The evolution of dinosaur tooth enamel microstructure

The evolution of tooth enamel microstructure in both extinct and extant mammalian groups has been extensively documented, but is poorly known in reptiles, including dinosaurs. Previous intensive sampling of dinosaur tooth enamel microstructure revealed that: (1) the three‐dimensional arrangement of enamel types and features within a tooth—the schmelzmuster—is most useful in diagnosing dinosaur clades at or around the family level; (2) enamel microstructure complexity is correlated with tooth morphology complexity and not necessarily with phylogenetic position; and (3) there is a large amount of homoplasy within Theropoda but much less within Ornithischia. In this study, the examination of the enamel microstructure of 28 additional dinosaur taxa fills in taxonomic gaps of previous studies and reinforces the aforementioned conclusions. Additionally, these new specimens reveal that within clades such as Sauropodomorpha, Neotheropoda, and Euornithopoda, the more basal taxa have simpler enamel that is a precursor to the more complex enamel of more derived taxa and that schmelzmusters evolve in a stepwise fashion. In the particularly well‐sampled clade of Euornithopoda, correlations between the evolution of dental and enamel characters could be drawn. The ancestral schmelzmuster for Genasauria remains ambiguous due to the dearth of basal ornithischian teeth available for study. These new specimens provide new insights into the evolution of tooth enamel microstructure in dinosaurs, emphasizing the importance of thorough sampling within broadly inclusive clades, especially among their more basal members.     

Biomechanical adaptations for burrowing in the incisor enamel microstructure of Geomyidae and Heteromyidae (Rodentia: Geomyoidea)

The enamel microstructure of fossil and extant Geomyoidea (Geomyidae, Heteromyidae) lower incisors incorporates three‐ or two‐layered schmelzmusters with uniserial, transverse Hunter‐Schreger bands having parallel and perpendicular or exclusively perpendicular oriented interprismatic matrix. Phylogenetically, these schmelzmusters are regarded as moderately (enamel type 2) to highly derived (enamel type 3). Our analysis detected a zone of modified radial enamel close to the enamel–dentine junction. Modified radial enamel shows a strong phylogenetic signal within the clade Geomorpha as it is restricted to fossil and extant Geomyoidea and absent in Heliscomyidae, Florentiamyidae, and Eomyidae. This character dates back to at least the early Oligocene (early Arikareean, 29 Ma), where it occurs in entoptychine gophers. We contend that this specialized incisor enamel architecture developed as a biomechanical adaptation to regular burrowing activities including chisel‐tooth digging and a fiber‐rich diet and was probably present in the common ancestor of the clade. We regard the occurrence of modified radial enamel in lower incisors of scratch‐digging Geomyidae and Heteromyidae as the retention of a plesiomorphic character that is selectively neutral. The shared occurrence of modified radial enamel is a strong, genetically anchored argument for the close phylogenetic relationship of Geomyidae and Heteromyidae on the dental microstructure level.     

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

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

On the earliest record of Cretaceous tyrannosauroids in western North America: implications for an Early Cretaceous Laurasian interchange event

The sudden appearance of Asian dinosaur clades within Lower Cretaceous strata of western North America has long been recognised as a biotic dispersion event related to initial establishment of a Beringian land bridge. To date, uncertainty exists regarding the timing of the Early Cretaceous Laurasian interchange event (EKLInE) and the pattern of associated biotic dispersal. Here, we report a tyrannosauroid premaxillary tooth (FMNH PR 2750) from the Cloverly Formation, Wyoming, USA, that pushes back the earliest Cretaceous record of the clade in North America. Although fragmentary, the tooth is consistent with mounting evidence for a pre-108 Ma initiation of EKLInE and earliest Albian emplacement of Beringia. Previous authors have considered the Aptian/Albian of western North America a depauperate dinosaur fauna, characterised by regional extinction and diversity decline. Documentation of Albian tyrannosauroids in the region indicates a more dynamic ecosystem than previously appreciated and marks an early start to faunal mixing between immigrant and endemic dinosaur clades. Finally, we find that the enamel microstructure of FMNH PR 2750 conforms to the morphotype of tyrannosaurids, yet exhibits poor columnar differentiation. This morphology bolsters prior interpretations on the phylogenetic utility of enamel microstructure and suggests a trend of increasing enamel complexity within Tyrannosauroidea.     

PHYLOGENETIC RELATIONSHIPS IN SEED PLANTS

Abstract— The phylogenetic relationships of nineteen extant and fossil seed plants are considered. Analysis of 31 characters produced ten topologically similar and equally parsimonious cladograms. A strict consensus tree derived from these cladograms places Lyginopteris as the sister taxon to the other seed plants included. Within this clade all the taxa considered, except medullosans and cycads, form a single monophyletic group defined by the presence of flattened seeds and saccate pollen ("platy-sperms"). Relationships between medullosans, cycads, and "platysperms" were not resolved, but within the "platysperm" clade conifers and cordaites ( Cordaixylon, Mesoxylon ) + Ginkgo form a monophyletic group ("coniferophytes"). The "higher platysperms" (glossopterids, Caytonia , corystosperms, Bennettitales, Pentoxylon , Gnetales, and angiosperms) are also monophyletic, but their relationship to "coniferophytes," peltasperms, and Callistophyton is unresolved. Pentoxylon is placed as sister taxon to the Bennettitales, and together they form the sister group to a clade in which Gnetales and angiosperm are sister taxa. The Bennettitales + Pentoxylon + Gnetales + angiosperms ("anthophytes") form a monophyletic sister group to the corystosperms. This analysis is compared with current classifications of seed plants. It does not support a close relationship between Bennettitales and cycads, it provides no evidence for seed plant polyphyly, and it strongly suggests that the current concept of seed ferns has little value in a phylogenetic context.     

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.     

Structural Morphology of Molars in Large Mammalian Herbivores: Enamel Content Varies between Tooth Positions

The distribution of dental tissues in mammalian herbivores can be very different from taxon to taxon. While grazers tend to have more elaborated and complexly folded enamel ridges, browsers have less complex enamel ridges which can even be so far reduced that they are completely lost. The gradient in relative enamel content and complexity of structures has so far not been addressed within a single species. However, several studies have noted tooth position specific wear rates in small mammals (rabbits, guinea pigs) which may be related to individual tooth morphology. We investigate whether differentiated enamel content by tooth position is also to be found in large herbivores. We use CT-scanning techniques to quantify relative enamel content in upper and lower molar teeth of 21 large herbivorous mammal species. By using a broad approach and including both perissodactyls and artiodactyls, we address phylogenetic intraspecific differences in relative enamel content. We find that enamel is highly unevenly distributed among molars (upper M1, M2, M3 and lower m1, m2, m3) in most taxa and that relative enamel content is independent of phylogeny. Overall, relative enamel content increases along the molar tooth row and is significantly higher in lower molars compared to upper molars. We relate this differential enamel content to prolonged mineralisation in the posterior tooth positions and suggest a compensatory function of m3 and M3 for functional losses of anterior teeth.     

An investigation into the cladistic relationships and monophyly of therocephalian therapsids (Amniota: Synapsida)

A comprehensive phylogenetic investigation was performed to elucidate the cladistic relationships and possible monophyly of therocephalian therapsids (Amniota: Synapsida). The phylogenetic positions of 30 therapsid taxa were examined under maximum parsimony, including 23 therocephalian genera. The analysis incorporated 110 cranial and postcranial characters in order to assess the interrelationships of basal therocephalians and eutherocephalians and their relationships to Cynodontia, representing the most complete review of therocephalian phylogeny to date. The analysis supports the hypothesis that Therocephalia represents the monophyletic sister taxon to Cynodontia, with as many as 15 morphological synapomorphies, in contrast with other recent analyses of lesser taxon sampling. The results also support the hypothesis that Scylacosauridae is more closely related to Eutherocephalia than to the basal therocephalian family Lycosuchidae, supporting a ‘Scylacosauria’ clade. The taxa suggested here to be neotenic forms (e.g. Ictidosuchoides and Ictidosuchops) are positioned near the base of a monophyletic Baurioidea. Neotenic development of the therocephalian feeding apparatus and evolutionary parallelism with cynodonts are suggested to have been important trends in the early evolution of baurioid therocephalians into the Late Permian and Early Triassic.     

The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow‐mouthed frogs (Anura,Microhylidae)

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum‐likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree‐alignment framework are generally better resolved and better supported than those inferred within a similarity‐alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model‐based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic.     

Primates: cladistic diagnosis and relationships

The morphological evidence for the phylogenetic relationships of euprimates, archaic primates, and related eutherian orders is reviewed following the methods of Hennigian phylogenetic systematics. Euprimates, the group including living primates and their closest common ancestor, is diagnosed by a suite of shared derived characters of the cranium and posteranium exhibiting relatively unique distributions among Eutheria. Plesiadapiformes, the group of archaic primates generally held to be the sister group to Euprimates, is not demonstrably monophyletic (with or without Microsyopidae). The Superorder Archonta (primates, tree shrews, bats, and colugos) is the only higher-level grouping including Euprimates that is based on uniquely derived morphological characters. Hypotheses of relationships within Archonta ally Euprimates with either tree shrews or some plesiadapiforms (paromomyids and plesiadapids), but the eurprimate-tree shrew clade receives more support from the distribution of derived characters among the taxa studied. Because the higher-level affinities of Euprimates are not well resolved, we advocate equating the Order Primates with the taxon Euprimates.     

A new juvenile specimen of Yunnanosaurus robustus (Dinosauria: Sauropodomorpha) from Early to Middle Jurassic of Chuxiong Autonomous Prefecture,Yunnan Province,China

An almost complete skeleton with partial cranial material (ZMNH-M8739) is recovered from the Early or Middle Jurassic of southwest China. ZMNH-M8739 is identified as a juvenile individual of basal sauropodomorph dinosaur, Yunnanosaurus robustus Young, 1951. The revised diagnoses are as follows: absence of anteroposterior expansion on the medial end of astragalus and dorsoventrally compressed medium shaft of the metatarsal IV. Unfused neural arch and finely grooved long bone surface texture indicate that this individual is in the immature growth stage. ZMNH-M8739 possesses the tooth–tooth wear facet on its mesial maxillary and dentary teeth. However, the distal maxillary teeth have coarse serrations. Such a characteristic dentition could represent a unique feeding mechanism of this animal. Finally, ZMNH-M8739 constitutes a monophyletic group with Y. robustus (holotype), and Y. huangi is nesting this clade in the phylogenetic tree of the present analysis. Comparison of juvenile and adult specimen reveals distinctive growth changes of Y. robustus. This clade is positioned in an unnamed clade at a sister taxon of Sauropoda. Finally, some members of the so-called prosauropod dinosaurs constitute a monophyletic group in the present result.     

Phylogenetic analysis of the Brachyura (Crustacea, Decapoda) based on characters of the foregut with establishment of a new taxon

The Brachyura, within the decapod crustaceans, is one of the most species-rich taxa with up to 10 000 species. However, its phylogenetic history, evolution and fossil record remain subjects of controversy. In our study, we examined the phylogenetic relationships of the Brachyura based on morphological characters of the foregut. The cladistic analysis supports a monophyletic Brachyura including the Dromiidae and Raninidae. A clade comprising Dromiidae and Dynomenidae forms the most basal assemblage within the Brachyura, followed by the Homolidae and Latreilliidae. As a result, neither Podotremata nor Archaeobrachyura form a clade. In contrast, foregut data suggest that the classical taxon Oxystomata, comprising Calappidae, Parthenopidae, Dorippidae, Leucosiidae, Cymonomidae and Raninidae, is monophyletic. This makes the Heterotremata paraphyletic or polyphyletic. A newly established taxon, Neobrachyura, embraces some representatives of the Heterotremata and the monophyletic Thoracotremata.     

New Species of Rotundomys (Cricetinae) from the Late Miocene of Spain and Its Bearing on the Phylogeny of Cricetulodon and Rotundomys

The material of Rotundomys (Rodentia, Cricetinae) from the Late Miocene fossiliferous complex of Cerro de los Batallones (Madrid, Spain) is described and compared with all species currently placed in the genera Rotundomys and Cricetulodon. Both the morphology and size variation encompassed in the collection of specimens from Batallones suggest they belong to a single taxon different from the other known species of these genera. A new species Rotundomys intimus sp. nov. is, therefore, named for it. A cladistic analysis, which is the first ever published concernig these taxa, has been conducted to clear up the phylogenetic position of the new species. Our results suggest that Rotundomys intimus sp. nov. inserts between R. mundi and R. sabatieri as a relatively primitive taxon inside the clade Rotundomys. The new taxon is more derived than R. mundi in having a transversal connection between the metalophulid and the anterolophulid on some m1 but more primitive than R. sabatieri and the most evolved species of Rotundomys (R. montisrotuni +R.bressanus) in its less developed lophodonty showing distinct cusps, shallower valleys, and the presence of a subdivided anteroloph on the M1. The species of Cricetulodon do not form a monophyletic group. As a member of Rotundomys, Rotundomys intimus sp. nov. is more derived than all of these taxa in its greater lophodonty and the complete loss of the anterior protolophule, mesolophs, and mesolophids.     

A new species of Azendohsaurus (Diapsida: Archosauromorpha) from the Triassic Isalo Group of southwestern Madagascar: cranium and mandible

Abstract: Here, we describe a new species of Azendohsaurus from the Middle–Late Triassic of Madagascar, extending the geographical range of a taxon known otherwise only by a single species from Morocco. Although Azendohsaurus has consistently been regarded as an early dinosaur (based on various advanced dental and gnathic features resembling those characterizing certain dinosaur subgroups), the relatively complete skeletal material, now available from Madagascar, argues strongly against its dinosaurian affinities. Rather, the retention of numerous primitive cranial and postcranial features indicates a surprisingly early divergence of Azendohsaurus within Archosauromorpha and an unusual mosaic of characters in this taxon. Features considered diagnostic of Sauropodomorpha thus are inferred to occur homoplastically in at least one clade of nondinosaurian archosauromorphs, indicating a complex evolution and distribution of features traditionally thought to be derived within archosaurs. Azendohsaurus has teeth resembling those of both early sauropodomorph and ornithischian dinosaurs, yet also possesses numerous inarguable basal archosauromorph cranial and postcranial attributes. This highlights the risk of uncritically referring isolated, Middle–Late Triassic (or even later), ‘leaf‐shaped’ teeth with denticles to the Dinosauria. Similarly, the occurrence of such teeth in an early diverging archosauromorph indicates that specializations for herbivory originated more frequently within this clade than conventionally assumed. For example, Azendohsaurus and numerous basal sauropodomorph dinosaur taxa share an array of convergently acquired features associated with herbivory, including tooth denticles, expanded tooth crowns, a downturned dentary and the articular located at the ventral margin of the mandible. Some of these features (denticles, expanded crowns and the ventrally deflected articular) are even more widespread among archosauromorphs, including aetosaurs, silesaurs and ornithischian dinosaurs. A downturned dentary also occurs in Trilophosaurus, a taxon further marked by unique specializations for herbivory, including transversely lophate, tricuspid teeth. An array of features associated with herbivory also occurs in rhynchosaurs and certain crocodilians (e.g. Simosuchus). This distribution suggests that craniodental features associated with herbivory were much more pervasive across the archosauromorph clade than previously recognized, possibly evolving at least six to eight times independently.     

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.     

Phylogenetic position of the adeleorinid coccidia (Myzozoa, Apicomplexa, Coccidia, Eucoccidiorida, Adeleorina) inferred using 18S rDNA sequences

Investigating the evolutionary relationships of the major groups of Apicomplexa remains an important area of study. Morphological features and host-parasite relationships continue to be important in the systematics of the adeleorinid coccidia (suborder Adeleorina), but the systematics of these parasites have not been well-supported or have been constrained by data that were lacking or difficult to interpret. Previous phylogenetic studies of the Adeleorina have been based on morphological and developmental characters of several well-described species or based on nuclear 18S ribosomal DNA (rDNA) sequences from taxa of limited taxonomic diversity. Twelve new 18S rDNA sequences from adeleorinid coccidia were combined with published sequences to study the molecular phylogeny of taxa within the Adeleorina and to investigate the evolutionary relationships of adeleorinid parasites within the Apicomplexa. Three phylogenetic methods supported strongly that the suborder Adeleorina formed a monophyletic clade within the Apicomplexa. Most widely recognized families within the Adeleorina were hypothesized to be monophyletic in all analyses, although the single Hemolivia species included in the analyses was the sister taxon to a Hepatozoon sp. within a larger clade that contained all other Hepatozoon spp. making the family Hepatozoidae paraphyletic. There was an apparent relationship between the various clades generated by the analyses and the definitive (invertebrate) host parasitized and, to lesser extent, the type of intermediate (vertebrate) host exploited by the adeleorinid parasites. We conclude that additional taxon sampling and use of other genetic markers apart from 18S rDNA will be required to better resolve relationships among these parasites.     

Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses

Despite many efforts to resolve evolutionary relationships among major clades of Cyprinidae, some nodes have been especially problematic and remain unresolved. In this study, we employ four nuclear gene fragments (3.3 kb) to infer interrelationships of the Cyprinidae.A reconstruction of the phylogenetic relationships within the family using maximum parsimony, maximum likelihood, and Bayesian analyses is presented. Among the taxa within the monophyletic Cyprinidae, Rasborinae is the basal-most lineage; Cyprinine is sister to Leuciscine. The monophyly for the subfamilies Gobioninae, Leuciscinae and Acheilognathinae were resolved with high nodal support. Although our results do not completely resolve relationships within Cyprinidae, this study presents novel and significant findings having major implications for a highly diverse and enigmatic clade of East-Asian cyprinids. Within this monophyletic group five closely-related subgroups are identified. Tinca tinca, one of the most phylogenetically enigmatic genera in the family, is strongly supported as having evolutionary affinities with this East-Asian clade; an established yet remarkable association because of the natural variation in phenotypes and generalized ecological niches occupied by these taxa.Our results clearly argue that the choice of partitioning strategies has significant impacts on the phylogenetic reconstructions, especially when multiple genes are being considered. The most highly partitioned model (partitioned by codon positions within genes) extracts the strongest phylogenetic signals and performs better than any other partitioning schemes supported by the strongest 2Δln Bayes factor. Future studies should include higher levels of taxon sampling and partitioned, model-based analyses.     

基于Rag1基因序列变异的鲤形目鱼类系统发育重建:采样策略对生命之树的影响

The phylogenetic relationships of species are fundamental to any biological investigation, including all evolutionary studies. Accurate inferences of sister group relationships provide the researcher with an historical framework within which the attributes or geographic origin of species (or supraspecific groups) evolved. Taken out of this phylogenetic context, interpretations of evolutionary processes or origins, geographic distributions, or speciation rates and mechanisms, are subject to nothing less than a biological experiment without controls. Cypriniformes is the most diverse clade of freshwater fishes with estimates of diversity of nearly 3,500 species. These fishes display an amazing array of morphological, ecological, behavioral, and geographic diversity and offer a tremendous opportunity to enhance our understanding of the biotic and abiotic factors associated with diversification and adaptation to environments. Given the nearly global distribution of these fishes, they serve as an important model group for a plethora of biological investigations, including indicator species for future climatic changes. The occurrence of the zebrafish, Danio rerio, in this order makes this clade a critical component in understanding and predicting the relationship between mutagenesis and phenotypic expressions in vertebrates, including humans. With the tremendous diversity in Cypriniformes, our understanding of their phylogenetic relationships has not proceeded at an acceptable rate, despite a plethora of morphological and more recent molecular studies. Most studies are pre-Hennigian in origin or include relatively small numbers of taxa. Given that analyses of small numbers of taxa for molecular characters can be compromised by peculiarities of long-branch attraction and nodal-density effect, it is critical that significant progress in our understanding of the relationships of these important fishes occurs with increasing sampling of species to mitigate these potential problems. The recent Cypriniformes Tree of Life initiative is an effort to achieve this goal with morphological and molecular (mitochondrial and nuclear) data. In this early synthesis of our understanding of the phylogenetic relationships of these fishes, all types of data have contributed historically to improving our understanding, but not all analyses are complementary in taxon sampling, thus precluding direct understanding of the impact of taxon sampling on achieving accurate phylogenetic inferences. However, recent molecular studies do provide some insight and in some instances taxon sampling can be implicated as a variable that can influence sister group relationships. Other instances may also exist but without inclusion of more taxa for both mitochondrial and nuclear genes, one cannot distinguish between inferences being dictated by taxon sampling or the origins of the molecular data.     

The phylogenetic position of the Prolecithophora (Rhabditophora, 'Platyhelminthes')

Complete 18S ribosomal DNA (rDNA) sequences and partial 28S rDNA sequences from a selection of rhabditophoran taxa were obtained and used in combination with literature data to determine the phylogenetic position of the Prolecithophora and of two families sometimes included in the Prolecithophora, the Urastomidae and the Genostomatidae. The results are largely compatible with earlier molecular studies when supported clades are considered, and adjusting for the denser taxonomic sampling of this study. The position of the Proseriata is not compatible with the taxon Seriata, which is rejected. The Rhabdocoela excluding the Fecampiida and the Neodermata is monophyletic. The phylogenetic position of the Neodermata cannot be determined, but its placement is not compatible with the proposed taxa Revertospermata and Mediofusata Kornakova & Joffe, 1999, which are rejected. The Urastomidae and the Genostomatidae in all analyses group with the Fecampiida, and it is our recommendation that these taxa be included in the Fecampiida. The amended Fecampiida always group separately from the Prolecithophora sensu stricto , the Rhabdocoela, and the Neodermata. Our analyses reveal the existence of a strongly supported clade consisting of Prolecithophora + Tricladida + the amended Fecampiida, and we propose the name Adiaphanida for this clade. Tentatively the sister group of the Prolecithophora is a clade consisting of the Tricladida + amended Fecampiida.