Taxonomy and sexual dimorphism of a new species of Loxoconcha (Podocopida: Ostracoda) from the Pleistocene of the Japan Sea

A new ostracod, Loxoconcha kamiyai sp. nov. in the Family Loxoconchidae, is described from the Pleistocene Omma Formation of Japan. Its geological and geographical distributions suggest that this species was once endemic to the Japan Sea, where it would have evolved until the Pliocene. Since the early Pleistocene, this species would have become extinct within this marginal sea during glacial maxima, probably due to its narrower salinity tolerances and geographical distributions than those of extant species inhabiting the euryhaline environments in other seas. The distributional patterns of pore systems in this species strongly suggest its closest phylogenetic affinities to a living species, Loxocorniculum mutsuense . These two species show a unique adult sexual dimorphism in the anterior element of the hingement. Taking the female hingement morphology as a standard, the male hingement can be explained in terms of heterochrony, i.e. paedomorphosis. Sexual hingement dimorphism with paedomorphosis occurs in only one phylogenetic group of the genus Loxoconcha , which is distinguished by the ontogenetic distributional patterns of pore systems. This morphology may represent relict primitive characters of ancient ostracods and could be an important character for evaluating the history of sexual dimorphism in ostracods since the Palaeozoic.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society , 2008, 153 , 239–251.     

Testing character correlation using pairwise comparisons on a phylogeny

In comparative biology, pairwise comparisons of species or genes (terminal taxa) are used to detect character associations. For instance, if pairs of species contrasting in the state of a particular character are examined, the member of a pair with a particular state might be more likely than the other member to show a particular state in a second character. Pairs are chosen so as to be phylogenetically separate, that is, the path between members of a pair, along the branches of the tree, does not touch the path of any other pair. On a given phylogenetic tree, pairs must be chosen carefully to achieve the maximum possible number of pairs while maintaining phylogenetic separation. Many alternative sets of pairs may have this maximum number. Algorithms are developed that find all taxon pairings that maximize the number of pairs without constraint, or with the constraint that members of each pair have contrasting states in a binary character, or that they have contrasting states in two binary characters. The comparisons chosen by these algorithms, although phylogenetically separate on the tree, are not necessarily statistically independent.     

Palaeozoic roots of the sigilliid ostracods

Podocopine ostracods rapidly increased in species diversity after the Palaeozoic, and 32 out of the 36 podocopine families are extant (Whatley et al., 1993), but the phyletic origins are known for only a few. The Sigilliacea are unique in having a long and detailed fossil record. The Sigilliidae known from the recent and Mesozoic faunas differ from others ostracods in having large adductor muscle scars with many spots, a character typical rather to Palaeozoic forms. Paleozoic Microcheilinellidae were morphologically close to the sigilliids, but details of their hingement and carapace margin structures were unknown until now.Silicified specimens of Microcheilinella mendelgrammi, new species, from the Early Carboniferous of southern China and Microcheilinella mandelstami, from the Middle Devonian of north-western Poland show merodont hingement and narrow calcified inner lamella. This makes their relationship to the Mesozoic, Tertiary, and recent sigilliids Saipanetta, Cardobairdia, Sigillium, and Kasella likely. The sigilliid lineage was thus established already in the Devonian.Tubulibairdia, with adont hingement and tubulous shell wall, and Microcheilinella s. s., with merodont hingement and no tubules, are distinct genera in different families.     

Propositions for a character-state-based biological taxonomy

A new procedure for defining taxa upon a single character state is developed. It is centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’. A taxon name/definition designates a monophyletic group until one of the following assumptions is falsified: (1) the character state typified by cladotypes is homologous in individuals that are designated as cladotypes, and (2) cohesion mechanisms isolated individuals exhibiting the type‐character‐state from those that do not. A taxon defined by a character state that is found to be a combination of several character states is to be redefined upon a character state shared by its cladotypes. If several character states are available, the character state that makes the taxon the least inclusive taxon including cladotypic species (i.e., species to which belong cladotypes) is to be preferred. Taxon names designate obsolete phylogenetic hypotheses if the first assumption is falsified (such names are to be kept for this purpose, i.e., they are not to be recycled in another definition). Rules governing adaptation of previously erected names are proposed. Main cases of taxa synonymy involve definitions based on different pairs of cladotypes but referring to the same type‐character‐state; and definitions based on the same character‐state initially hypothesised as acquired by convergence in cladotypic species pairs, but later demonstrated as originating from a unique ancestor. Taxa could be synonyms if a permanent splitting event did not segregate individuals exhibiting a new character state, qualified as type‐character‐state, from individuals already assigned to a previously erected taxon. This procedure accommodates potentially any species concept, but is not tied to any; it is an extension of the composite species concept. Species are treated in a different way than other taxa: they are defined as sets of individuals belonging to the same evolving (segments of) metapopulation lineages as a holotype specimen, and do not need a defining character state.     

Ultrastructure of pigmented eyes in Dorvilleidae (Annelida,Errantia, Eunicida) and their importance for understanding the evolution of eyes in polychaetes

Among polychaetes, the errant forms are the only group known so far possessing true multicellular eyes in adults which are preceded by bicellular larval eyes in many species. Most likely, two pairs of such eyes showing a specific structure belong to the ground pattern of Errantia = Aciculata. However, these eyes have primarily been investigated in only two subgroups of Errantia, but data on the third main taxon, Eunicida, are available for only two taxa. In the present investigation, the eyes in two additional species of Eunicida, the dorvilleids Protodorvillea kefersteini and Schistomeringos neglecta, were studied. In P. kefersteini, usually described as possessing one pair of small eyes, two pairs could be detected, whereas in S. neglecta only one pair was found. Each eye is made up of rhabdomeric photoreceptor cells, pigment cells and unpigmented supportive cells. Lenses or vitreous bodies are absent. From their structure most likely all eyes represent adult eyes and even the small anterior eyes in P. kefersteini structurally resemble miniaturized adult eyes. Neither persisting larval eyes nor unpigmented rhabdomeric ocelli were found in the two species. The observations in Dorvilleidae confirm the hypothesis of a common origin of adult eyes in Errantia.     

Assessing Riparian Quality Using Two Complementary Sets of Bioindicators

Biological indicators are being increasingly used to rapidly monitor changing river quality. Among these bioindicators are macroinvertebrates. A short-coming of macroinvertebrate rapid assessments is that they use higher taxa, and therefore lack taxonomic resolution and species-specific responses. One subset of invertebrate taxa is the Odonata, which as adults, are sensitive indicators of both riparian and river conditions. Yet adult Odonata are not necessarily an umbrella taxon for all other taxa. Therefore, we investigated whether the two metrics of aquatic macroinvertebrate higher taxa and adult odonate species might complement each other, and whether together they provide better clarity on river health and integrity than one subset alone. Results indicated that both metrics provide a similar portrait of large-scale, overall river conditions. At the smaller spatial scale of parts of rivers, Odonata were highly sensitive to riparian vegetation, and much more so than macroinvertebrate higher taxa. Odonate species were more sensitive to vegetation structure than they were to vegetation composition. Landscape context is also important, with the odonate assemblages at point localities being affected by the neighbouring dominant habitat type. Overall, benthic macroinvertebrates and adult Odonata species provide a highly complementary pair of metrics which together provide large spatial scale (river system) and small spatial scale (point localities) information on the impact of stressors such as riparian invasive alien trees. As adult Odonata are easy to sample and are sensitive to disturbance at both small and large spatial scales, they are valuable indicators for rapid assessment of river condition and riparian quality.     

Ostracods of the genus Palaeocytheridea Mandelstam in the Middle and Upper Jurassic of Europe: 1. Development of ideas on the content of the genus and the results of its revision

The analysis of ostracods (Crustacea) of the genus Palaeocytheridea, widespread in the Boreal and Tethyan regions of Europe, allows establishing several correlated sequences in the Middle Jurassic of these regions, thus showing the stratigraphical significance of this genus. However M.I. Mandelstam misdescribed the hinge in carapace valves of the ostracod genus Palaeocytheridea in his characterization of the type species of P. bakirovi Mandelstam, 1947, and subsequently P.S. Lyubimova (1955) replaced the original type species by Eucythere denticulata Sharapova, 1937, thus confusing the understanding of the content of the genus Palaeocytheridea and triggering the assignment to it of more than 90 forms, belonging not only to different genera but also to different families. The revision reveals 11 valid Palaeocytheridea species, belonging to the two subgenera: Palaeocytheridea s. str. and Malzevia subgen. nov. One species, Palaeocytheridea kalandadzei sp. nov., is described as new. This paper, the first of the series of three papers dealing with ostracods of the genus Palaeocytheridea, considers the history of the development of ideas on the content of the genus, presents the results of its revision, and describes new taxa.     

Repeated convergent evolution of parthenogenesis in Acariformes (Acari)

The existence of old species‐rich parthenogenetic taxa is a conundrum in evolutionary biology. Such taxa point to ancient parthenogenetic radiations resulting in morphologically distinct species. Ancient parthenogenetic taxa have been proposed to exist in bdelloid rotifers, darwinulid ostracods, and in several taxa of acariform mites (Acariformes, Acari), especially in oribatid mites (Oribatida, Acari). Here, we investigate the diversification of Acariformes and their ancestral mode of reproduction using 18S rRNA. Because parthenogenetic taxa tend to be more frequent in phylogenetically old taxa of Acariformes, we sequenced a wide range of members of this taxon, including early‐derivative taxa of Prostigmata, Astigmata, Endeostigmata, and Oribatida. Ancestral character state reconstruction indicated that (a) Acariformes as well as Oribatida evolved from a sexual ancestor, (b) the primary mode of reproduction during evolution of Acariformes was sexual; however, species‐rich parthenogenetic taxa radiated independently at least four times (in Brachychthonioidea (Oribatida), Enarthronota (Oribatida), and twice in Nothrina (Oribatida), (c) parthenogenesis additionally evolved frequently in species‐poor taxa, for example, Tectocepheus, Oppiella, Rostrozetes, Limnozetes, and Atropacarus, and (d) sexual reproduction likely re‐evolved at least three times from species‐rich parthenogenetic clusters, in Crotonia (Nothrina), in Mesoplophora/Apoplophora (Mesoplophoridae, Enarthronota), and in Sphaerochthonius/Prototritia (Protoplophoridae, Enarthronota). We discuss possible reasons that favored the frequent diversification of parthenogenetic taxa including the continuous long‐term availability of dead organic matter resources as well as generalist feeding of species as indicated by natural variations in stable isotope ratios.     

Ontogeny and phylogeny in temnospondyls: a new method of analysis

A new method has been devised to compare the ontogeny and phylogeny of some of the better documented tetrapods from the Stephanian to the Trias. This approach is based on global parsimony analysis of several temnospondyl amphibians, in which some ontogenetic sequences have been highlighted. Forty-one homologous morphoanatomical character states have been separated into larval, juvenile and adult stages of each of six tetrapod species. The taxonomic congruence (TC) approach involves comparing trees based on larval, juvenile and adult character states. These so-called 'ontotrees' are not congruent, either in their topologies or in the distribution of the character states. The total evidence (TE) approach involves a combined analysis of all the character states observed in the various growth stages of the taxa, and is secondarily used in order to test this taxonomic incongruence. In this case, the TE result corroborates the TC analysis: the TE tree is robust and reveals a few homoplasies which cause the taxonomic incongruence. This is interpreted as either the result of heterochronic events in temnospondyl evolution, or as the product of inaccurate identification of larval and metamorphic fossil forms.     

Flower Development and the Evolution of Self-fertilization in <Emphasis Type="Italic">Amsinckia</Emphasis>: The Role of Heterochrony

We studied the development of 26 flower traits under natural conditions in three clades of the genus Amsinckia (Boraginaceae). Each clade contained both a derived highly self-fertilizing taxon and an ancestral more highly outcrossing taxon. The more outcrossing taxa contained two flower morphs—pins and thrums—with opposite positioning of the sex organs (heterostyly). The highly selfing taxa had smaller flowers with sex organs in close proximity (homostyly). Growth trajectories were quantified over the entire or nearly the entire period from primordium initiation to flower opening. These trajectories were compared in the heterochronic framework and, in contrast with previous studies, character size was tracked over time rather than relative to another character. We focused on three hypotheses: (1) The distinct developmental trajectories leading to pins and thrums should be similar in all clades, while the trajectories leading to homostylous flowers might differ among clades. This was supported. Specifically, contrasting growth rates of stamen and pistil heights in heterostylous flowers caused pin and thrum flowers to have the reciprocal arrangement of anther and stigma heights. From the viewpoint of heterochrony, the decreased size (paedomorphosis) of the homostylous morph, compared to pins and thrums, resulted from decreased growth rate (neoteny) and earlier offset (progenesis) in all clades. Nevertheless, multiple heterochronic processes were involved in the mosaic development and evolution of homostylous flowers. (2) We tested the hypothesis that small, self-fertilizing flowers have reduced development times, one of the proposed selective advantages of increased self-fertilization rates. We found in contrast that developmental duration of homostylous flowers was either the same (two clades) or longer (one clade) compared to duration of pins and thrums. (3) Finally, we tested von Baer’s Law, which proposes that developmental differences among closely related taxa should arise later in development than differences among more distantly related taxa. Von Baer’s Law was supported strongly among homostyles, moderately among thrums and weakly among pins.     

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.     

Temporal,spatial and ecological dynamics of speciation among amphi‐Beringian small mammals

Aim

Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

Location

Beringia, the nexus of the northern continents.

Methods

We used approximate Bayesian computation methods to test for simultaneous divergence among eight pairs of taxa, using cytochrome b gene sequences. We calculated coalescence times for eastern and western components of each pair and for the combined pairs, and relate dates to Quaternary climatic periodicity and combinations of environmental events and physical barriers. Population growth and expansion statistics were used to test evolutionary responses among taxa, including range shifts, persistence or periodic extirpation. Species distribution models (SDMs) for each taxon were used to predict their geographical ranges during the present interglacial, Last Glacial Maximum and previous interglacial.

Results

Multiple divergence events across Beringia were primarily coincident with extreme glacial cycles of the late Quaternary. Structure within Beringia is spatially consistent with at least three environmental barriers arising at different times: the Kolyma Uplands, Bering Strait and portions of the Bering Isthmus. Levels of divergence varied substantially, indicating evolutionary processes spanning deep and shallow time‐scales. The different demographics among taxa reflect their distinct ecological responses. SDMs predicted regional distributional changes through time and different spatial responses among taxa.

Main conclusions

Beringia predominantly constituted a dispersal corridor during the early Quaternary and a major centre of endemism in the late Quaternary. Coincident with severe glacial cycles, small mammal species were ‘caught’ in Beringia and diversified over multiple climatic phases. Relative genetic differentiation across Beringia appears to be related to ecological differences reflecting a gradual adaptation to Beringian environments through time. Some methodological constraints associated with resolving recent (late Quaternary) isolation events or drawing inferences from a single locus are discussed.     

Conserved relative timing of cranial ossification patterns in early mammalian evolution

We analyzed a comprehensive data set of ossification sequences including seven marsupial, 13 placental and seven sauropsid species. Data are provided for the first time for two major mammalian clades, Chiroptera and Soricidae, and for two rodent species; the published sequences of three species were improved with additional sampling. The relative timing of the onset of ossification in 17 cranial elements was recorded, resulting in 136 event pairs, which were treated as characters for each species. Half of these characters are constant across all taxa, 30% are variable but phylogenetically uninformative, and 19% potentially deliver diagnostic features for clades of two or more taxa. Using the conservative estimate of heterochronic changes provided by the program Parsimov, only a few heterochronies were found to diagnose mammals, marsupials, or placentals. A later onset of ossification of the pterygoid with respect to six other cranial bones characterizes therian mammals. This result may relate to the relatively small size of this bone in this clade. One change in relative onset of ossification is hypothesized as a potential human autapomorphy in the context of the sampling made: the earlier onset of the ossification of the periotic with respect to the lacrimal and to three basicranial bones. Using the standard error of scaled ranks across all species as a measure of each element's lability in developmental timing, we found that ossification of early, middle, and late events are similarly labile, with basicranial traits the most labile in timing of onset of ossification. Despite marsupials and placental mammals diverging at least 130 Ma, few heterochronic shifts in cranial ossification diagnose these clades.     

Phylogeny of Dicranophoridae (Rotifera: Monogononta) – a maximum parsimony analysis based on morphological characters

This study presents the first phylogenetic analysis of Dicranophoridae (Rotifera: Monogononta), a species rich rotifer family of about 230 species currently recognized. It is based on a maximum parsimony analysis including 77 selected ingroup and three outgroup taxa and a total of 59 phylogenetically informative morphological characters. Character coding is based on personal investigation of material collected by the authors and an extensive survey of the literature. Apart from covering general body organization, character coding primarily relies on scanning electron microscopic preparations of the mastax jaw elements. Our study suggests monophyly of Dicranophoridae with a clade of Dicranophorus and Dorria as the sister taxon of all other dicranophorid species. Monophyly of Encentrum , the most species rich genus within Dicranophoridae, cannot be demonstrated. Within Dicranophoridae our study identifies the monophyletic taxa Caudosubbasifenestrata, Intramalleata, Praeuncinata and Proventriculata, each based on unambiguous character transformations evolved in their stem lineages. However, resolution within Praeuncinata and Proventriculata is very limited. Although some terminal clades within Praeuncinata and Proventriculata are recognized, basal splits remain obscure. Probably, other characters such as DNA sequence data are needed to further our understanding of phylogenetic relationships within these poorly resolved taxa.     

NULL MODELS FOR THE NUMBER OF EVOLUTIONARY STEPS IN A CHARACTER ON A PHYLOGENETIC TREE

Random trees and random characters can be used in null models for testing phylogenetic hypothesis. We consider three interpretations of random trees: first, that trees are selected from the set of all possible trees with equal probability; second, that trees are formed by random speciation or coalescence (equivalent); and third, that trees are formed by a series of random partitions of the taxa. We consider two interpretations of random characters: first, that the number of taxa with each state is held constant, but the states are randomly reshuffled among the taxa; and second, that the probability each taxon is assigned a particular state is constant from one taxon to the next. Under null models representing various combinations of randomizations of trees and characters, exact recursion equations are given to calculate the probability distribution of the number of character state changes required by a phylogenetic tree. Possible applications of these probability distributions are discussed. They can be used, for example, to test for a panmictic population structure within a species or to test phylogenetic inertia in a character's evolution. Whether and how a null model incorporates tree randomness makes little difference to the probability distribution in many but not all circumstances. The null model's sense of character randomness appears more critical. The difficult issue of choosing a null model is discussed.     

A revision of the Afrotropical taxa of the genus Amerila Walker (Lepidoptera: Arctiidae)

This paper comprises a complete revision of the Afrotropical species of the genus Amerila ( Rhodogastria auct.), based on adult morphology. Examination of type material for most described taxa has resulted in numerous taxonomic changes. From a total of forty-seven previously described African taxa, thirty-five species including five newly described species and two new subspecies are recognized. For ten taxa, lectotypes have been selected, and for one species a neotype had to be designated. For each species, in addition to synonymy, a brief diagnosis based on external characters and genitalia is given, and the known distribution summarized. All species are illustrated by photographs and illustrations of male genitalia (except A.rufifemur , the male of which is unknown), and a key for determination of males by external characters is provided.     

Testing "species pair" hypotheses: evolutionary processes in the lichen-forming species complex Porpidia flavocoerulescens and Porpidia melinodes

Pairs of taxa are commonly found in lichen-forming ascomycetes that differ primarily in their reproductive modes: one taxon reproduces sexually, the other vegetatively. The evolutionary processes underlying such "species pairs" are unknown. The species pair formed by Porpidia flavocoerulescens (sexual) and Porpidia melinodes (vegetative) was chosen to investigate four previously proposed hypotheses. These hypotheses posit that species pairs are either two monophyletic, independently evolving species with contrasting reproductive mode; a single outcrossing species polymorphic with regard to its reproductive modes; a sexual mother lineage frequently giving rise to asexual spin-offs; or a complex of cryptic species. The phylogenetic patterns observed within the species pair in the present study were analyzed using stringent hypothesis testing and visualizations of relationships and conflict based on tree and network reconstructions. DNA sequences at the three analyzed loci revealed the same four to five deeply divergent lineages. A detailed analysis of DNA-sequence variability revealed closely linked gene loci, but high levels of conflict within each of the gene fragments, as well as between observed genetic lineages. The observed patterns of phylogenetic relationships, linkage, and conflict are not congruent with any of the previously proposed species pair hypotheses. Rather, it is proposed that the observed results can be explained by conflicting reproductive and nutritional requirements imposed by an obligate symbiotic lifestyle. These interacting constraints produce recurring selective sweeps within predominantly vegetatively reproducing lineages and are the main forces that shape the evolution within the investigated species pair.     

The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca)

Comparisons of mitochondrial gene sequences and gene arrangements can be informative for reconstructing high-level phylogenetic relationships. We determined the complete sequence of the mitochondrial genome of Siphonodentalium lobatum, (Mollusca, Scaphopoda). With only 13,932 bases, it is the shortest molluscan mitochondrial genome reported so far. The genome contains the usual 13 protein-coding genes, two rRNA and 22 tRNA genes. The ATPase subunit 8 gene is exceptionally short. Several transfer RNAs show truncated TpsiC arms or DHU arms. The gene arrangement of S. lobatum is markedly different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod. Phylogenetic analyses of all available complete molluscan mitochondrial genomes based on amino acid sequences of 11 protein-coding genes yield trees with low support for the basal branches. None of the traditionally accepted molluscan taxa and phylogenies are recovered in all analyses, except for the euthyneuran Gastropoda. S. lobatum appears as the sister taxon to two of the three bivalve species. We conclude that the deep molluscan phylogeny is probably beyond the resolution of mitochondrial protein sequences. Moreover, assessing the phylogenetic signal in gene order data requires a much larger taxon sample than is currently available, given the exceptional diversity of this character set in the Mollusca.