Overlap Indices: Tools to quantify the amount of anatomical overlap among groups of incomplete terminal taxa in phylogenetic analyses

Phylogenetic analyses of morphological data are often characterized by missing data due to incomplete operational taxonomic units, as in fossils. This incomplete knowledge derives from various reasons, including—in the case of fossils—the numerous filters an organism has to pass through during taphonomy, fossilization, weathering and collecting. Whereas several methods have been proposed to address issues raised by the inclusion of incomplete terminal taxa, until recently no tool existed to easily quantify the amount of anatomical overlap within a particular clade. The Overlap Indices provide such values and might prove useful for comparative cladistics. We herein describe these new indices and their applications in detail and provide an example file for their calculation. A case study of diplodocid sauropod dinosaurs shows how the Overlap Indices will help to explore and quantify, which one of a number of conflicting tree topologies is supported by more anatomical traits, which skeletal regions are underrepresented in a particular phylogenetic matrix, and which taxon would improve character state score completeness.     

小腹茧蜂亚科的雄外生殖器及族级单元系统发育的研究

对分布在东洋区和古北区的小腹茧蜂亚科 (膜翅目: 茧蜂科)21个属的67个种及外群折脉茧蜂属 (膜翅目: 茧蜂科) 2个种的雄外生殖器的5个性状进行了比较研究。在形态学研究的基础上,通过选用头部、胸部和腹部(包括雌雄外生殖器的性状) 等34个性状,运用支序分析的方法探讨了分布在东洋区和古北区的小腹茧蜂亚科21个属以及它们所属的族间的系统发育关系,并对Mason (1981) 的分类系统进行了重新评价。雄外生殖器和支序分析基本上证实并恢复了由Mason (1981) 确定的2个主要分支,即绒茧蜂族Apantelini+小腹茧蜂族Microgastrini和拱茧蜂族Fornicini+盘绒茧蜂族Cotesiini+侧沟茧蜂族MicroplitinI。绒茧蜂族Apantelini、拱茧蜂族Fornicini和侧沟茧蜂族Microplitini为单系群也被支持,但小腹茧蜂族Microgastrini和盘绒茧蜂族Cotesiini是否为单系群尚难于在树形图中体现,而且族内各属间的分支关系有变动。因此,尽管Mason的族级分类单元有一些欠缺,但仍是可信、实用的,不同意Walker等 (1990) 认为不应再使用Mason分族系统的观点。     

A new subfamily of Trichomycteridae (Teleostei, Siluriformes), lower loricarioid relationships and a discussion on the impact of additional taxa for phylogenetic analysis

The Copionodontinae is described as a new subfamily of the neotropical catfish family Trichomycteridae. It comprises two new genera and three new species from north-eastern Brazil: Copionodon gen. nov. (including C. pecten sp. nov. and C. orthiocarinatus sp. nov. ) and Glaphyropoma gen nov. (including G. rodriguesi sp. nov. ) The Copionodontinae can be diagnosed externally by the anterior position of the dorsal fin, the presence of a well-developed adipose fin, and the strongly spatulate shape of the jaw teeth. The subfamily is hypothesized as monophyletic on the basis of several synapomorphies in internal and external anatomy. Copionodontines have the plesiomorphic condition of several characters, relative to all other trichomycterids, including the presence of ductus pneumaticus; the possession of separate pterosphenoids, sphenotics and prootics; the presence of the intercalarium; the complete infraorbital latero-sensory canal; the presence of the interhyal; and the wide lateral opening of the swimbladder capsule. Elsewhere within trichomycterids, these primitive traits are found only in Trichogenes. These and other characters support the hypothesis that copionodontines are the plesiomorphic sister group of all other trichomycterids, and that Trichogenes is their next successive sister group. Contrary to the currently accepted hypothesis, the monotypic Nematogenyidae is proposed as the sister group of the Trichomycteridae, and not of all remaining loricarioids. This change is to a major extent induced by the inclusion of copionodontines and Trichogenes in the analysis of lower loricarioid relationships. The present case is given as an example of the impact that undiscovered taxa, fossil or Recent, may have upon hypotheses of phylogenetic relationships.     

European cave shrimp species (Decapoda: Caridea: Atyidae), redefined after a phylogenetic study; redefinition of some taxa,a new genus and four new Troglocaris species

Endemic atyids of southern Europe have been ascribed to Dugastella, and to subterranean Typhlatya and Troglocaris: Dugastella is epigean, and Typhlatya and Troglocaris are subterranean. An extensive collection from all centres of distribution in southern Europe (excepting the Caucasus) was morphologically examined. A taxonomic redefinition of the group, at different levels, is based on recently published and newly generated molecular phylogeny, whereas newly established taxa have also been morphologically defined. The accordance between the phylogenetic tree and the geographical distributions suggested that a re‐evaluation of some traditionally used morphological characters should generate the most parsimonious solution: this enabled a novel taxonomic division. Gallocaris gen. nov. is erected for the French Troglocaris inermis Fage, 1937, which is more closely related to the epigean Dugastella valentina (Ferrer Galdiano, 1924) than to its supposed congeners. Both western Mediterranean Typhlatya species are closely related to their Caribbean congeners. All other European cave shrimps constitute a monophylum, Troglocaris, which is divisible into subgenera (already with available names): the holo‐Dinaric Troglocaris (Troglocaris) Dormitzer, 1853, south‐eastern mero‐Dinaric Troglocaris (Troglocaridella) Babi?, 1922, and Troglocaris (Spelaeocaris) Matja?i?, 1956, and the Caucasian Troglocaris (Xiphocaridinella) Sadovsky, 1930. Four new species are described: Troglocaris (Troglocaris) bosnica sp. nov. , Troglocaris (Spelaeocaris) prasence sp. nov. , Troglocaris (Spelaeocaris) kapelana sp. nov. , and Troglocaris (Spelaeocaris) neglecta sp. nov. The distribution of all established species is shown, and the value of the morphological characters is discussed. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 786–818.     

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

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

Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

Large-scale phylogenetic analyses reveal fagalean diversification promoted by the interplay of diaspores and environments in the Paleogene

The order Fagales (ca. 1325 species, 32 genera) is one of the most important orders of woody angiosperms in both tropical and temperate forests. Fagalean plants have diverse diaspores and dispersal modes, and have abundant macrofossil records. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of Fagales to date based on five plastid loci. We reconstructed the phylogenetic relationships within Fagales using parsimony, likelihood and Bayesian approaches. We inferred the evolutionary shifts of diaspore types, dispersal modes, habitats, and pollination syndromes, and estimated divergence times and rates of diversification. Fossil fruit records of Fagales were also reviewed. Our results suggest that fagalean families are all monophyletic and 29 of the 32 genera are monophyletic. The majority of inter-familial and inter-generic relationships were well resolved. Our evolutionary reconstructions indicate that winged diaspore is synapomorphic, and animal dispersal system is symplesiomorphic in Fagales. Within the order, the families diverged in the mid-Cretaceous but mainly diversified after the Cretaceous–Paleogene (K–Pg) boundary. The overwhelming majority of winged and wingless fruited genera diverged or diversified during the Paleogene, reflecting adaptation to wind and animal dispersals, respectively. Correlated evolution analyses strongly supported the correlated transitions between dispersal mode and habitat. The winged fruited groups often inhabit open habitats and are commonly dispersed abiotically, whereas the wingless fruits usually inhabit closed habitats and have a vertebrate-dispersal mode. Environmental changes triggered increased diversification of Fagales in the Paleogene together with evolution of diaspores and dispersal modes. Additionally, our paleobotanically calibrated time-scale for Fagales may be useful for ecological and physiological studies.     

Phylogeny reconstruction in the neogene bryozoan metrarabdotos: A paleontologic evaluation of methodology

An adequate stratigraphic record can not only aid in both cladistic and stratophenetic reconstruction of phytogenies, but can also serve in estimating the temporal consistency of the resulting phylogenetic trees. For hypothetical data sets, cladistically constructed trees can be as consistent with the temporal distribution of sampled populations or species as those constructed stratophenetically. Empirical testing in taxonomic groups with sufficiently dense fossil records is needed to show whether, and under what conditions, this potential can be realized. A stratophenetic tree and cladistic trees based on several approaches to character weighting were constructed for Caribbean Neogene species of the bryozoan Metrarabdotos with multiple‐character data from closely spaced sequential populations. The modular morphology and highly punctuated evolutionary pattern of these species blur the distinction between continuous and discrete characters, so that all available characters are potentially of equal significance in establishing phytogenies, rather than just those with discrete states conventionally used in cladistic analysis. However, only the cladistic trees generated with all characters weighted to emphasize contribution to species discrimination have temporal consistencies that are clearly significant statistically and approach that of the stratophenetic tree in magnitude. These results provide a start toward establishing general guidelines for cladistic analysis of taxa with stratigraphie records too sparse for stratophenetic reconstruction.     

The status and phylogenetic relationships of “Zanclodon”arenaceus: the earliest known phytosaur?

“Zanclodon”arenaceus has been suggested to represent the oldest reliably dated phytosaur. The type and only specimen, a mandibular fragment of an archosaur from the Schilfsandstein (Carnian; Late Triassic) of Southwest Germany, is described in detail for the first time. “Z.”arenaceus is characterized by a great elongation of the mandible and symphysis, and labiolingually flattened, serrated teeth, a combination that is so far unique among Triassic archosaurs. The previous assignment to the enigmatic reptilian genusZanclodon is unsubstantiated. “Z.”arenaceus shares with Phytosauria both these mandibular characters, but differs in numerous other characters, including most of the autapomorphic mandibular and dental features of Phytosauria. Thus, “Z.”arenaceus is not a phytosaur as currently defined. A cladistic analysis identified “Z.”arenaceus as the sister-taxon of Phytosauria, but because of the limited data available and numerous homoplasies that occur among mandibular characters of archosaurs a closer relationship with other archosaur taxa is a reasonable alternative. It seems unjustified to redefine Phytosauria, or to propose a more inclusive taxon to include “Z.”arenaceus, and therefore the species is assessed as Archosauriaincertae sedis.     

Polygyrid relations: a phylogenetic analysis of 17 subfamilies of land snails (Mollusca: Gastropoda: Stylommatophora)

The family of polygyrid land snails in North America is significant for its sympatric shell convergences, diversity of mating systems and complex zoogeography; its monophyly and its relation to other families has long been questionable. Cladistic analysis has been performed on one representative each of 17 subfamilies, including all three polygyrid subfamilies and one or more subfamilies each from all ten of the families that have been proposed as the polygyrid sister groups. Eighteen anatomical synapomorphies are used, of which eight are newly discovered, four are differently assessed from previous studies, and six are traditional. The resulting strict consensus tree of alternative maximum-parsimony cladograms is: (Acavidae (Ammonitellidae Corillidae ((Discidae Oreohelicidae) (Helminthoglyptidae Bradybaenidae Polygyridae (Thysanophoridae (Camaenidae Sagdidae)))))).
According to this working hypothesis, the Polygyridae are monophyletic, and their sister group remains unresolved, although the Acavidae, Ammonitellidae, Corillidae, Discidae and Oreohelicidae can be ruled out. Of the five classifications of stylommatophoran families that have been proposed in the past 12 years, the consensus tree is closest to that of Nordsieck. For future morphological work, three regions are recommended as potentially rich in unused phylogenetic information: the fertilization pouch-seminal receptacle complex, the ureter at the pneumostome and the ventral-chain ganglia. Simultaneous dissection, wkh side-by-side comparisons, is recommended over other methods for detecting homologies in land snails. Molecular characters should be exploited, because of the scarcity and the frequent homoplasy of morphological characters.     

A phylogenetic revision of the true bug genus Heraeus (Hemiptera: Rhyparochromidae: Myodochini), with the description of two new genera and 30 new species

Prior to this study, the genus Heraeus Stål, 1862 included 14 species, all of which are restricted to the Western Hemisphere. Three species are known from the Nearctic Region, nine from the Neotropical Region, and two mainly tropical elements are distributed in both regions. In this contribution, we consider Heraeus cincticornis Stål, 1874 a junior synonym of Heraeus elegans (Walker, 1873), select a lectotype for Heraeus coquilletti Barber, 1914, and neotype for Lygaeus triguttatus Guérin‐Méneville, 1857, and describe 28 new species. In addition, the two new genera, Baranowskiobius gen. nov., to include H. elegans (Baranowskiobius elegans comb. nov.) and two new species, and Paraheraeus gen. nov., to include Heraeus eximius Distant, 1882 (Paraheraeus eximius comb. nov.), are described. Previously described species and new taxa are (re)described and illustrated, including male genitalia. Scanning electron micrographs, general habitus photographs, and distribution maps are included for all species studied. A phylogenetic analysis comprising 46 terminal taxa and 50 morphological characters was performed, and five species groups were hypothesized, including the coquilletti, caliginosus, guttatus, illitus, and plebejus groups. All known species of Heraeus and the new genera are included in the phylogenetic analysis. The type species of the genera Myodocha Latreille, 1807, Orthaea Dallas, 1852, and Paisana Dellapé, 2008 are used as out‐groups.     

Exploratory phylogenetic and biogeographic analyses within three land-snail families in southeastern-most Madagascar

For Madagascan vicariance biogeography and phylogeny‐based conservation, four land snail groups have been predicted as most readily informative: Acavidae, Boucardicus (Cyclophoridae), Reticulapex (Charopidae), and Streptaxidae. Acavids have been evaluated in a previous paper; this paper uses recently described taxa from three mountains in southeastern Madagascar to evaluate the other three groups, based on shell and reproductive characters. Phylogenetic analyses, using appropriate outgroups, were performed on all 17 Boucardicus (31 characters, 120 states), all nine Reticulapex (21 characters, 53 states), and all 15 streptaxids (19 characters, 68 states) known from the three mountains. The Boucardicus cladogram was marginally robust; it supported monophyly of the genus, and it implied evolutionary trends toward larger, more colour‐patterned, more globose shells hatched from larger eggs; toward a dorsally and more weakly papillate penis with a large, external gland; and toward a broad‐based, tightly convoluted fertilization pouch‐seminal receptacle complex with an internal, muscular funnel. A convergence in high‐spired shells supported the recent synonymization of Madecataulus under Boucardicus. According to the cladogram, a three‐lobed apertural peristome was plesiomorphic, was lost, then reappeared convergently. Among the 12 dissected species of Boucardicus, morphology of the female reproductive system was extremely variable (11 of 14 character states autapomorphic). The Reticulapex cladogram supported monophyly of the genus but gave no robust resolution among species. Recent surveys also indicate that Reticulapex is rare to absent in northern Madagascar. The streptaxid cladogram suggested a sister‐group relationship between the endemic clades Par‐vedentulina and Streptostele (Makroconche), but provided no robust resolution among species within either clade or within Gulella. Anatomical material is relatively scarce for Madagascan streptaxids. Vicariance‐biogeographic analysis resulted in the area cladogram (northern Vohimena mountain chain (southern Vohimena chain (southern Anosy chain))). The Vohimena chain, already known for its significantly greater diversity and endemism than the Anosy chain, thus also séems to harbour the older, more plesiomorphic species; this heightens the urgency for conservation and further survey within the Vohimena chain. Acavids (115 species known) remain the most accessible of Madagascar's major, widespread land‐snail groups for island‐wide phylogenetics and biogeography, mainly because of existing frozen‐tissue collections, which have a limited shelf life. Boucardicus (177 species and 6 subspecies known) is clearly the second most accessible.     

Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices

Implied weighting, a method for phylogenetic inference that actively seeks to downweight supposed homoplasy, has in recent years begun to be widely utilized in palaeontological datasets. Given the method's purported ability at handling widespread homoplasy/convergence, we investigate the effects of implied weighting on modelled phylogenetic data. We generated 100 character matrices consisting of 55 characters each using a Markov Chain morphology model of evolution based on a known phylogenetic tree. Rates of character evolution in these datasets were variable and generated by pulling from a gamma distribution for each character in the matrix. These matrices were then analysed under equal weighting and four settings of implied weights (k = 1, 3, 5, and 10). Our results show that implied weighting is inconsistent in its ability to retrieve a known phylogenetic tree. Equally weighted analyses are found to generally be more conservative, retrieving higher frequency of polytomies but being less likely to generate erroneous topologies. Implied weighting is found to generally resolve polytomies while also propagating errors, resulting in an increase in both correctly and incorrectly resolved nodes with a tendency towards higher rates of error compared to equal weighting. Our results suggest that equal weights may be a preferable method for parsimony analysis.     

Bayesian analyses in phylogenetic palaeontology: interpreting the posterior sample

Establishing hypotheses of relationships is a critical prerequisite for any macroevolutionary analysis, but different approaches exist for achieving this goal. Amongst palaeontologists using morphological data the Bayesian approach is increasingly preferred over parsimony, but this shift also alters the way we think about samples of trees. Here we revisit stratigraphic congruence as a comparator between Bayesian and parsimony samples, but in a new visual context: treespace. Such spaces represent an ordination of unique topologies that can also be extended to create a ‘landscape’ where altitude represents some comparative measure (here congruence with stratigraphy). By co-opting existing visualization tools and applying them to a meta-analysis of 128 cladistic data sets we show that there is no consistent favouring of either Bayesian or parsimony according to stratigraphic congruence metrics, and further that empirical treespace visualizations suggest a complex variety of topological landscapes. We conclude by arguing that treespaces should become a standard exploratory tool in phylogenetic analysis.     

赤眼蜂属系统进化研究进展

赤眼蜂是一类重要的天敌昆虫,该属包括的种类达180多种,并且广泛地分布于世界各地。通过对形态特征的分析,赤眼蜂属的系统发育研究在不同的研究者中得到不同的分类系统。由于赤眼蜂的个体微小,仅04mm左右,现有的化石记录稀少,并且可用作系统发育研究的形态特征很少,导致该类群的系统发育研究仍有许多不清楚的地方。同时,近年来分子生物学的发展为赤眼蜂系统发育研究提供了很好的途径,也取得了一些共识。但仍然未能提出一套精确的、更可靠的分类系统。作者对近年来的赤眼蜂属系统进化研究进行了综述。     

Shifting ditypic site analysis: Heuristics for expanding the phylogenetic range of nucleotide sequences in Sankoff analyses

Summary We describe and illustrate a simple heuristic approach to the Sankoff methods for construction of parsimonious evolutionary trees from nucleotide sequence data. The procedure is intended to permit more valid inferences, particularly from relatively short sequences, concerning relationships among taxa separated for long time intervals. The procedure is based on the freat variability of evolutionary plasticity among sites in the molecules and removes from consideration the more highly variable sites. Editing is accomplished after classifying sites in carefully aligned arrays of sequences. Only “ditypic sites,” i.e., sites observed in only two evolutionary states within the array, are used in making phylogenetic inferences. This strategy makes possible the construction of good approximations to the most parsimonious Steiner strees, by means of efficient programs that require “dense species arrays,” i.e., species sets that differ from each other by relatively small numbers of differences in conservative sites. The technique is illustrated with 5S and 5.8S rRNA sequence data from published catalogs.     

Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers

Nuclear introns are increasingly used as phylogenetic markers. Here, we present a multidisciplinary approach towards optimal locus selection and amplification using Asian pitvipers as an example of a non‐model taxon, and raise the profile of length variant heterozygotes (LVHs) in intron loci. Taxon‐specific primers were identified using a bioinformatic approach, and also designed from existing exon primed, intron crossing (EPIC) primer amplifications. Eleven further universal EPIC primer pairs were assayed using a range of PCR optimization strategies. Taxon‐specific primers yielded the most consistent amplifications, but assaying a large number of universal EPIC primers yielded another appropriate locus for phylogenetic purposes. Modified Taq DNA polymerases such as JumpStart?Taq either significantly improved the specificity and yield of EPIC PCR amplifications (of low copy number nuclear targets), or resulted in amplifications that were not significantly worse than those derived from a generic Taq DNA polymerase. Finally, LVHs were detected in all loci that were sequenced suggesting that they are relatively common in introns. This study provides an efficient and cost effective template for the successful identification of intron markers for molecular systematics which is universally applicable to other non‐model taxon groups. © The Willi Hennig Society 2005.     

Determination of phylogenetic position ofPipizini (Diptera: Syrphidae): based on molecular biological and morphological data

Based on the sequence analysis of 5.8S subunit and internal transcribed spacers (ITS) of ribosomal RNA gene (rDNA), the molecular phylogenetic tree of representative species of Pipizini and three groups of Syrphidae with different feeding habits (seven species belong to six genera) was constructed. Meanwhile, the phylogenetic tree of tribes (including Pipizini and other 17 tribes of Syrphidae) was constructed using morphological characteristics of adults and larvae and the number of chromosomes. Both the results show that the relationship between Pipizini and predatory groups is closer than that between Pipizini and saprophagous groups. So it is suggested that Pipizini be transferred from Milesiinae to Syrphinae.     

SeqMaT: A sequence manipulation tool for phylogenetic analysis

Most bioinformatics tools require specialized input formats for sequence comparison and analysis. This is particularly true for molecular phylogeny programs, which accept only certain formats. In addition, it is often necessary to eliminate highly similar sequences among the input, especially when the dataset is large. Moreover, most programs have restrictions upon the sequence name. Here we introduce SeqMaT, a Sequence Manipulation Tool. It has the following functions: data format conversion,sequence name coding and decoding,redundant and highly similar sequence removal, anddata mining utilities. SeqMaT was developed using Java with two versions, web-based and standalone. A standalone program is convenient to manipulate a large number of sequences, while the web version will guarantee wide availability of the tool for researchers and practitioners throughout the Internet. AVAILABILITY: The database is available for free at http://glee.ist.unomaha.edu/seqmat.