attempt to rigorously test global ornithischian phylogeny. Parsimony analysis is carried out with 46 taxa and 221 characters. Although the strict component consensus tree shows poor resolution in a number of areas, application of reduced consensus methods provides a well-resolved picture of ornithischian interrelationships. Surprisingly, Heterodontosauridae is placed as the most basal group of all well-known ornithischians, phylogenetically distant from a stem-defined Ornithopoda, creating a topology that is more congruent with the known ornithischian stratigraphical record. There is no evidence for a monophyletic 'Fabrosauridae', and Lesothosaurus (the best-known 'fabrosaur') occupies an unusual position as the most basal member of Thyreophora. Other relationships within Thyreophora remain largely stable. The primitive thyreophoran Scelidosaurus is the sister taxon of Eurypoda (stegosaurs and ankylosaurs), rather than a basal ankylosaur as implied by some previous studies. The taxonomic content of Ornithopoda differs significantly from previous analyses and basal relationships within the clade are weakly supported, requiring further investigation. 'Hypsilopho-dontidae' is paraphyletic, with some taxa (Agilisaurus, Hexinlusaurus, Othnielia) placed outside of Ornithopoda as non-cerapodans. Ceratopsia and Pachycephalosauria are monophyletic and are united as Marginocephalia; however, the stability of these clades is reduced by a number of poorly preserved basal taxa. This analysis reaffirms much of the currently accepted ornithischian topology. Nevertheless, in-stability in the position and content of several clades (notably Heterodontosauridae and Ornithopoda) indicates that considerable future work on ornithischian phylogeny is required and causes problems for several current phylogenetic definitions.
A phylogenetic analysis of 123 morphological characters of basal waterfowl (Aves: Anseriformes) and other selected avian orders confirmed that the screamers (Anhimae: Anhitn-idae) are the sister-group of other waterfowl (Anseres), and that the magpie goose (Anseranatidae: Anseranas semipalmata) is the sister group of other modern waterfowl exclusive of screamers (Anatidae sensu stricto). The analysis also supports the traditional hypothesis of the gallinaceous birds (Galliformes) as the sister group of the Anseriformes. Presbyornis, a fossil from the early Eocene of Wyoming and averred by Olson & Feduccia as showing that the Anseriformes were derived from shorebirds (Charadriiformes), was found to represent the sister group of the Anatidae. Associated hypotheses by Olson & Feduccia concerning the implications of Presbyornis for the phylogenetic relationships of flamingos (Phoenicopteriformes), the position of the Anhimidae within the waterfowl, relationships among modern Anatidae, and a plausible evolutionary scenario for waterfowl also are rejected. Analyses revealed that cranial characters were critical to the establishment of the Galliformes as the sister group of the Anseriformes; exclusion of the Anhimidae, especially in combination with Anseranas, also undermined the support for this inference. Placement of Presbyornis as the sister group of the Anatidae casts doubt on the role suggested by Feduccia of ‘transitional shorebirds' in the origin of modern avian orders, and calls into question the concept of ‘fossil mosaics’. The phylogenetic hypothesis is used to reconstruct an evolutionary scenario for selected ecomorphological characters in the galliform-anseriform transition, to predict the most parsimonious states of these characters for Presbyornis, and to propose a phylogenetic classification of the higher-order taxa of waterfowl. This re-examination of Presbyornis also is used to exemplify the fundamental methodological shortcomings of the intuitive approach to the reconstruction of phylogenetic relationships.
Abstract — Consensus in cladistics is reviewed. Consensus trees, which summarize the agreement in grouping among a set of cladograms, are distinguished from compromise trees, which may contain groups that do not appear in all the cladograms being compared. Only a strict or Nelson tree is an actual consensus. This distinction has implications for the concept of support for cladograms: only those branches supported under all possible optimizations are unambiguously supported. We refer to such cladograms as strictly supported, in contrast to the semistrictly (ambiguously) supported cladograms output by various current microcomputer programs for cladistic analysis. Such semistrictly supported cladograms may be collapsed, however, by a variety of options in various programs. Consideration of collapsibility and optimization on multifurcations leads to some conclusions on the use of consensus. Consensus tree length provides information about character conflict that occurs between, not within, cladograms. We propose the clade concordance index, which employs the consensus tree length to measure inter-cladogram character conflict for all characters among a set of cladograms.
Most recently Lorenzen and Sieg (1991) claimed massive critique on computer parsimony programs. It is shown that PA UP version 3.0 overcomes the stated problems of PAUP version 2.4 in recognizing polytomies in original trees. Additional potential solutions of the given matrix are considered as correct trees. Parsimony programs offer potential solutions which should be further analyzed under evolutionary considerations. However, principal problems of parsimony programs occur in all cases of horizontal gene transfer respectively reticulate genealogy, it may be caused by bacterial conjugation, endo- or ectocytobiosis, gene transfer by vectors, or in the case of hybrid genesis. Kürzlich wurde von Lorenzen und Sieg (1991) massive Kritik an den zur Verfügung stehenden Computerprogrammen auf Parsimony-Basis geäußert. Es wird dargelegt, daß die neue Version (3.0) von PAUP die angesprochenen Probleme von PAUP 2.4 überwindet, indem Polytomien in den Kladogrammen erkannt und geduldet werden. Zusätzliche potentielle Lösungen des Problems werden als echte Lösungsmöglichkeiten angesehen, Parsimony-Programme offerieren potentielle Lösungen, die unter evolutionären Gesichtspunkten analysiert werden sollten. Grundsätzliche Probleme mit Parsimony-Programmen treten jedoch in allen Fällen von horizontalen Gentransfers beziehungsweise beim Vorliegen netzartiger Genealogien auf, wie sie etwa durch bakterielle Konjugation, Endo- oder Ektozytobiose, Gentransfer durch Vektoren, oder durch Hybridgenese hervorgerufen werden.
The basic assumptions underlying the computer parsimony programs PHYLIP, PAUP and HENNIG 86 include that of zero value branches (handled as zero value assumptions) and, in PHYLIP, that of strict dichotomy within a diagram of relationships. As both assumptions are not needed in phylogenetic systematics, the principle of parsimony requires discarding them. It is argued that, in phylogenetic systematics, each hypothesis of relationships must cover two essential aspects, that of branching order and that of character interpretations. The homology index is introduced which may facilitate a selection among equally parsimonious hypotheses of relationships. Proposal for improving the computer parsimony programs are made. Zu den Grundannahmen der Computer-Sparsamkeitsprogramme PHYLIP, PAUP und HENNIG 86 gehören die der unbegründeten Verzweigungen (als Nullwertannahmen behandelt) und – bei PHYLIP – die der strikten Dichotomie innerhalb eines Verwandtschaftsdiagrammes. In der phylogenetischen Systematik sind beide Annahmen überflüssig und müssen daher gemäß dem Prinzip der Sparsamkeit gestrichen werden. Es wird begründet, daß in jeder Verwandtschaftshypothese der phylogenetischen Systematik sowohl das Verzweigungsmuster als auch die Beurteilung der Merkmale unverzichtbare Bestandteile sind. Es wird der Homologie-Index eingeführt, der die Auswahl zwischen gleichermaßen sparsamen Verwandtschaftshypothesen erreichtern kann. Vorschläge zur Verbesserung der genannten Computer-Sparsamkeitsprogramme werden unterbreitet.
Lorenzen and Sieg (1991) claimed that the computer parsimony programs PHYLIP, PAUP and HENNIG86 failed in finding all most parsimonious trees and produced erroneous solutions when applied to a simple character data matrix. We maintain that the three programs do find all the shortest trees and that the alleged deficiencies in them are due to Lorenzen and Sieg's unfamiliarity with these programs and the interpretation of the results. Lorenzen und Sieg (1961) behaupten, daß die Computerparsimony-Programme PHYLIP, PAUP und HENNIG86 bei der Ermittlung der sparsamsten Stammbaumzweige versagen und zu irrigen Lösungen führen, wenn sie bei einer simple character data matrix Anwendung finden. Wir behaupten, daß die drei Programme zu den kürzesten Zweigen führen und daß die angebliche Unzulänglichkeit auf der Unvertrautheit von Lorenzen und Sieg mit diesen Programmen und der Interpretation der Ergebnisse beruht.
Recently Lorenzen and Sieg (1991) criticized cladistic computer programs as unreliable because they fail to find “all most parsimonious trees of relationships” and they find “wrong” ones. These authors suggest criteria which a “perfect parsimony program” should meet. Their analysis is flawed because of their: 1. peculiar definition of parsimony and relationship, 2. use of an outdated version of PAUP, and 3. misinterpretation of the programs' output. It is shown that PAUP and HENNIG86 by and large meet their criteria and find all most parsimonious cladograms for the hypothetical data set used by Lorenzen and Sieg. In einer kürzlich publizierten Arbeit charakterisieren Lorenzen und Sieg kladistische Computer-Programme als nicht zuverlässig, weil sie nicht nur nicht alle sparsamsten Stammbäume finden, sondern zudem auch falsche Stammbäume produzieren. Lorenzen und Sieg schlagen Kriterien vor, die von “perfekten kladistischen Programmen” erfüllt werden sollen. Ihre Kritik ist verfehlt, weil sie letztlich das Resultat einer 1. ungebräuchlichen Definition vom Sparsamkeitsprinzip und Verwandtschaftsdiagramm ist, 2. in ihrer Studie eine veraltete Version von PAUP benutzt haben und 3. die Ergebnisdateien der Programme falsch ausgewertet haben. Es wird gezeigt, daß PAUP und HENNIG 86 die von Lorenzen und Sieg aufgestellten Kriterien weitestgehend erfüllen und alle sparsamsten Stammbäume für den hypothetischen Datensatz finden, den Lorenzen und Sieg in ihrer Arbeit verwendeten.