The phylogenetic relationships of sauropod dinosaurs

A data-matrix of 205 osteological characters for 26 sauropod taxa is subjected to cladistic analysis. Two most parsimonious trees are produced, differing only in the relationships between Euhelopus, Omeisaurus and Mamenchisaurus. The monophyly of the Euhelopodidae (including Shunosaurus) is supported by seven synapomorphies. The Cetiosauridae (Patagosaurus, Cetiosaurus and Haplocanthosaurus) is paraphyletic with respect to the Neosauropoda. The latter clade divides into two major radiations–the ‘Brachiosauria’ (Camarasaurus, brachiosaurids and titanosauroids), and the Diplodocoidea (nemegtosaurids, dicraeosaurids, diplodocids and Rebbachisaurus). Further evidence for the inclusion of Opisthocoelwaudia in the Titanosauroidea is presented. Phuwiangosaurus, a problematic sauropod from Thailand, may represent one of the most plesiomorphic titanosauroids. ‘Peg’-like teeth have evolved at least twice within the Sauropoda. The postspinal lamina, on the neural spines of middle and caudal dorsal vertebrae, represents a neomorph rather than a fusion of pre-existing structures. Forked chevrons may have evolved convergently in the Euhelopodidae and the diplodocid-dicraeosaurid clade, or they may have been acquired early in sauropod evolution and subsequently lost in the ‘Brachiosauria’. The strengths and weaknesses of the data-matrix and tree topologies are explored using bootstrapping, decay analysis and randomization tests. Several nodes are only poorly supported, but this seems to reflect the large proportion of missing data in the matrix (～46%), rather than an abnormally high level of homoplasy. The results of the randomization tests indicate that the ‘data-matrix’ probably contains a strong phylogenetic ‘signal’. The relationships of some forms, such as Haplocanthosaurus, are influenced by the inclusion or exclusion of certain taxa with unusual combinations of character states. Such a result suggests that there are dangers inherent in the view that ‘higher’ level sauropod phylogeny can be accurately reconstructed using only a small number of well-known taxa.     

Phylogeny of extant and fossil Juglandaceae inferred from the integration of molecular and morphological data sets

It is widely acknowledged that integrating fossils into data sets of extant taxa is imperative for proper placement of fossils, resolution of relationships, and a better understanding of character evolution. The importance of this process has been further magnified because of the crucial role of fossils in dating divergence times. Outstanding issues remain, including appropriate methods to place fossils in phylogenetic trees, the importance of molecules versus morphology in these analyses, as well as the impact of potentially large amounts of missing data for fossil taxa. In this study we used the angiosperm clade Juglandaceae as a model for investigating methods of integrating fossils into a phylogenetic framework of extant taxa. The clade has a rich fossil record relative to low extant diversity, as well as a robust molecular phylogeny and morphological database for extant taxa. After combining fossil organ genera into composite and terminal taxa, our objectives were to (1) compare multiple methods for the integration of the fossils and extant taxa (including total evidence, molecular scaffolds, and molecular matrix representation with parsimony [MRP]); (2) explore the impact of missing data (incomplete taxa and characters) and the evidence for placing fossils on the topology; (3) simulate the phylogenetic effect of missing data by creating "artificial fossils"; and (4) place fossils and compare the impact of single and multiple fossil constraints in estimating the age of clades. Despite large and variable amounts of missing data, each of the methods provided reasonable placement of both fossils and simulated "artificial fossils" in the phylogeny previously inferred only from extant taxa. Our results clearly show that the amount of missing data in any given taxon is not by itself an operational guideline for excluding fossils from analysis. Three fossil taxa (Cruciptera simsonii, Paleoplatycarya wingii, and Platycarya americana) were placed within crown clades containing living taxa for which relationships previously had been suggested based on morphology, whereas Polyptera manningii, a mosaic taxon with equivocal affinities, was placed firmly as sister to two modern crown clades. The position of Paleooreomunnea stoneana was ambiguous with total evidence but conclusive with DNA scaffolds and MRP. There was less disturbance of relationships among extant taxa using a total evidence approach, and the DNA scaffold approach did not provide improved resolution or internal support for clades compared to total evidence, whereas weighted MRP retained comparable levels of support but lost crown clade resolution. Multiple internal minimum age constraints generally provided reasonable age estimates, but the use of single constraints provided by extinct genera tended to underestimate clade ages.     

Effects of iodine deficiency on mental and psychomotor abilities

The allometric relationships between canine base area, first molar and summed molar crown area, and the glabella–opisthocranion distance, and the direct allometric relationships between canine and molar size have been established in five primate taxa. Separate sex and combined sex ‘intraspecific’, and ‘interspecific’ regression and ‘best fit’ allometry coefficients were computed. This analysis showed that for any increase in glabella–opisthocranion length, the rate of increase in canine size exceeds the rate of increase in molar area, and ‘best fit’ solutions indicate that canine base area is positively allometric when related directly to molar crown area. These results were compared with data available for the ‘gracile’ australopithecine, A. africanus, and two ‘robust’ australopithecine taxa, A. boisei and A. robustus. The differences in canine and molar size which occur between the ‘gracile’ taxon and the two ‘robust’ taxa do not correspond to any of the trends in the comparative allometric models. Data on glabella–opisthocranion length for the fossils, meagre though they are, show that while the proportional increase in molar crown area between the taxa corresponds to comparative allometry models, the reduced canine size in the ‘robust’ taxa is against comparative allometric trends. These results indicate that, at least in terms of canine/molar proportions, the differences between the ‘gracile’ and ‘robust’ australopithecines are not merely allometric and may indicate significant dietary or behavioural differences.     

Phylogeny of Arvicolinae (Mammalia,Cricetidae): utility of morphological and molecular data sets in a recently radiating clade

Phylogenetic relationships within the Arvicolinae are examined based on two genes (mitochondrial cytb, nuclear GHR exon 10) and 296 morphological, developmental, behavioural, ecological and cytogenetic characters. To inspect the phylogenetic ‘behaviour’ of individual taxa, basic maximum‐parsimony and Bayesian phylogenetic analyses were accompanied by experiments based on different data‐partition combinations, ‘slow–fast’ character weighting, and inclusion/exclusion of individual problematic taxa. Ellobius, Prometheomys and Lagurus are the most basal arvicolines; Dicrostonyx, Phenacomys and Arborimus form a clade (Dicrostonychini s.lat.); the ‘core arvicolines’ include three subclades: Lemmini (Synaptomys, Lemmus, Myopus), Clethrionomyini (Eothenomys, Myodes) and Arvicolini (Arvicola, Chionomys, Stenocranius and Microtus, the last with six monophyletic subgenera: Alexandromys, ‘Neodon’, Mynomes, Lasiopodomys, Terricola, and Microtus s.str.). Position of Ondatra and Dinaromys is uncertain, probably compromised by highly homoplastic morphological characters.     

Chondrichthyan‐like scales from the Middle Ordovician of Australia

Abstract: Microvertebrate sampling of the Stairway Sandstone (Darriwilian, Middle Ordovician, central Australia) has yielded scales that are chondrichthyan‐like in their overall construction, and Tantalepis gatehousei gen. et sp. nov. is erected here to describe these specimens. Tantalepis gatehousei gen. et sp. nov. is the stratigraphically oldest microsquamous taxon described thus far, and the ‘shark‐like’ appearance of the scales may extend the chondrichthyan lineage back into the Middle Ordovician. The presence of ‘shark‐like’ scales in the fossil record some 50 myr prior to the first articulated chondrichthyan body fossils and 44 myr before the first clearly identifiable chondrichthyan teeth suggests there is a considerable scope for the recovery of articulated specimens with which to document the early history of crown gnathostomes. Traditional hypotheses of phylogenetic relationships among early jawed vertebrates were recently challenged by the proposal of a radically different tree topology. However, the development of a new data set specifically addressing scale‐based characters is required before taxa such as Tantalepis, that are based upon disarticulated remains alone, can be firmly placed within the emerging, revised, evolutionary narrative.     

A new phylogeny of Stegosauria (Dinosauria,Ornithischia)

The stegosaurs are some of the most easily recognizable dinosaurs, but are surprisingly rare as fossils. Consequently much remains unknown about their palaeobiology, and every new stegosaurian find contributes to our understanding of the evolution of the clade. Since the last attempt to examine the evolutionary relationships of Stegosauria, new specimens have come to light, including the most complete individual of Stegosaurus ever found, new taxa have been described and, perhaps most importantly, new methods for analysis of cladistic datasets have been produced. In the light of these new data and technological advances, the phylogenetic relationships of the stegosaurs and basal armoured dinosaurs are investigated. The inclusion of continuous data results in much better resolution than was previously obtained, and the resulting single most parsimonious tree supports re‐erection of the genera Miragaia and Hesperosaurus, which had previously been synonymized with Dacentrurus and Stegosaurus respectively. The recently described genus Alcovasaurus is resolved as a basal thyreophoran, but this is most likely a consequence of a very high degree of missing data and the questionable ontogenetic stage of the specimen. Examination of the effects of continuous data on the analysis suggest that while it contains a phylogenetic signal congruent with that of discrete data and provides better resolution than discrete data alone, it can affect topologies in unpredictable ways, particularly in areas of the tree where there are large amounts of missing data. The phylogeny presented here will form the basis for future work on the palaeobiology of the plated dinosaurs.     

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling

Background

Phylogenies are essential to many areas of biology, but phylogenetic methods may give incorrect estimates under some conditions. A potentially common scenario of this type is when few taxa are sampled and terminal branches for the sampled taxa are relatively long. However, the best solution in such cases (i.e., sampling more taxa versus more characters) has been highly controversial. A widespread assumption in this debate is that added taxa must be complete (no missing data) in order to save analyses from the negative impacts of limited taxon sampling. Here, we evaluate whether incomplete taxa can also rescue analyses under these conditions (empirically testing predictions from an earlier simulation study).

Methodology/Principal Findings

We utilize DNA sequence data from 16 vertebrate species with well-established phylogenetic relationships. In each replicate, we randomly sample 4 species, estimate their phylogeny (using Bayesian, likelihood, and parsimony methods), and then evaluate whether adding in the remaining 12 species (which have 50, 75, or 90% of their data replaced with missing data cells) can improve phylogenetic accuracy relative to analyzing the 4 complete taxa alone. We find that in those cases where sampling few taxa yields an incorrect estimate, adding taxa with 50% or 75% missing data can frequently (>75% of relevant replicates) rescue Bayesian and likelihood analyses, recovering accurate phylogenies for the original 4 taxa. Even taxa with 90% missing data can sometimes be beneficial.

Conclusions

We show that adding taxa that are highly incomplete can improve phylogenetic accuracy in cases where analyses are misled by limited taxon sampling. These surprising empirical results confirm those from simulations, and show that the benefits of adding taxa may be obtained with unexpectedly small amounts of data. These findings have important implications for the debate on sampling taxa versus characters, and for studies attempting to resolve difficult phylogenetic problems.     

Fossils impact as hard as living taxa in parsimony analyses of morphology

Systematists disagree whether data from fossils should be included in parsimony analyses. In a handful of well-documented cases, the addition of fossil data radically overturns a hypothesis of relationships based on extant taxa alone. Fossils can break up long branches and preserve character combinations closer in time to deep splitting events. However, fossils usually require more interpretation than extant taxa, introducing greater potential for spurious codings. Moreover, because fossils often have more "missing" codings, they are frequently accused of increasing numbers of MPTs, frustrating resolution and reducing support. Despite the controversy, remarkably little is known about the effects of fossils more generally. Here we provide the first systematic study, investigating empirically the behavior of fossil and extant taxa in 45 published morphological data sets. First-order jackknifing is used to determine the effects that each terminal has on inferred relationships, on the number of MPTs, and on CI' and RI as measures of homoplasy. Bootstrap leaf stabilities provide a proxy for the contribution of individual taxa to the branch support in the rest of the tree. There is no significant difference in the impact of fossil versus extant taxa on relationships, numbers of MPTs, and CI' or RI. However, adding individual fossil taxa is more likely to reduce the total branch support of the tree than adding extant taxa. This must be weighed against the superior taxon sampling afforded by including judiciously coded fossils, providing data from otherwise unsampled regions of the tree. We therefore recommend that investigators should include fossils, in the absence of compelling and case specific reasons for their exclusion.     

Global interrelationships of Plesiosauria (Reptilia,Sauropterygia) and the pivotal role of taxon sampling in determining the outcome of phylogenetic analyses

Previous attempts to resolve plesiosaurian phylogeny are reviewed and a new phylogenetic data set of 66 taxa (67% of ingroup taxa examined directly) and 178 characters (eight new) is presented. We recover two key novel results: a monophyletic Plesiosauridae comprising Plesiosaurus dolichodeirus, Hydrorion brachypterygius, Microcleidus homalospondylus, Occitanosaurus tournemirensis and Seeleyosaurus guilelmiimperatoris; and five plesiosaurian taxa recovered outside the split between Plesiosauroidea and Pliosauroidea. These taxa are Attenborosaurus conybeari, ‘Plesiosaurus’macrocephalus and a clade comprising Archaeonectrus rostratus, Macroplata tenuiceps and BMNH 49202. Based on this result, a new name, Neoplesiosauria, is erected for the clade comprising Plesiosauroidea and Pliosauroidea. Taxon subsamples of the new dataset are used to simulate previous investigations of global plesiosaurian relationships. Based on these simulations, most major differences between previous global phylogenetic hypotheses can be attributed to differences in taxon sampling. These include the position of Leptocleididae and Polycotylidae and the monophyly or paraphyly of Rhomaleosauridae. On this basis we favour the results recovered by our, larger analysis. Leptocleididae and Polycotylidae are sister taxa, forming a monophyletic clade within Plesiosauroidea, indicating that the large‐headed, short‐necked ‘pliosauromorph’ body plan evolved twice within Plesiosauria. Rhomaleosauridae forms the monophyletic sister taxon of Pliosauridae within Pliosauroidea. Problems are identified with previous phylogenetic definitions of plesiosaurian clades and new, stem‐based definitions are presented that should maintain their integrity over a range of phylogenetic hypotheses. New, rank‐free clade names Cryptoclidia and Leptocleidia are erected to replace the superfamilies Cryptoclidoidea and Leptocleidoidea. These were problematic as they were nested within the superfamily Plesiosauroidea. The incongruence length difference test indicates no significant difference in levels of homoplasy between cranial and postcranial characters.     

The impact of missing data on real morphological phylogenies: influence of the number and distribution of missing entries

Here we explore the effect of missing data in phylogenetic analyses using a large number of real morphological matrices. Different percentages and patterns of missing entries were added to each matrix, and their influence was evaluated by comparing the accuracy and error of most parsimonious trees. The relationships between accuracy and error and different parameters (e.g. the number of taxa and characters, homoplasy, support) were also evaluated. Our findings, based on real matrices, agree with the simulation studies, i.e. the negative effect increases with the percentage of missing entries, and decreases with the addition of more characters. This indicates that the main problem is the lack of information, not just the presence of missing data per se. Accuracy varies with different distribution patterns of missing entries; the worst case is when missing data are concentrated in a few taxa, while the best is when the missing entries are restricted to just a few characters. The results expand our knowledge of the missing data problem, corroborate many of the findings previously published using simulations, and could be useful for empirical or theoretical studies. © The Willi Hennig Society 2009.     

The phylogeny of leaf beetles (Chrysomelidae) inferred from mitochondrial genomes

The high-level classification of Chrysomelidae (leaf beetles) currently recognizes 12 or 13 well-established subfamilies, but the phylogenetic relationships among them remain ambiguous. Full mitochondrial genomes were newly generated for 27 taxa and combined with existing GenBank data to provide a dataset of 108 mitochondrial genomes covering all subfamilies. Phylogenetic analysis under maximum likelihood and Bayesian inference recovered the monophyly of all subfamilies, except that Timarcha was split from Chrysomelinae in some analyses. Three previously recognized major clades of Chrysomelidae were broadly supported: the ‘chrysomeline’ clade consisting of (Chrysomelinae (Galerucinae + Alticinae)); the ‘sagrine’ clade with internal relationships of ((Bruchinae + Sagrinae) + (Criocerinae + Donaciinae)), and the ‘eumolpine’ clade comprising (Spilopyrinae (Cassidinae (Eumolpinae (Cryptocephalinae + Lamprosomatinae)))). Relationships among these clades differed between data treatments and phylogenetic algorithms, and were complicated by two additional deep lineages, Timarcha and Synetinae. Various topological tests favoured the PhyloBayes software as the preferred inference method, resulting in the arrangement of (chrysomelines (eumolpines + sagrines)), with Timarcha placed as sister to the chrysomeline clade and Synetinae as a deep lineage splitting near the base. Whereas mitogenomes provide a solid framework for the phylogeny of Chrysomelidae, the basal relationships do not agree with the topology of existing molecular studies and remain one of the most difficult problems of Chrysomelidae phylogenetics.     

Phylogenetic structure and biogeography of the Pacific Rim clade of Sphagnum subgen. Subsecunda: haploid and allodiploid taxa

Although it is an uncommon distribution in seed plants, many bryophytes occur around the Pacific Rim of north‐western North America and eastern Asia. This work focuses on a clade of peatmosses (Sphagnum) that is distributed around the Pacific Rim region, with some individual species found across the total range. The goals were to infer divergent phylogenetic relationships among haploid species in the clade, assess parentage of allopolyploid taxa, and evaluate alternative hypotheses about inter‐ and intraspecific geographical range evolution. Multiple data sets and analyses resolved an ‘Alaska’ clade, distributed across western North America, eastern China and Japan, and an ‘Asia’ clade that includes western Chinese, Thai, Korean, eastern Chinese and Japanese lineages. Allopolyploids have arisen at least four times in the Pacific Rim clade of Sphagnum subgen. Subsecunda; it appears that all allopolyploid origins involved closely related haploid parental taxa. Biogeographical inferences were impacted by topological uncertainty and especially by the biogeographical model utilized to reconstruct ancestral areas. Most analyses converge on the conclusion that the ancestor to this clade of Pacific Rim Sphagnum species was widespread from Alaska south to eastern Asia, but a northern origin for the Alaska subclade was supported by one of the two biogeographical models we employed, under which it was robust to phylogenetic uncertainty.     

Combining Molecular Data with Classical Morphology for Uncultured Phagotrophic Euglenids (Excavata): A Single‐Cell Approach

Phagotrophic euglenids are one of the most diverse and important forms of heterotrophic flagellates in sediment systems, and are key to understanding the evolution of photosynthetic euglenids and ‘primary osmotrophs’, yet relatively little is known about their biodiversity and phylogenetic relationships. A wealth of light microscopy‐based information is available, but little progress has been made in associating this with molecular sequence data. We established a protocol to obtain light microscopy data and molecular data from single euglenid cells isolated from environmental samples. Individual cells from freshwater and marine benthic samples were isolated and rinsed by micropipetting, documented using high‐resolution photomicroscopy, then subjected to single‐cell nested PCR using taxon‐specific primers in combination with universal eukaryotic primers, generating > 75% or full‐length SSU rDNA sequences. As a proof‐of‐principle eight individuals were characterised and subjected to phylogenetic analyses. Many of these cells were identified as Anisonema or Dinema, and grouped with existing sequences assigned to these taxa, and with a ‘Peranema sp.’ sequence that we could now clearly demonstrate was misidentified or misannotated. Another cell is Heteronema c.f. exaratum, the first ‘skidding heteronemid’ for which sequence data are available. This is not closely related to Heteronema scaphurum, and intriguingly, branches as the sister group to primary osmotrophs. A cell similar to Ploeotia vitrea (the type of this genus), shows no particular phylogenetic affinity to Ploeotia costata, the best studied Ploeotia species. Our experimental protocol provides a useful starting point for future analyses on euglenid biodiversity (including environmental sequence surveys), and their evolution and systematics.     

Phylogeny of New Zealand hepialid moths (Lepidoptera: Hepialidae) inferred from a cladistic analysis of morphological data

The phylogeny of the New Zealand hepialid moths was estimated from a cladistic analysis of sixty‐three morphological characters, from all life cycle stages. One hundred and sixteen maximum parsimony trees were produced. The phylogenetic reconstruction indicated that the currently recognized generic concepts, and the four informal lineages hypothesized in a previous morphological taxonomic revision, were monophyletic. The relationships of species within genus Wiseana were not fully resolved. Analysis of a data set of thirty‐nine adult male characters from the New Zealand taxa and the Australian genera Jeana, Oxycanus and Trictena supported the monophyly of the New Zealand ‘Oxycanus’ s.s lineage.     

The phylogenetic affinities of the Socotra Bunting Emberiza socotrana

The monophyly of the African ‘brown bunting’ complex was corroborated by a recent molecular study. However, the little-known Socotran endemic Emberiza socotrana, which is morphologically similar to the other taxa in this complex, was not included. Here we present a hypothesis of the phylogenetic relationships of the Socotra Bunting based on one mitochondrial gene and one nuclear intron. We found the Socotra Bunting to be deeply nested within the African ‘brown bunting’ complex and, although morphologically most similar to E. capensis, it proved to be more closely related to the E. striolata/sahari and E. tahapisi/goslingi species groups. The phylogenetic uniqueness of the Socotra Bunting underpins once more the evolutionary importance of the Endemic Bird Area of Socotra, which is often considered the ‘Galápagos of the Indian Ocean’.     

The past and the present through phylogenetic analysis: the rove beetle tribe Othiini now and 99 Ma

In order to classify and taxonomically describe the first two fossil Othiini (Coleoptera: Staphylinidae: Staphylininae) species from three well‐preserved specimens in Cretaceous Burmese amber, a phylogenetic analysis was conducted, combining extant and extinct taxa. A dataset of 76 morphological characters scored for 33 recent species across the subfamilies Staphylininae and Paederinae was analysed using maximum parsimony and Bayesian inference methods. The many differing phylogenetic hypotheses for higher‐level relationships in the large rove beetle subfamilies Staphylininae and Paederinae were summarized and their hitherto known fossil record was reviewed. Based on the analyses, the new extinct genus Vetatrecus gen.n. is described with two new species: V. adelfiae sp.n. and V. secretum sp.n. Both species share character states that easily distinguish them from all recent Othiini and demonstrate a missing morphological link between subfamilies Staphylininae and Paederinae. This is the first morphology‐based evidence for the paraphyly of Staphylininae with respect to Paederinae, suggested earlier by two independent molecular‐based phylogenies of recent taxa. Our newly discovered stem lineage of Othiini stresses the importance of fossils in phylogenetic analyses conducted with the aim of improving the natural classification of extant species. It also suggests that the definitions of Staphylininae and Paederinae, long‐established family‐group taxa, may have to be reconsidered. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:817F39C4-F36B-4FD9-96CD-5F8FB064C39E .     

Increasing the number of molecular markers resolves the phylogenetic relationship of ‘Cepaea’ vindobonensis (Pfeiffer 1828) with Caucasotachea Boettger 1909 (Gastropoda: Pulmonata: Helicidae)

‘Cepaea’ vindobonensis has been shown to be closely related to Caucasotachea in recent molecular studies. The phylogenetic relationships within this clade and especially the phylogenetic position of ‘Cepaea’ vindobonensis were, however, not well resolved. Our phylogenetic analyses on the basis of an increased number of molecular genetic loci from the mitochondrial and nuclear genomes unambiguously demonstrate that ‘Cepaea’ vindobonensis represents the sister group of the Caucasotachea taxa, with C. leucoranea from the Caspian region of Azerbaijan and Iran being the sister species of the remaining Caucasian and eastern Pontic Caucasotachea species. We argue for the inclusion of ‘Cepaea’ vindobonensis in Caucasotachea rather than for a re‐erection of a monotypic genus Austrotachea for the species because of the overall low degree of morphological differentiation and the low number of species in the group.