Phylogeny of the ovenbird genus Upucerthia: a case of independent adaptations for terrestrial life

In view of the amount of adaptive radiation among ovenbirds, Furnariinae, the traditional taxonomy needs scrutiny. We used nuclear DNA data to study relationships of the genus Upucerthia . Five species belong in the Furnariini, as traditionally assumed. The other species represent two independent cases of specialisation for terrestrial life, in response to formation of arid habitats in the southern Andes, within the paraphyletic assemblage of arboreal species referred to as Philydorini.     

INTRAGENOMIC NUCLEOTIDE POLYMORPHISM AMONG SMALL SUBUNIT (18S) RDNA PARALOGS IN THE DIATOM GENUS SKELETONEMA (BACILLARIOPHYTA)1

Morphological features of the siliceous cell wall traditionally have been used to diagnose and classify species of diatoms, though an increasing number of studies distinguish new species, in part, by phylogenetic analysis of rDNA sequences. Intragenomic sequence variation is common among the hundreds to thousands of rDNA cistrons present within a genome, and this variation has strong potential to obscure species boundaries based on rDNA sequences. We screened six Skeletonema culture strains for intragenomic nucleotide polymorphisms in the small subunit (SSU) rDNA gene and found that all strains had polymorphic sites, with proportions ranging from 0.57% to 1.81%. In all cases, transitions accounted for more than 70% of nucleotide differences at polymorphic sites. Polymorphic sites were split nearly evenly in the SSU rRNA molecule between the base‐paired regions of helices (52%) and the unpaired regions of loops and bulges (48%). Phylogenetic analysis showed that SSU rDNA genotypes were monophyletic for two of the six culture strains examined. Genotypes from the other four culture strains either showed little or no phylogenetic structure compared with genotypes of other conspecific culture strains or had phylogenetic structure that was incongruent with existing species boundaries. Moderate to strong support for monophyly was recovered for four of the seven species included in the analysis. Phylogenetic results combined with the low sequence divergence of SSU rDNA genotypes within species suggest that concerted evolution has not proceeded to completion in these species and/or that the rate at which variation is being generated exceeds the rate at which concerted evolution is expunging variation.     

Intercontinental dispersal by a microendemic burrowing reptile (Dibamidae)

Intercontinental dispersal via land bridge connections has been important in the biogeographic history of many Holarctic plant and animal groups. Likewise, some groups appear to have accomplished trans-oceanic dispersal via rafting. Dibamid lizards are a clade of poorly known fossorial, essentially limbless species traditionally split into two geographically disjunct genera: Dibamus comprises approximately 20 Southeast Asian species, many of which have very limited geographical distributions, and the monotypic genus Anelytropsis occupies a small area of northeastern Mexico. Although no formal phylogeny of the group exists, a sister-taxon relationship between the two genera has been assumed based on biogeographic considerations. We used DNA sequence data from one mitochondrial and six nuclear protein-coding genes to construct a phylogeny of Dibamidae and to estimate divergence times within the group. Surprisingly, sampled Dibamus species form two deeply divergent, morphologically conserved and geographically concordant clades, one of which is the sister taxon of Anelytropsis papillosus. Our analyses indicate Palaearctic to Nearctic Beringian dispersal in the Late Palaeocene to Eocene. Alternatively, a trans-Pacific rafting scenario would extend the upper limit on dispersal to the Late Cretaceous. Either scenario constitutes a remarkable long-distance dispersal in what would seem an unlikely candidate.     

An inbreeding model of associative overdominance during a population bottleneck

Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situations have been considered. In the present study, associative overdominance is related to the distribution of individual inbreeding levels (i.e., genomic autozygosity). Our model integrates the effects of physical linkage and variation in inbreeding history among individual pedigrees. Hence, linkage and identity disequilibrium, traditionally presented as alternatives, are summarized within a single framework. This allows studying nonequilibrium situations in which both occur simultaneously. The model is applied to the case of an infinite population undergoing a sustained population bottleneck. The effects of bottleneck size, mating system, marker gene diversity, deleterious genomic mutation parameters, and physical linkage are evaluated. Bottlenecks transiently generate much larger associative overdominance than observed in equilibrium finite populations and represent a plausible explanation of empirical results obtained, for instance, in marine species. Moreover, the main origin of associative overdominance is random variation in individual inbreeding whereas physical linkage has little effect.     

Local ranges of phytosociological associations: are they reflected in numerical classification?

In the tradition of European phytosociology, delimitations of vegetation units such as associations are mostly based on data from small areas where more detailed vegetation sampling has been carried out. Such locally delimited vegetation units are often accepted in large-scale synthetic classifications, e.g. national vegetation monographs, and tentatively assigned to a small geographical range, forming groups of similar (vicarious) vegetation units in different small areas. These vicarious units, however, often overlap in species composition and are difficult to recognize from each other. We demonstrate this issue using an example of the classification of dry grasslands (Festuco-Brometea) in the Czech Republic. The standard vegetation classification of the Czech Republic supposes that the majority of accepted associations (66 out of 68) have a restricted distribution in one of the two major regions, Bohemia or Moravia. We compared the classification into traditional associations with the numerical classification of 1440 phytosociological relevés from the Czech Republic, in order to test whether the traditionally recognized associations with small geographical ranges are reflected in numerical classification. In various comparisons, the groups of relevés identified by numerical analysis occupied larger areas than the traditional associations. This suggests that with consistent use of total species composition as the vegetation classification criterion, the resulting classification will usually include more vegetation units with larger geographical ranges, while many of the traditional local associations will disappear.     

Manipulating flux through plant metabolic pathways

The past two years have seen a marked increase in patent applications for novel methods of altering the level and spectrum of commercially important products in plants. Results from these studies have proven surprising, showing that in many cases those enzymes traditionally thought of as flux-controlling have no impact on product formation when they are directly altered by genetic manipulation. In many cases, successful induction of increased flux throughout an entire pathway has been achieved by targeting one of the terminal enzymes in the pathway.     

Disentangling the morphological stasis in two rotifer species of the <Emphasis Type="Italic">Brachionus plicatilis</Emphasis> species complex

The taxonomic uncertainty surrounding cryptic species complexes has traditionally been resolved using lengthy experimental approaches, while, since the advent of PCR based techniques the number of cryptic species described in a variety of taxa is increasing steadily. Here we formally describe a new rotifer species of the Brachionus plicatilis complex: Brachionus manjavacas n.sp., disentangling what was known as a morphological stasis. Detailed morphological analyses demonstrated significant differences in body shape and size between B. manjavacas and B. plicatilis s.s., analysed by geometric morphometrics; unfortunately these statistical differences are not taxonomically reliable because of wide overlaps. Size and asymmetry of masticatory apparatus, named trophi, observed by SEM, gave similar results, with taxonomic ambiguity. Only the shape of small pieces of the trophi, named satellites, were consistently different between the species. On a strictly classical taxonomical basis it is absolutely useful to name new species on morphological bases, as we did, and to assess their status as distinct entities. Nevertheless, the two species are broadly similar; therefore, we do not suggest using the small differences in shape of satellites of trophi to identify the species for further ecological studies, but to continue discriminating them on genetic marker bases. Handling editor: K. Martens     

MITOCHONDRIAL DNA HOMOGENEITY IN THE PHENOTYPICALLY DIVERSE REDPOLL FINCH COMPLEX (AVES: CARDUELINAE: CARDUELIS FLAMMEA-HORNEMANNI)

Breeding redpoll finches (Aves: Carduelinae) show extensive plumage and size variability and, in many cases, a plumage polymorphism that is not related to age or sex. This has been ascribed to extreme phenotypic variation within a single taxon or to moderate variability within distinct taxa coupled with hybridization. The predominant view favors the recognition of two largely sympatric species: Carduelis flammea, comprised of four well-marked subspecies—flammea, cabaret, islandica, and rostrata; and C. hornemanni, comprised of two subspecies—hornemanni and exilipes. We studied representative samples of these putative subspecies (except islandica) for variation in mitochondrial DNA (mtDNA). Using 20 informative restriction enzymes that recognized 124 sites (642 base pairs [bp] of sequence or ≈ 3.7% of the molecule), we identified 17 RFLP haplotypes in the 31 individuals surveyed. The haplotypes formed a simple phylogenetic network with most clones diverging by a single site difference from a common haplotype found in almost half of the individuals. Within populations and taxa, levels of mtDNA diversity were similar to those observed in other avian species. The pattern of mtDNA divergence among populations was statistically unrelated to their geographic or traditional taxonomic relationships, and the estimated distance between the two traditionally recognized species was very small relative to those typically observed among avian sister species.     

Molecular characterisation and development of rapid molecular methods to identify species of Gracilariaceae from the Atlantic coast of Morocco

In Gracilariaceae, species identification is traditionally based on gross morphology; therefore the taxonomic status of terete individuals remains frequently problematic due to the lack of diagnostic characters to identify specimens. Different morphospecies have been recorded along the Atlantic coast of Morocco; however, no clear diagnostic characters were available to discriminate between terete species. Rapid molecular techniques have been developed recently to resolve many taxonomic problems and to re-assess the global diversity and biogeography in algae. In this study, molecular markers were used as DNA barcoding to characterise species. The sequence of the Rubisco spacer allowed identification of six species of Gracilariaceae: Gracilaria gracilis, Gracilaria dura, Gracilaria conferta, Gracilaria vermiculophylla, Gracilaria multipartita and Gracilariopsis longissima. In order to identify species with certainty, two simple and rapid methods based on the amplification of rDNA ITS and PCR-RFLP of the large subunit of the Rubisco were developed.     

Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System

Background

The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN) system of BOLD (Barcode of Life Datasystems), a method that supports automated, rapid species delineation and identification.

Methodology/Principal Findings

This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88%) in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93%) were found to possess diagnostic barcode sequences at the European level while only three species pairs (3%) were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads) shared BINs, while specimens from the remaining species (18%) were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies.

Conclusions/Significance

This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed regional variation of uncertain taxonomic significance.     

Two new species of Charianthus (Melastomataceae: Miconieae) from the Lesser Antilles

In the course of a phylogenetic analysis and systematic revision ofCharianthus, it was discovered thatC. purpureus, as traditionally circumscribed, is polyphyletic, consisting of three morphologically diagnosable entities. Thus two new species,Charianthus dominicensis andC. grenadensis, are described and illustrated. Each is endemic to the Lesser Antillean island for which it is named—Dominica and Grenada, respectively.Charianthus, the only vascular plant genus endemic to the Lesser Antilles, comprises six species of nectariferous, hummingbird-pollinated shrubs and small trees.     

Little evidence for sympatric speciation in island birds

It has been suggested that the presence of sister species in small circumscribed areas, such as isolated lakes or islands, might imply that these species originated sympatrically. To investigate this possibility in birds, we searched for endemic, congeneric species on isolated islands in the ocean. Among 46 islands and small archipelagos chosen because they contain at least one species of endemic land bird, we identified seven pairs of endemic congeners (excluding flightless rails). Of these seven, only four pairs are potentially sister species and thus possible candidates for sympatric speciation. However, three of these four pairs have always been considered the results of double invasion from a mainland source (in two of these cases, molecular-phylogenetic work has either confirmed a double invasion or is ambiguous). The one remaining pair may have speciated allopatrically on a small archipelago. Additional phylogenetic studies are required to understand these cases, and our results should also be considered in light of the large number of island-bird extinctions in historic time. We conclude that, at present, there is little evidence for sympatric speciation in island birds.     

ON SPECIES and OTHER TAXA

Abstract— It is argued that taxa, whether Linnaean or phylogenetic, belong to Popper's worlds 2 and 3, the worlds of knowledge, but that they represent entities residing in world 1, the world of objects, namely, classes of living beings. The Linnaean taxa are concepts, and thus untestable, whereas phylogenetic taxa are statements, the monophyletic taxa being true, and the paraphyletic and polyphyletic ones false statements. The taxa are neither strictly nor numerically universal statements, but probabilistic ones which cannot be falsified by single observations. It is suggested that the classical "species problem" is due to the fact that "species" has been used in three different senses. First, traditionally it has been assumed that the specific "essence" of an organism is that by which it is what it is. When we know the species, we know the organism. Second, the species are terminal taxa in the phylogenetic hierarchy. This implies that it is only a very small part of the "essence" of the organism which distinguishes the species. The remaining part characterizes the succession of superior taxa in the phylogenetic lineage which ends with the species in question. Third, the species has been regarded to be the "evolutionary unit." This idea may be refuted for two reasons: (1) since concepts and statements cannot evolve, species cannot evolve either, and (2) it is generally in very small isolated populations that evolutionary innovations are first established. In Linnean systematics the superior taxa are allotted categorical rank. The fact that the classification is constrained by this conventional stipulation implies that the superior taxa are often man-made artifacts. In the phylogenetic hierarchy, composed of monophyletic taxa, the ontological states of the taxa is completely independent of their numerical rank; the kingdom is as "real" as the species.     

Mitochondrial DNA coding region sequences support the phylogenetic distinction of two Indian wolf species

Two small endangered populations of Indian wolves were recently shown to be distant from other wolf and dog mtDNA lineages characterized so far. None of the inner branches in the tree of canid species based on partial hypervariable D-loop sequences were, however, statistically supported by the data raising the question whether the two Indian wolf lineages represent two new species, occupying an intermediate position between Canis latrans and C. lupus or have diverged from the sub-species of C. lupus due to isolation and drift. Here we report complete D-loop, cytochrome b, and 16S rRNA sequences data for 23 additional wolves from India analysed in the context of other canid species. Extended analyses of D-loop data and partial sequences of 16S rRNA showed highly reticulated pattern and were unable to resolve unambiguously the phylogenetic relationship of Indian wolves among other canid species. The phylogenetic reconstructions of cytochrome b sequences, however gave significant statistical support for the inner branches supporting genetic distinction of the two Indian wolf lineages within themselves as well as from all other wolves of the world, including individuals belonging to subspecies C. lupus chanco and C. lupus pallipes to which the two Indian wolf populations have been traditionally assigned. Their genetic differentiation relative to worldwide variation of wolves supports the suggestion to treat them as separate wolf species, C. himalayensis and C. indica .     

Genetic differentiation and phylogeographical structure of the Brachionus calyciflorus complex in eastern China

Spatio-temporal patterns and processes of genetic differentiation in passively dispersing zooplankton are drawing much attention from both ecologists and evolutionary biologists. Two opposite phylogeographical scenarios have already been demonstrated in rotifers, which consist of high levels of genetic differentiation among populations even on small geographical scales on the one hand and the traditionally known cosmopolitanism that is associated with high levels of gene flow and long-distance dispersal via diapausing stages on the other hand. Here, we analysed the population genetic structure and the phylogeography of the Brachionus calyciflorus species complex in eastern China. By screening a total of 318 individuals from ten locations along a 2320-km gradient and analysing samples from two growing seasons, we aimed at focusing on both small- and large-scale patterns. We identified eight cryptic species and verified species status of two of these by sexual reproduction tests. Samples in summer and winter yielded different cryptic species. The distribution patterns of these genetically distinct cryptic species were diverse across eastern China, from full cosmopolitanism to local endemism. The two most abundant cryptic species BcWIII and BcSW showed a pattern of strong genetic differentiation among populations and no significant isolation by distance. Long-distance colonization, secondary contact and recent range expansion are probably responsible for the indistinct pattern of isolation by distance. Our results suggest that geographical distance is more important than temporal segregation across seasons in explaining population differentiation and the occurrence of cryptic species. We explain the current phylogeographical structure in the B. calyciflorus species complex by a combination of recent population expansion, restricted gene flow, priority effects and long-distance colonization.     

Phylogeny of the water strider genus Rheumatobates (Heteroptera: Gerridae)

The genus Rheumatobates comprises thirty‐seven species and subspecies of New World water striders belonging to subfamily Rhagadotarsinae. Among species, males vary dramatically in the degree and nature of modifications of the antennae, three pairs of legs and abdominal and genital segments. Characters describing this modification have traditionally been used to differentiate and group species. The general assumption has been that modified species belong to one group and unmodified species to another. These two ‘species groups’ are subdivided into ‘subgroups’, but little effort has been made to resolve relationships among them. We conduct the first numerical cladistic analysis of Rheumatobates using a data set comprised of 102 characters, primarily describing modification of male external morphology. To address concerns about the inclusion of characters to be optimized on the phylogeny, characters describing modification of antennae and hind legs were included and then excluded in separate analyses. A preferred phylogeny was chosen from the four equally parsimonious cladograms found after successive reweighting of characters. There was good resolution at all levels of the phylogeny. Most of the major clades and terminal relationships were moderately to strongly supported, whereas the basal relationships were less well supported. The general assumption that unmodified and modified species form two monophyletic groups was not supported. However, traditionally recognized ‘subgroups’ within the modified species group were largely upheld. The analysis also suggested several major clades and relationships among these clades that were not previously recognized. The exclusion of characters describing modification of antennae and hind legs did not change the resolved major clades of the reconstructed phylogeny.     

Landscape configuration and diversity hotspots in wintering sparrows

Community-level studies with finches have traditionally viewed local resources as the primary constrainst on local diversity. Patches have been considered to be self-contained and embedded in landscapes that were neutral with respect to the ecological processes under investigation. This study uses a factorial design to examine the relative roles of patch content and patch context in determining patterns of species richness. Sparrows were surveyed in small fallow patches that varied in both weed cover and the type of adjacent habitat. Species richness and total sparrow abundance were significantly influenced by both factors. Individual species were also influnced by both factors; however, responses were species-specific. Because occupation of particular plot types was conditional on their association with specific habitat types, the spatial patterning of species assemblages results from the configuration of patch types within the landscape.     

Morphology and molecular phylogeny of Pseudotrichonympha hertwigi and Pseudotrichonympha paulistana (Trichonymphea, parabasalia) from neotropical rhinotermitids

Pseudotrichonympha is a large hypermastigote parabasalian found in the hindgut of several species of rhinotermitid termites. The genus was discovered more than 100 years ago, and although over a dozen species have since been described, this represents only a small fraction of its likely diversity: the termite genera from which Pseudotrichonympha is known are all species rich, and in most cases their hindgut symbionts have not been examined. Even formally described species are mostly lacking in detailed microscopic data and/or sequence data. Using small subunit ribosomal RNA gene sequences and light and scanning electron microscopy we describe here the morphology and molecular phylogenetic position of two Pseudotrichonympha species: the type species for the genus, Pseudotrichonympha hertwigi from Coptotermes testaceus (described previously in line drawing only), and Pseudotrichonympha paulistana from Heterotermes tenuis (described previously based on light microscopy only).     

Body temperature patterns in two syntopic elephant shrew species during winter

We measured body temperature (T_b) in free-ranging individuals of two species of elephant shrews, namely western rock elephant shrews (Elephantulus rupestris) and Cape rock elephant shrews (E. edwardii), during winter in a winter-rainfall region of western South Africa. These syntopic species have similar ecologies and morphologies and thus potential for large overlaps in diet and habitat use. Unexpectedly, they displayed different T_b patterns. Western rock elephant shrews were heterothermic, with all individuals decreasing T_b below 30 °C on at least 34% of nights. The level of heterothermy expressed was similar to other species traditionally defined as daily heterotherms and was inversely related to T_a, as is commonly seen in small heterothermic endotherms. In contrast, Cape rock elephant shrews rarely allowed their T_b to decrease below 30 °C. The level of heterothermy was similar to species traditionally defined as homeotherms and there was no relationship between the level of heterothermy expressed and T_a. In both species, the minimum daily T_b was recorded almost exclusively at night, often shortly before sunrise, although in some individuals minimum T_b occasionally occurred during the day. The interspecific variation in T_b patterns among Elephantulus species recorded to date reiterates the importance of ecological determinants of heterothermy that interact with factors such as body mass and phylogeny.