Electron microscopical observations on vitellocytes and germocytes inNematoplana coelogynoporoides (Plathelminthes,Proseriata)

Summary Fine-structural features of vitellaria and germaria inNematoplana coelogynoporoides are documented and compared with those of other free-living plathelminths with ectolecithal eggs. Emphasis is mainly put on the pattern of eggshell material, yolk bodies deposited in vitellocytes, and marginal granules of the female germ cells. In this species, encompassed in the taxon Proseriata Unguiphora, the eggshell granules show a meandering pattern also known from species of the taxon Proseriata Lithophora. In contrast, the yolk globules exhibit crystalline components unknown from the Lithophora. The marginal granules in the ooplasm have an extremely large diameter. They consist of a flocculent core and a crescent-shaped cortex. Marginal granules of this appearance have not been found in any other taxon of free-living Neoophora.Abbreviations cc crystalline component - co cortex - gER granular endoplasmic reticulum - go Golgi complex - gl glycogen - lp lipid droplet - mg marginal granule - n nucleus - nl nucleolus - sg eggshell granule - sp spermatozoa - yg yolk globule     

Quo vadis eohippus? The systematics and taxonomy of the early Eocene equids (Perissodactyla)

The systematics and taxonomy of early Eocene equids are investigated. A paraphyletic sequence of equid taxa is recovered from a phylogenetic analysis of 40 taxa and 121 characters. This analysis supports the identification of Hyracotherium as a primitive equoid and its restriction to the genotype, Hyracotherium leporinum . Sifrhippus gen. nov. is erected for the sister taxon of all other equids, Hyracotherium sandrae Gingerich. Minippus gen. nov., the next more-derived equid clade, is erected for two small equids, M. index Cope and M. jicarillai nov. species. Arenahippus gen. nov. is erected for the next three sequentially more-derived equid taxa, A. grangeri Kitts, A. aemulor Gingerich, and A. pernix Marsh. The genus Xenicohippus , which is the next more-derived equid clade, is redefined to include X. craspedotum Cope. Eohippus Marsh, the next more-derived equid taxon, is resurrected for E. angustidens Cope. Pliolophus , the only early Eocene equid from Europe, is identified as the sister taxon to Protorohippus , a sequence of successively more-derived equid taxa consisting of P. montanum Wortman and P. venticolum Cope. Protorohippus venticolum is identified as the sister taxon of Orohippus . Systemodon Cope is resurrected for S. tapirinum Cope. This taxon has historically been placed within Hyracotherium yet this analysis allies it with Cymbalophus near the base of the perissodactyl radiation. © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 134 , 141–256.     

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.     

Phylogenetic relationships of the enigmatic land snail genus Prestonella: the missing African element in the Gondwanan superfamily Orthalicoidea (Mollusca: Stylommatophora)

The land snail superfamily Orthalicoidea, although generally assumed to be of Gondwanan origin, is considered by the majority of recent authors to be absent from the African continent. However, two poorly-known African genera, Aillya and Prestonella , have historically been referred to the orthalicoid family Bulimulidae s.l. Anatomical study of Aillya has subsequently shown it to be morphologically distinct from the Bulimulidae and referable to a family of its own, outside the Orthalicoidea, but Prestonella has remained an enigmatic taxon of unknown affinity. Using molecular and morphological evidence, we demonstrate conclusively that Prestonella is indeed a member of the Bulimulidae s.l. We thus confirm that this family is represented in Africa, and that it has a classical disjunct, tri-continental southern distribution. Thus, either the origin of the family must at the least predate the separation of Africa and South America in the Mid Cretaceous (under a vicariance scenario) or there must have been subsequent dispersal between the isolated Gondwanan fragments. In view of the limited dispersal ability of terrestrial snails, we consider the former more likely. Anatomically, Prestonella exhibits many character states thought to be plesiomorphic, suggesting a relationship with the subfamily Bulimulinae. Bayesian analysis of nuclear DNA sequence data places it as sister group (posterior probability = 1.0) to an Australasian clade comprising Bothriembryon and Placostylus . However, taxon sampling within the Orthalicoidea is currently inadequate to permit meaningful resolution of subfamilial affinity using molecular data. Similarly, although those orthalicoid taxa for which molecular data are available comprise a well-supported clade, the relationships of this clade to other stylommatophoran clades remain unresolved.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 203–221.     

Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

Progress in nemertean biology: development and phylogeny

This paper reviews progress in developmental biology and phylogenyof the Nemertea, a common but poorly studied spiralian taxonof considerable ecological and evolutionary significance. Analysesof reproductive biology (including calcium dynamics during fertilizationand oocyte maturation), larval morphology and development anddevelopmental genetics have significantly extended our knowledgeof spiralian developmental biology. Developmental genetics studieshave in addition provided characters useful for reconstructingmetazoan phylogeny. Reinvestigation of the cell lineage of Cerebratuluslacteus using fluorescent tracers revealed that endomesodermforms from the 4d cell as in other spiralians and that ectomesodermis derived from the 3a and 3b cells as in annelids, echiuransand molluscs. Studies examining blastomere specification showthat cell fates are established precociously in direct developersand later in indirect developers. Morphological characters usedto estimate the phylogenetic position of nemerteans are criticallyre-evaluated, and cladistic analyses of morphology reveal thatconflicting hypotheses of nemertean relationships result becauseof different provisional homology statements. Analyses thatinclude disputed homology statements (1, gliointerstitial cellsystem 2, coelomic circulatory system) suggest that nemerteansform the sister taxon to the coelomate spiralian taxa ratherthan the sister taxon to Platyhelminthes. Analyses of smallsubunit rRNA (18S rDNA) sequences alone or in combination withmorphological characters support the inclusion of the nemerteansin a spiralian coelomate clade nested within a more inclusivelophotrochozoan clade. Ongoing evaluation of nemertean relationshipswith mitochondrial gene rearrangements and other molecular charactersis discussed.     

The early evolution of titanosauriform sauropod dinosaurs

Titanosauriformes was a globally distributed, long‐lived clade of dinosaurs that contains both the largest and smallest known sauropods. These common and diverse megaherbivores evolved a suite of cranial and locomotory specializations perhaps related to their near‐ubiquity in Mesozoic ecosystems. In an effort to understand the phylogenetic relationships of their early (Late Jurassic–Early Cretaceous) members, this paper presents a lower‐level cladistic analysis of basal titanosauriforms in which 25 ingroup and three outgroup taxa were scored for 119 characters. Analysis of these characters resulted in the recovery of three main clades: Brachiosauridae, a cosmopolitan mix of Late Jurassic and Early Cretaceous sauropods, Euhelopodidae, a clade of mid‐Cretaceous East Asian sauropods, and Titanosauria, a large Cretaceous clade made up of mostly Gondwanan genera. Several putative brachiosaurids were instead found to represent non‐titanosauriforms or more derived taxa, and no support for a Laurasia‐wide clade of titanosauriforms was found. This analysis establishes robust synapomorphies for many titanosauriform subclades. A re‐evaluation of the phylogenetic affinities of fragmentary taxa based on these synapomorphies found no body fossil evidence for titanosaurs before the middle Cretaceous (Aptian), in contrast to previous reports of Middle and Late Jurassic forms. Purported titanosaur track‐ways from the Middle Jurassic either indicate a substantial ghost lineage for the group or – more likely – represent non‐titanosaurs. Titanosauriform palaeobiogeographical history is the result of several factors including differential extinction and dispersal. This study provides a foundation for future study of basal titanosauriform phylogeny and the origins of Titanosauria. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 624–671.     

The anatomy of the basal ornithischian dinosaur Eocursor parvus from the lower Elliot Formation (Late Triassic) of South Africa

Ornithischia is a morphologically and taxonomically diverse clade of dinosaurs that originated during the Late Triassic and were the dominant large‐bodied herbivores in many Cretaceous ecosystems. The early evolution of ornithischian dinosaurs is poorly understood, as a result in part of a paucity of fossil specimens, particularly during the Triassic. The most complete Triassic ornithischian dinosaur yet discovered is Eocursor parvus from the lower Elliot Formation (Late Triassic: Norian–Rhaetian) of Free State, South Africa, represented by a partial skull and relatively complete postcranial skeleton. Here, the anatomy of Eocursor is described in detail for the first time, and detailed comparisons are provided to other basal ornithischian taxa. Eocursor is a small‐bodied taxon (approximately 1 m in length) that possesses a plesiomorphic dentition consisting of unworn leaf‐shaped crowns, a proportionally large manus with similarities to heterodontosaurids, a pelvis that contains an intriguing mix of plesiomorphic and derived character states, and elongate distal hindlimbs suggesting well‐developed cursorial ability. The ontogenetic status of the holotype material is uncertain. Eocursor may represent the sister taxon to Genasauria, the clade that includes most of ornithischian diversity, although this phylogenetic position is partially dependent upon the uncertain phylogenetic position of the enigmatic and controversial clade Heterodontosauridae. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 648–684.     

Improved bootstrap confidence limits in large-scale phylogenies,with an example from Neo-Astragalus (Leguminosae)

Phylogenetic analyses of large data sets pose special challenges, including the apparent tendency for the bootstrap support for a clade to decline with increased taxon sampling of that clade. We document this decline in data sets with increasing numbers of taxa in Astragalus, the most species-rich angiosperm genus. Support for one subclade, Neo-Astragalus, declined monotonically with increased sampling of taxa inside Neo-Astragalus, irrespective of whether parsimony or neighbor-joining methods were used or of which particular heuristic search algorithm was used (although more stringent algorithms tended to yield higher support). Three possible explanations for this decline were examined, including (1) mistaken assignment of the most recent common ancestor of the taxon sample (and its bootstrap support) with the most recent common ancestor of the clade from which it was sampled; (2) computational limitations of heuristic search strategies; and (3) statistical bias in bootstrap proportions, especially that from random homoplasy distributed among taxa. The best explanation appears to be (3), although computational shortcomings (2) may explain some of the problem. The bootstrap proportion, as currently used in phylogenetic analysis, does not accurately capture the classical notion of confidence assessments on the null hypothesis of nonmonophyly, especially in large data sets. More accurate assessments of confidence as type I error levels (relying on iterated bootstrap methods) remove most of the monotonic decline in confidence with increasing numbers of taxa.     

Phylogenetic relationships within Adiaphanida (phylum Platyhelminthes) and the status of the crustacean‐parasitic genus Genostoma

The existence of the platyhelminth clade Adiaphanida—an assemblage comprising the well‐studied order Tricladida as well as two lesser known taxa, Prolecithophora and the obligate parasitic Fecampiida—is among the more surprising results of flatworm molecular systematics. Each of these three clades is itself largely well‐defined from a morphological point of view, although Adiaphanida at large, despite its strong support in molecular phylogenetic analyses, lacks known morphological synapomorphies. However, one taxon, the genus Genostoma, a parasite of the leptostracan crustacean Nebalia, rests uneasily within its current classification within the fecampiid family Genostomatidae; ultrastructural investigations on this taxon have uncovered a spermatogenesis reminiscent of Kalyptorhynchia, and a dorsal syncytium resembling the neodermatan tegument. Here, we provide molecular sequence data (nearly complete 18S and 28S rRNA) from a representative of Genostoma, with which we test hypotheses on the phylogenetic position of this taxon within Platyhelminthes, expanding upon a recently published phylum‐wide analysis, and applying novel alignment algorithms and substitution models. These analyses unequivocally position Genostoma as the sister group of Prolecithophora. However, even in taxon‐rich analyses, support for the position of the root of Adiaphanida is lacking, highlighting the need for new data types to study the phylogeny of this clade. Interestingly, our analyses also do not recover the monophyly of several taxa previously proposed, notably Continenticola within Tricladida and Protomonotresidae within Prolecithophora. In light of this phylogeny and the distinctive morphology (especially, spermatogenesis) of Genostoma, we advocate for a redefinition of the family Genostomatidae, outside of both Fecampiida and Prolecithophora, to encompass the members of this unique genus of parasites. Within Fecampiida, the family Piscinquilinidae fam. nov. is erected to accommodate the vertebrate‐parasitic Piscinquilinus, formerly Genostomatidae.     

The osteology and phylogeny of the Hawaiian finch radiation (Fringillidae: Drepanidini), including extinct taxa

The monophyly and phylogeny of the adaptive radiation of Hawaiian finches (Fringillidae: Drepanidini; honeycreepers, auct.) were studied using parsimony analysis of comparative osteology, combined with Templeton (Wilcoxon signed‐ranks) tests of alternative phylogenetic hypotheses. Eighty‐four osteological characters were scored in 59 terminal taxa of drepanidines, including 24 fossil forms, and in 30 outgroup species. The optimal phylogenetic trees show considerable agreement, and some conflict, with independently derived ideas about drepanidine evolution. The monophyly of a large Hawaiian radiation was upheld, although one fossil taxon from Maui fell outside the drepanidine clade. The finch‐billed species were placed as basal drepanidine taxa, and continental cardueline finches (Carduelini) were identified as the radiation's closest outgroups. The study found anatomical as well as phylogenetic evidence that the radiation had a finch‐billed ancestor. The optimal trees identify the red‐and‐black plumage group as a clade, and suggest that the tubular tongue evolved only once in the radiation. Because comparative osteology provides too few characters to strongly support all the nodes of the tree, it was helpful to evaluate statistical support for alternative hypotheses about drepanidine relationships using the Templeton test. Among the alternatives that received significant statistical support are a relationship of the drepanidines with cardueline finches rather than with the Neotropical honeycreepers (Thraupini), classification of the controversial genera Paroreomyza and Melamprosops as drepanidines, and a secondary loss of the tubular tongue in Loxops mana. The hypothesis of monophyly for all the Hawaiian taxa in the study was not rejected statistically. The study provides a framework for incorporating morphological and palaeontological information in evolutionary studies of the Drepanidini. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 141 , 207–255.     

‘Back to Africa’: increased taxon sampling confirms a problematic Australia‐to‐Africa bee dispersal event in the Eocene

Colletidae is a predominantly southern hemisphere bee family with a Late Cretaceous origin and with an inferred ancestral region covering late Gondwanan South America, Antarctica and Australia. One highly diverse colletid subfamily, Euryglossinae, is entirely restricted to Australia and the strictly Afrotropical subfamily Scrapterinae has been inferred as its sister clade. This has led to suggestions that Scrapterinae represents a highly unusual post‐Gondwanan dispersal from Australia to Africa, but phylogenetic studies to date have included only minimal representatives from each subfamily. Here we greatly increase the level of species sampling of both subfamilies and develop a molecular phylogeny based on one mitochondrial and two nuclear genes. Our results indicate that the broad results of earlier studies are robust to substantially greater taxon sampling, and we infer a divergence date between the two subfamilies in the early Eocene. Dispersal pathways between Africa and Australia during that time are problematic, with several studies suggesting dispersals via the now largely submerged Kerguelen and Crozet Plateaus. Our results contribute another example of a puzzling sister‐clade relationship between African and Australian taxa and indicate the need to better understand southern hemisphere subaerial configurations, including Antarctica, and ocean and wind currents at those times.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

Australian parasitic Ogyris butterflies: east–west divergence of highly‐specialized relicts

Not all butterflies are innocuous plant‐feeders. A small number of taxa in the family Lycaenidae have graduated from mutualistic partnerships with ants to predatory or parasitic associations. These highly‐specialized life histories, involving butterfly larvae living inside ant colonies, are often associated with rarity and vulnerability to extinction. In the present study, we examined the evolutionary relationships of a poorly‐known group of seven taxa herein referred to as the idmo‐group within the Australian lycaenid genus Ogyris. The idmo‐group has a relictual distribution across southern Australia and includes taxa with highly‐specialized phytophagous and myrmecophagous life histories. A phylogeny based on mitochondrial DNA (cytochrome oxidase I and cytochrome b] and the nuclear DNA locus elongation factor 1α (EF1α), generally agrees with current taxonomy and supports the recent elevation of endangered taxon Ogyris halmaturia to full species status. The transition to myrmecophagy was dated to the mid‐Miocene (approximately 16 Mya), when southern Australia experienced a humid climate and extensive mesic biome. The arid Nullarbor Plain, a major biogeographical feature of central southern Australia, divides the remnants of this mesic biome into south‐eastern and south‐western isolates. Late‐Miocene to Pliocene divergence estimates for polytypic Ogyris species across the Nullarbor were older than estimates made for similarly distributed birds, butterflies, mammals, and reptiles, which mostly date to the Pleistocene. The concept of highly‐specialized life histories as evolutionary dead‐end strategies is well exemplified by the idmo‐group. Data compiled on the known extant subpopulations for idmo‐group taxa show that all of these extraordinary butterflies are scarce and several face imminent threat of extinction. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 473–484.     

The interrelationships of all major groups of Platyhelminthes: phylogenetic evidence from morphology and molecules

We used a data matrix of 65 morphological characters from 25 ingroup and 6 outgroup taxa, and an alignment comprising complete 18S rDNA sequences from 82 species of parasitic and free-living Platyhelminthes and from 19 species of lower invertebrates to analyse phylogenetic relationships of various platyhelminth taxa. Of the 1358 unambiguously alignablc molecular positions, 995 were variable and 757 were phylogenctically informative (parsimony criterion); complete 18S rDNA sequences ranged in length from 1755 to 2873 bp. Main conclusions are: Ncodermata are monophylctic, and the Trematoda, Monogenca and Cestoda within them are monophylctic as well. The sister group of the Ncodermata is all the other Ncoophora; the Kalyptorhynchia, Typhloplanida, Dalyelliida and Tcmnocephalida form one clade, and the last three another. Monophyly of the Seriata is rejected, but Polycladida/ Macrostomida/Haplopharyngida are monophylctic, as arc the last two taxa. As a consequence, validity of the taxon Trepaxonemata is rejected. Further studies must show the correct position of the Acocla and Nemertodermatida. It is stressed that morphological and molecular data in some respects lead to contradictory results, for instance concerning the position of the Fecampiidac/ Urastoma/Ichthyophaga and the relative position of the Lccithoepitheliata. Denser sampling of taxa for molecular data, complementary sequences from independent genes, and inclusion of additional morphological data are necessary to resolve these contradictions.     

Craniodental anatomy of late Oligocene archaeohyracids (Notoungulata,Mammalia) from Bolivia and Argentina and new phylogenetic hypotheses

The rich Deseadan fauna from the locality of Salla Luribay (Bolivia) documents the last occurrence of archaeohyracids, a poorly known group of small typotherian notoungulates. Exceptionally, archaeohyracid remains are extremely abundant in the Salla deposits and are assigned to a single new species Archaeohyrax suniensis sp. nov . The anatomy of the new taxon is presented and the ontogeny of the cheek teeth is described. Archaeohyrax patagonicus Ameghino, 1897 from the Deseadan of Patagonia is also redescribed and compared with the new Bolivian species. Additionally, juvenile teeth of Sallatherium altiplanense (Hegetotheriidae) are described because they provide crucial phylogenetic information for understanding the phylogeny of archaeohyracids. A cladistic analysis performed on archaeohyracids and hegetotheriids supports for the first time the existence of a clade of late archaeohyracids (post‐Mustersan), which is the sister taxon of all hegetotheriids. It also argues for the origin of mesotheriids within archaeohyracids and for the existence of a hegetotheriine clade. These conclusions fit well with temporal data known for each taxa. Nevertheless, the present analysis also underlines the fact that the lack of data concerning the cranial anatomy of many archaeohyracids (Eohyrax, Pseudhyrax, Archaeotypotherium, Protarchaeohyrax) weakens the phylogenetic signal. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 458–509.     

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.     

The articulation of annelids

The aim of this paper is to assess the monophyly of the Annelida. Also, recent cladistic analyses of metazoan taxa, using a variety of data, have shown incongruities with regards to annelids and associated taxa that should be resolved. The Platyhelminthes is selected as the taxon to root our minimal length trees and polarise our characters in a parsimony analysis; ingroup taxa being Mollusca, Nemertea, Sipuncula, Echiura, Pogonophora, Vestimentifera, Euarthropoda, Onycho-phora, and the groups most commonly regarded as true ‘annelids’, the Clitellata and Polychaeta. We use 13 characters and a total of 33 states. This results in 18 minimal length trees of 23 steps. The consensus tree has the topology (Platyhelminthes (Nemertea (Sipuncula Mollusca (Echiura (Polychaeta (Vestimcntifera Pogonophora) Clitellata (Euarthropoda Onychophora)))))). The name Articulata is applied to the Clitellata, Euarthropoda, Onychophora, Pogonophora, Polychaeta, and Vestimentifera. The Vestimentifera is the sister group to, or more likely a clade within, the frenulate pogonophores, and the name Pogonophora is retained for this group. In half of the 18 minimal length trees, the traditionally formulated Annelida, i.e. Polychaeta and Clitellata, is paraphyletic if the Pogonophora are excluded. In the remaining minimal length trees, a monophyletic Annelida cannot be formulated. The name Annelida should not be used unless relationships within the Articulata are resolved to show it is a monophyletic taxon. The taxon name Articulata, originally formulated to include the Annelida and Arthropoda by Cuvier, is defined as the clade stemming from the first ancestor to show repetition of homologous body structures derived by teloblastic growth with a pygidial growth zone (segmentation) and longitudinal muscles broken into bands. The Articulata is considered, on current evidence, to consist of four monophyletic groups; the Arthropoda, Clitellata, Polychaeta, and Pogonophora, though the latter group may be a clade of polychaetes. If this is shown, the Pogonophora should revert to the original family name Lamellisabellidae Uschakov, 1933. An indented classification reflective of the cladistic pattern is provided. Other recent hypotheses about metazoan systematics arc analysed.     

Molecular phylogeny of hinge‐beak shrimps (Decapoda: Caridea: Rhynchocinetes and Cinetorhynchus) and allies: a formal test of familiar and generic monophyly using a multilocus phylogeny

The Rhynchocinetidae (‘hinge‐beak’ shrimps) is a family of marine caridean decapods with considerable variation in sexual dimorphism, male weaponry, mating tactics, and sexual systems. Thus, this group is an excellent model with which to analyse the evolution of these important characteristics, which are of interest not only in shrimps specifically but also in animal taxa in general. Yet, there exists no phylogenetic hypothesis, either molecular or morphological, for this taxon against which to test either the evolution of behavioural traits within the Rhynchocinetidae or its genealogical relationships with other caridean taxa. In this study, we tested (1) hypotheses on the phylogenetic relationships of rhynchocinetid shrimps, and (2) the efficacy of different (one‐, two‐, and three‐phase) methods to generate a reliable phylogeny. Total genomic DNA was extracted from tissue samples taken from 17 species of Rhynchocinetidae and five other species currently or previously assigned to the same superfamily (Nematocarcinoidea); six species from other superfamilies were used as outgroups. Sequences from two nuclear genes (H3 and Enolase) and one mitochondrial gene (12S) were used to construct phylogenies. One‐phase phylogenetic analyses (SATé‐II) and classical two‐ and three‐phase phylogenetic analyses were employed, using both maximum likelihood and Bayesian inference methods. Both a two‐gene data set (H3 and Enolase) and a three‐gene data set (H3, Enolase, 12S) were utilized to explore the relationships amongst the targeted species. These analyses showed that the superfamily Nematocarcinoidea, as currently accepted, is polyphyletic. Furthermore, the two major clades recognized by the SATé‐II analysis are clearly concordant with the genera Rhynchocinetes and Cinetorhynchus, which are currently recognized in the morphological‐based classification (implicit phylogeny) as composing the family Rhynchocinetidae. The SATé‐II method is considered superior to the other phylogenetic analyses employed, which failed to recognize these two major clades. Studies using more genes and a more complete species data set are needed to test yet unresolved inter‐ and intrafamilial systematic and evolutionary questions about this remarkable clade of caridean shrimps. © 2014 The Linnean Society of London     

Phylogenetics and morphological evolution of coral‐dwelling barnacles (Balanomorpha: Pyrgomatidae)

Pyrgomatid barnacles are a family of balanomorphs uniquely adapted to symbiosis on corals. The evolution of the coral‐dwelling barnacles is explored using a multi‐gene phylogeny (COI, 16S, 12S, 18S, and H3) and phenotypic trait‐mapping. We found that the hydrocoral associate Wanella should be excluded, while some archaeobalanids in the genus Armatobalanus should be included in the Pyrgomatidae. Three well supported clades were recovered: clade I is the largest group and is exclusively Indo‐West Pacific, clade II contains two plesiomorphic Indo‐West Pacific genera, while clade III is comprised of East and West Atlantic taxa. Some genera did not form reciprocally monophyletic groups, while the genus Trevathana was found to be paraphyletic and to include members of three other apomorphic genera/tribes. The highly unusual coral‐parasitic hoekiines appear to be of recent origin and rapidly evolving from Trevathana sensu lato. Pyrgomatids include six‐, four‐, and one‐plated forms, and exhibit convergent evolutionary tendencies towards skeletal reduction and fusion, loss of cirral armature, and increased host specificity. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 162–179.