Descriptions of two new silversides, Hypoatherina golanii and Hypoatherina lunata, from the Indo-West Pacific (Atheriniformes: Atherinidae)

Two new atherinid fishes, Hypoatherina golanii and Hypoatherina lunata, are described based on specimens collected from the wide range of the Indo-West Pacific. The former species is known from the Red Sea and was confused with Hypoatherina barnesi because it has a somewhat wide midlateral band and overlapping meristic counts. Hypoatherina golanii is distinguished from its congeners by the midlateral scales with an indented posterior margin, posterior margin of anterior predorsal scales with a spatular outgrowth, posterior margin of axillary scales without a distinct projection, and posterior end of maxilla not slanted downward. Hypoatherina lunata is distributed in the waters of southern Japan (Okinawa and Kagoshima prefectures) and Indonesia (North Sulawesi, Maluku, and Papua), but was confused with Hypoatherina woodwardi. Hypoatherina lunata is distinguished from its congeners in having a distinct crescent marking in front of the eye and the anus usually situated anterior to the tip of the pelvic fin.     

Molecular phylogeny suggests polyphyly of both the turban shells (family Turbinidae) and the superfamily Trochoidea (Mollusca: Vetigastropoda)

Bayesian and parsimony phylogenetic analyses of sequence from two nuclear and two mitochondrial genes suggest that neither the molluscan superfamily Trochoidea, nor the family Turbinidae are monophyletic. The family Turbinidae s.l. divides into two main groups. The first group includes taxa previously referred to the five subfamilies Angariinae, Colloniinae, Phasianellinae, Tricoliinae, Gabrieloninae, and the liotiine genus Cinysca; these subfamilies are here recognized as Angariidae, Colloniidae, and Phasianellidae (with subfamilies Phasianellinae, Tricoliinae, and Gabrieloninae). The second group, which corresponds to Turbinidae sensu stricto, includes Prisogasterinae, Turbininae, and the liotiine genus Liotina, all of which are more closely related to trochids than they are to the first group. Several morphological studies have suggested previously that the family Phasianellidae is distinct from Turbinidae. However, this is the first study to suggest that Phasianellidae forms a group with some taxa previously thought of as turbinids, but excluding the nominotypical genus Turbo and its allies. The family Turbinidae has traditionally been described as the only family in the Vetigastropoda group that has a calcified operculum. The non-monophyly of Turbinidae suggests that calcareous opercula may have arisen independently more than once within the Vetigastropoda.     

Molecular phylogenetics of Australo-Papuan possums and gliders (family Petauridae)

Phylogenetic relationships within the possums of the family Petauridae, including their affinities with the family Pseudocheiridae, were inferred from DNA sequences obtained for the mitochondrial ND2 gene (1040 bp) combined with previously published partial 12S rDNA sequences. Short, deep internodes characterize some of the divergences obtained. The robustness of these nodes was assessed by several methods such as exclusion of taxa and partitioning of characters. In all analyses a monophyletic Pseudocheiridae was evident, whereas a monophyletic Petauridae was not as well supported. Within the Petauridae, Gymnobelideus was more closely related to Dactylopsila-Dactylonax than to Petaurus. This supports the results obtained from microcomplement fixation of albumin and DNA-DNA hybridization studies but conflicts with morphological data.     

Morphological and molecular phylogenetics in the genus Leptopilina (Hymenoptera: Cynipoidea: Eucoilidae)

We have conducted cladistic analyses of the genus Leptopilina , a group of Drosophila parasitoids studied intensively by (behavioural) ecologists. Twenty-three morphological characters were scored in ten Leptopilina and two outgroup species. At the same time, DNA sequences for the second ribosomal internal transcribed spacer (ITS2) were gathered for eight Leptopilina and one outgroup species. Both data sets yielded phylogenetic trees which were largely compatible. A 'total evidence' analysis resulted in a single tree that provides a relatively robust phylogenetic reconstruction of the group, which may serve as a basis for historically interpreting the distribution of ecological and behavioural traits.     

A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): extreme polyphyly in a group of Andean specialists

The unparalleled avian diversity of the Neotropics has long been argued to be in large part the evolutionary consequence of the incredible habitat diversity and rugged topography of the Andes mountains. Various scenarios have been proposed to explain how the Andean context could have generated lineage diversification (e.g. vicariant speciation or parapatric speciation across vertical ecological gradients), yet further study on Andean taxa is needed to reveal the relative importance of the different processes. Here we use mitochondrial and nuclear DNA sequences to derive the first phylogenetic hypothesis for Phrygilus (Sierra-Finches), one of the most species-rich genera of mainly Andean passerines. We find strong evidence that the genus is polyphyletic, comprising four distantly related clades with at least nine other genera interspersed between them (Acanthidops, Catamenia, Diglossa, Haplospiza, Idiopsar, Melanodera, Rowettia, Sicalis and Xenodacnis). These four Phrygilus clades coincide with groups previously established mainly on the basis of plumage characters, suggesting single evolutionary origins for each of these. We consider the history of diversification of each clade, analyzing the timing of splitting events, ancestral reconstruction of altitudinal ranges and current geographical distributions. Phrygilus species origins date mainly to the Pleistocene, with representatives diversifying within, out of, and into the Andes. Finally, we explored whether Phrygilus species, especially those with broad altitudinal and latitudinal Andean distributions, showed phylogeographic structure. Our best-sampled taxon (Phrygilus fruticeti) exhibited no clear pattern; however, we found deep genetic splits within other surveyed species, with Phrygilus unicolor being the most extreme case and deserving of further research.     

Molecular phylogenetics of the butterflyfishes (Chaetodontidae): taxonomy and biogeography of a global coral reef fish family

Marine butterflyfishes (10 genera, 114 species) are conspicuously beautiful and abundant animals found on coral reefs worldwide, and are well studied due to their ecological importance and commercial value. Several phylogenies based on morphological and molecular data exist, yet a well-supported molecular phylogeny at the species level for a wide range of taxa remains to be resolved. Here we present a molecular phylogeny of the butterflyfishes, including representatives of all genera (except Parachaetodon) and at least one representative of all commonly cited subgenera of Chaetodon (except Roa sensuBlum, 1988). Genetic data were collected for 71 ingroup and 13 outgroup taxa, using two nuclear and three mitochondrial genes that total 3332 nucleotides. Bayesian inference, parsimony, and maximum likelihood methods produced a well-supported phylogeny with strong support for a monophyletic Chaetodontidae. The Chaetodon subgenera Exornator and Chaetodon were found to be polyphyletic, and the genus Amphichaetodon was not the basal sister group to the rest of the family as had been previously proposed. Molecular phylogenetic analysis of data from 5 genes resolved some clades in agreement with previous phylogenetic studies, however the topology of relationships among major butterflyfish groups differed significantly from previous hypotheses. The analysis recovered a clade containing Amphichaetodon, Coradion, Chelmonops, Chelmon, Forcipiger, Hemitaurichthys, Johnrandallia, and Heniochus. Prognathodes was resolved as the sister to all Chaetodon, as in previous hypotheses, although the topology of subgeneric clades differed significantly from hypotheses based on morphology. We use the species-level phylogeny for the butterflyfishes to resolve long-standing questions regarding the use of subgenera in Chaetodon, to reconstruct molecular rates and estimated dates of diversification of major butterflyfish clades, and to examine global biogeographic patterns.     

Implications of climate change for the reproductive capacity and survival of New World silversides (family Atherinopsidae)

The New World silversides (family Atherinopsidae) are found in marine, estuarine and inland waters of North, Central and South America, where they are ecologically important as forage fishes and sometimes economically important for commercial and recreational fisheries. This report reviews the knowledge of the reproductive attributes of temperate and subtropical atherinopsids in relation to temperature and discusses the potential effects of climate change on their reproduction and adaptive responses. Their reproductive cycles are primarily entrained by photoperiod with high temperature acting as a limiting factor. They are generally multiple spawners which release successive batches of eggs in spring, but some species can spawn also in autumn and even summer when temperatures do not increase excessively. The decoupling of temperature patterns and photoperiod with further global warming and associated asymmetric thermal fluctuations could lead to spawning at times or temperatures that are unsuitable for larval development and growth. Many members of this family show temperature-dependent sex determination (TSD), where the phenotypic sex of an individual is determined partly or wholly by the temperature experienced during gonadal sex differentiation, and high-temperature induced germ cell degeneration and decreased fertility. The predicted short-term reproductive responses of atherinopsids to climate change therefore include acceleration, shortening or overall disruption of spawning activity, and also more subtle, but nonetheless equally population-threatening, dysfunctions such as highly skewed sex ratios and partial or total loss of fertility. In the case of species with TSD, asymmetric thermal fluctuations could also cause larvae to encounter temperatures lower than normal during early development and be feminized. Such dysfunctions have been documented already in natural populations but are confined so far to landlocked, inland water habitats, perhaps because they impose more severe thermal fluctuations and limitations to migration and dispersal. The severity and recurrence of these dysfunctions with further climate change will depend both on the magnitude, speed and pattern of change and on how much (or how fast) physiological and behavioural traits can evolve to match the new conditions imposed by the climate, which is largely unknown. In this regard, compelling evidence is shown that numerous traits, including the sex determination system, are capable of rapid evolution and could mitigate the negative effects of temperature increases on population viability in atherinopsids.     

Phylogenetic relationships among New Caledonian Sapotaceae (Ericales): molecular evidence for generic polyphyly and repeated dispersal

The phylogeny of a representative group of genera and species from the Sapotaceae tribe Chrysophylleae, mainly from Australia and New Caledonia, was studied by jackknife analyses of sequences of nuclear ribosomal DNA. The phylogeny conflicts with current opinions on generic delimitation in Sapotaceae. Pouteria and Niemeyera, as presently circumscribed, are both shown to be nonmonophyletic. In contrast, all species currently assigned to these and other segregate genera confined to Australia, New Caledonia, or neighboring islands, form a supported clade. Earlier classifications in which more genera are recognized may better reflect relationships among New Caledonian taxa. Hence, there is need for a revision of generic boundaries in Chrysophylleae, and particularly within the Pouteria complex, including Leptostylis, Niemeyera, Pichonia, Pouteria pro parte (the main part of section Oligotheca), and Pycnandra. Section Oligotheca have been recognized as the separate genus Planchonella, a monophyletic group that needs to be resurrected. Three clades with strong support in our jackknife analysis have one Australian species that is sister to a relatively large group of New Caledonian endemics, suggesting multiple dispersal events between this small and isolated tropical island and Australia. The phylogeny also suggests an interesting case of a relatively recent and rapid radiation of several lineages of Sapotaceae within New Caledonia.     

Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.     

Evolution of host specialization in the Adelgidae (Insecta: Hemiptera) inferred from molecular phylogenetics

The Adelgidae form a small group of insects in the Aphidoidea. They are cyclically parthenogenetic with host alternating, multiple-generation complex life cycles and are restricted to certain host genera in the Pinaceae. Species that host alternate always have Picea as the primary host where sexual reproduction and gall formation occur, and another genus in the Pinaceae as the secondary host where a series of parthenogenetic generations are produced. Other species that do not host alternate complete their entire life cycle on one host and only reproduce parthenogenetically. We studied relationships within Adelgidae using DNA sequences from the mitochondrial COI, COII, and cytb genes, and the nuclear EF1alpha gene. Analysis of the combined data resulted in a well-resolved phylogeny in which the major adelgid clades correspond neatly to their association with secondary host genera. Specialization on each secondary host genus occurred only once and was followed by diversification on the host genus. Molecular dating of divergence times in the Adelgidae suggest that diversification among host genera occurred in the Late Cretaceous and Early Tertiary when the Pinaceae genera were diverging. It is not clear, however, whether the Adelgidae and Pinaceae co-diversified because the relationships among the Pinaceae genera are not fully resolved. We discuss implications for adelgid taxonomy, life cycle evolution, and evolution of the interaction between adelgids and their host plants.     

Molecular evidence for the polyphyly of Olearia (Astereae: Asteraceae)

 Analyses of ITS sequences for 49 species of Olearia, including representatives from all currently recognised intergeneric sections, and 43 species from 23 other genera of Astereae, rooted on eight sequences from Anthemideae, provide no support for the monophyly of this large and morphologically diverse Australasian genus. Eighteen separate lineages of Olearia are recognised, including seven robust groups. Three of these groups and another eight species are placed within a primary clade incorporating representatives of Achnophora, Aster, Brachyscome, Calotis, Camptacra, Erigeron, Felicia, Grangea, Kippistia, Lagenifera, Minuria, Oritrophium, Peripleura, Podocoma, Remya, Solidago, Tetramolopium and Vittadinia. The remaining four groups and three individual species lie within a sister clade that also includes Celmisia, Chiliotrichum, Damnamenia, Pleurophyllum and Pachystegia. Relationships within each primary clade are poorly resolved. There is some congruence between this molecular estimate of the phylogeny and the distribution of types of abaxial leaf-hair, which is the basis of the present sectional classification of Olearia, but all states appear to have arisen more than once within the tribe. It is concluded that those species placed within the second primary clade should be removed from the genus, but the extent to which species placed within the first primary clade constitute a monophyletic group can only be resolved with further sequence data. Received November 12, 2001; accepted April 29, 2002 Published online: November 22, 2002 Addresses of authors: Edward W. Cross, Centre for Plant Biodiversity Research, CSIRO, GPO Box 1600, Canberra, ACT 2601, Australia (E-mail: ed.cross@csiro.au); Christopher J . Quinn, Royal Botanic Gardens, Mrs Macquaries Rd., Sydney, NSW 2000, Australia; Steven J. Wagstaff, Landcare Research, PO Box 69, Lincoln 8152, New Zealand.     

Detection of selection utilizing molecular phylogenetics: a possible approach

The neutral theory of molecular evolution (Kimura 1985) is the basis for most current statistical tests for detecting selection, mainly using polymorphism data within species, divergence data between species, and/or genomic structures like linkage disequilibrium (Wang et al. 2006). In most cases informative tests can only be constructed with ample variations within these parameters and many common tests are difficult to formulate when identity-by-descent is not clear, for example in gene families or repetitive elements. With the current progress being made toward whole-genome sequencing and re-sequencing efforts, as well as protein sequencing via tandem mass spectrometry where genomic sequencing is lacking, we felt it was necessary to re-visit possible methods for rapid screening and detection of evolutionary outliers. These outliers might be of interest for other research, such as candidate gene association studies or genome annotations, drug- and disease-target searches, and functional studies. We focused on methods that would work on both protein and nucleotide data, could be used on large gene or protein domain families, and could be generated quickly in order for “first pass” annotation of large scale data. For these reasons, we chose properties of trees generated routinely in molecular phylogenetic studies; genetic distance, tree shape and balance, and internal node statistics (Heard 1992). Our current research looking at protein domain family data and phylogenetic trees from PFAM (Finn et al. 2008) suggests this approach towards detecting evolutionary outliers is feasible, but additional work will be necessary to determine the parameters that suggest either positive or negative selection is occurring in specific gene families. This is particularly true when other factors such as rapid duplication and deletion of genes containing these domains is taking place, and we suggest phylogenetic statistics may be useful in combination with existing methodologies for detailed studies of gene family data.     

The mushroom family Psathyrellaceae: evidence for large-scale polyphyly of the genus Psathyrella

Psathyrella is the archetypal little brown mushroom genus with few easily discernable characters causing it to be considered a "clean-up" genus for other small brown-spored saprotrophic species found worldwide. While molecular studies have demonstrated that mushroom genera based on homoplastic morphological characters are artificial, the degree of phylogenetic heterogeneity contained within Psathyrella and Psathyrellaceae has never been appropriately addressed. For this study, 132 ribosomal sequences from approximately one-tenth of the known Psathyrella species worldwide, including representatives of most subgeneric subdivisions, and three closely related coprinoid genera (Parasola, Coprinopsis, Coprinellus) were evaluated using multiple phylogenetic methods, including likelihood, with Agaricaceae as the outgroup. Our results indicated that Psathyrella was polyphyletic. Conservatively, the genus can be separated into 11 clades of which five can be raised to generic status. Most species of Psathyrella, including its type species P. gracilis, formed a large clade with Coprinellus, which appeared to be derived from within Psathyrella. Generic limits of Parasola, Lacrymaria, and Coprinopsis should be reevaluated. Several taxa previously synonymized based on morphological features were phylogenetically distinct. Morphological features traditionally used to subdivide Psathyrella appeared to be mostly convergent (homoplasious) when traced upon the resulting phylogenies, although several had high RI values. These results were interpreted in light of the two major taxonomic treatments of Psathyrella and revealed substantial inconsistencies between the molecular- and morphology-derived inferences of relationships.     

Classical and molecular cytogenetics of Atherinella brasiliensis (Teleostei, Atheriniformes) from South coast of Brazil

Cytogenetic studies were performed on specimens of Atherinella brasiliensis from Laranjeiras Bay (Paraná State, Brazil). All specimens had a diploid number of 48 chromosomes, with a karyotype constituted by 4m+14sm+18st+12a and fundamental number of 84. The C-positive heterochromatin was distributed over the nucleolar organizer regions (NORs) in the centromeric regions and on short arms of metacentric and submetacentric chromosomes. Most of this heterochromatin was AT-rich, except in the NORs, which were rich in GC, as detected by double staining with chromomycin A₃/4'-6-diamin-2-phenylindole. Single NORs were located at terminal positions of a submetacentric pair, as confirmed by fluorescent in situ hybridization with 18S rDNA probes. Both techniques showed a size heteromorphism between the homologous chromosomes. The 5S rDNA clusters were located in terminal positions on two chromosomal pairs and also displayed a size heteromorphism. Despite the conserved diploid number, the data on the karyotype microstructure help characterize the cytogenetic profile of this group.     

Molecular phylogenetics reveals a pattern of biome conservatism in New World anchovies (family Engraulidae)

Evolutionary transitions between marine and freshwater biomes are relatively rare events, yielding a widespread pattern of biome conservatism among aquatic organisms. We investigated biome transitions in anchovies (Engraulidae), a globally distributed clade of economically important fishes. Most anchovy species are near-shore marine fishes, but several exclusively freshwater species are known from tropical rivers of South America and were previously thought to be the product of six or more independent freshwater invasions. We generated a comprehensive molecular phylogeny for Engraulidae, including representatives from 15 of 17 currently recognized genera. Our data support previous hypotheses of higher-level relationships within Engraulidae, but show that most New World genera are not monophyletic and in need of revision. Ancestral character reconstruction reveals that New World freshwater anchovies are the product of a single marine to freshwater transition, supporting a pattern of biome conservatism. We argue that competition is the principal mechanism that regulates aquatic biome transitions on a continental scale.     

Comparative anatomy, morphology, and molecular phylogenetics of the African genus Satanocrater (Acanthaceae)

? Premise of the study: Anatomical and morphological features of Satanocrater were studied to test hypotheses of xeric adaptations in the genus, which is endemic to arid tropical Africa. These features, together with molecular data, were used to test the phylogenetic placement of Satanocrater within the large plant family Acanthaceae. ? Methods: We undertook a comparative study of four species of Satanocrater. Carbon isotope ratios were generated to test a hypothesis of C(4) photosynthesis. Molecular data from chloroplast (trnG-trnS, trnG-trnR, psbA-trnH) and nuclear (Eif3E) loci were used to test the placement of Satanocrater within Acanthaceae. ? Key results: Anatomical features reflecting xeric adaptations of species of Satanocrater included a thick-walled epidermis, thick cuticle, abundant trichomes and glandular scales, stomata overarched by subsidiary cells, tightly packed mesophyll cells, and well-developed palisade parenchyma on both leaf surfaces. Although two species had enlarged bundle sheath cells, a feature often implicated in C(4) photosynthesis, isotope ratios indicated all species of Satanocrater use the C(3) pathway. Molecular data resolved Satanocrater within tribe Ruellieae with strong support. Within Ruellieae, our data suggest that pollen morphology of Satanocrater may represent an intermediate stage in a transition series. ? Conclusions: Anatomical and morphological features of Satanocrater reflect adaptation to xeric environments and add new information about the biology of xerophytes. Morphological and molecular data place Satanocrater in the tribe Ruellieae with confidence. This study adds to our capacity to test hypotheses of broad evolutionary and ecological interest in a diverse and important family of flowering plants.     

Historical biogeography at the crossroads of the northern continents: molecular phylogenetics of red-backed voles (Rodentia: Arvicolinae)

Evolutionary relationships of red-backed voles and their relatives were examined and used to test biogeographic hypotheses. Sequences of the mitochondrial cytochrome b gene were obtained for 25 individuals representing Alticola macrotis, Clethrionomys californicus, C. gapperi, C. glareolus, C. rutilus, and C. rufocanus. These were combined with 21 partial sequences from GenBank for C. regulus, C. rex, C. rufocanus, C. rutilus, Eothenomys imaizumii, E. melanogaster, Phaulomys andersoni, and P. smithii. Complete sequences of three species of Microtus (M. montanus, M. oeconomus, and M. pennsylvanicus), representative species of other arvicoline genera (Myopus, Synaptomys, Arvicola, Ellobius, Ondatra, Lemmus, Dicrostonyx, and Phenacomys), and a sigmodontine representative (Peromyscus) were included as outgroups. We used maximum parsimony, maximum likelihood, distance, and Bayesian based methods and conducted statistical tests on proposed hypotheses of phylogenetic relationships and biogeographic histories. A close relationship of species representing the genera Alticola, Clethrionomys, and Eothenomys was supported (Clethrionomyini); however, the genus Clethrionomys was paraphyletic with respect to both Alticola and Eothenomys. Three major clades were identified as Asian (Eothenomys andersoni, E. smithii, C. rex, C. regulus, and C. rufocanus), Trans-beringian (Alticola macrotis, C. californicus, C. gapperi, C. glarelolus, and C. rutilus), and Taiwanese (E. melanogaster). These results are consistent with the fossil record which indicates an initial diversification in Asia followed by colonization of the Nearctic on at least two occasions. The holarctic species, C. rutilus, appears to have either reinvaded Asia from North America or colonized North America more recently (late Pleistocene) than the two species of Clethrionomys (C. gapperi and C. californicus) that are endemic to North America (early to mid-Pleistocene). Finally, C. gapperi, appears to be comprised of an eastern and a western species, the former with affinities to the Asian C. glareolus and the latter more closely related to C. californicus.