For organisms living in the intertidal zone, temperature is an important selective agent that can shape species distributions and drive phenotypic variation among populations. Littorinid snails, which occupy the upper limits of rocky shores and estuaries worldwide, often experience extreme high temperatures and prolonged aerial emersion during low tides, yet their robust physiology--coupled with morphological and behavioral traits--permits these gastropods to persist and exert strong grazing control over algal communities. We use a mechanistic heat-budget model to compare the effects of behavioral and morphological traits on the body temperatures of five species of littorinid snails under natural weather conditions. Model predictions and field experiments indicate that, for all five species, the relative contribution of shell color or sculpturing to temperature regulation is small, on the order of 0.2-2 °C, while behavioral choices such as removing the foot from the substratum or reorienting the shell can lower body temperatures by 2-4 °C on average. Temperatures in central California rarely exceeded the thermal tolerance limits of the local littorinid species during the study period, but at sites where snails are regularly exposed to extreme high temperatures, the functional significance of the tested traits may be important. The mechanistic approach used here provides the ability to gauge the importance of behavioral and morphological traits for controlling body temperature as species approach their physiological thresholds.

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef-associated clade-the diverse and colorful Calcinus hermit crabs-to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for approximately 90% of 56 putative species, including nine undescribed,"cryptic" taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that >2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan "diversity center." Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification.

Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases.

A phylogenetic analysis of all 17 extant species of the clawed lobster genus Metanephrops based on mitochondrial 12S rRNA, 16S rRNA and cytochrome c oxidase I, and nuclear histone H3 gene sequences supports the morphological groupings of two of the traditional groups of the genus (the binghami and japonicus groups) but refutes monophyly of the other two groups (the arafurensis and thomsoni groups). The results in general support a recent morphology-based cladistic analysis of this genus except that this study suggests M. neptunus to be a basal rather than a derived species as indicated in the morphological analysis. This species is genetically diverse over its geographical range. Moreover, the two color forms of M. thomsoni are genetically distinct, most likely representing different species. The molecular phylogeny and current distribution pattern of the extant species, together with the fossil record, suggest that the genus originated in the Antarctica in the Cretaceous, followed by diversification and dispersal along the continental shelf of different continents as a result of the vicariant events associated with the breakup of the Southern Temperate Gondwana since Late Cretaceous.

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.'conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.

Comparisons among patterns exhibited by functionally distinct genetic markers have been widely used to infer the impacts of demography and selection in structuring genetic variation in natural populations. However, such multilocus comparisons remain an indirect evaluation of selection at particular candidate loci; ideally, the identification of a candidate gene by comparative genetic methodologies should be complemented by functional analyses and experimental manipulations of genotypes in the laboratory or field. We examined genotype frequency variation among replicated intertidal habitats at two spatial scales in the grazing snail Littorina obtusata. Both of the candidate allozyme markers varied predictably with environment, and these patterns were consistent at both spatial scales. Three of four reference loci were spatially homogeneous, but one microsatellite exhibited significant structure at both geographical and mesoscales. To initiate a direct examination of whether the observed genotype frequency variation at one of the candidate markers, mannose-6-phosphate isomerase (MPI), was impacted by differential survivorship of genotypes, we conducted a series of laboratory-based thermal stress assays using snails from two geographically disparate source populations. When snails were exposed to bouts of thermal/desiccation stress, patterns of mortality were nonrandom with respect to MPI genotype. Furthermore, patterns of mortality in the laboratory manipulation coincided with the observed distribution of genotypes in the field. The data suggest the operation of selection at the Mpi or a linked locus, but functional studies and further experimentation are required to establish the relationship between MPI genotype and fitness across heterogeneous intertidal environments.

The Antarctic biota is highly endemic, and the diversity and abundance of taxonomic groups differ from elsewhere in the world. Such characteristics have resulted from evolution in isolation in an increasingly extreme environment over the last 100 Myr. Studies on Antarctic species represent some of the best examples of natural selection at the molecular, structural and physiological levels. Analyses of molecular genetics data are consistent with the diversity and distribution of marine and terrestrial taxa having been strongly influenced by geological and climatic cooling events over the last 70 Myr. Such events have resulted in vicariance driven by continental drift and thermal isolation of the Antarctic, and in pulses of species range contraction into refugia and subsequent expansion and secondary contact of genetically distinct populations or sister species during cycles of glaciation. Limited habitat availability has played a major role in structuring populations of species both in the past and in the present day. For these reasons, despite the apparent simplicity or homogeneity of Antarctic terrestrial and marine environments, populations of species are often geographically structured into genetically distinct lineages. In some cases, genetic studies have revealed that species defined by morphological characters are complexes of cryptic or sibling species. Climate change will cause changes in the distribution of many Antarctic and sub-Antarctic species through affecting population-level processes such as life history and dispersal.

Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five segments), 12S rRNA, cytochrome c oxidase subunit I, histone H3 and elongation factor 1alpha. The alignment has a combined length of 3995 base positions for 36 taxa, comprising 29 Caenogastropoda representing all of its major lineages and seven outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. The results generally support monophyly of Caenogastropoda and Hypsogastropoda (Caenogastropoda excepting Architaenioglossa, Cerithioidea and Campanilioidea). Within Hypsogastropoda, maximum likelihood and Bayesian analyses identified a near basal clade of nine or 10 families lacking an anterior inhalant siphon, and Cerithiopsidae s.l.(representing Triphoroidea), where the siphon is probably derived independently from other Hypsogastropoda. The asiphonate family Eatoniellidae was usually included in the clade but was removed in one Bayesian analysis. Of the two other studied families lacking a siphon, the limpet-shaped Calyptraeidae was associated with this group in some analyses, but the tent-shaped Xenophoridae was generally associated with the siphonate Strombidae. The other studied hypsogastropods with an anterior inhalant siphon include nine families, six of which are Neogastropoda, the only traditional caenogastropod group above the superfamily-level with strong morphological support. The hypotheses that Neogastropoda are monophyletic and that the group occupies a derived position within Hypsogastropoda are both contradicted, but weakly, by the molecular analyses. Despite the addition of large amounts of new molecular data, many caenogastropod lineages remain poorly resolved or unresolved in the present analyses, possibly due to a rapid radiation of the Hypsogastropoda following the Permian-Triassic extinction during the early Mesozoic.

The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability. Members of the recA/RAD51 family have functions that have differentiated during evolution. However, the evolutionary history and relationships of these members remains unclear. Homolog searches in prokaryotes and eukaryotes indicated that most eubacteria contain only one recA. However, many archaeal species have two recA/RAD51 homologs (RADA and RADB), and eukaryotes possess multiple members (RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, XRCC3, and recA). Phylogenetic analyses indicated that the recA/RAD51 family can be divided into three subfamilies:(i) RADalpha, with highly conserved functions;(ii) RADbeta, with relatively divergent functions; and (iii) recA, functioning in eubacteria and eukaryotic organelles. The RADalpha and RADbeta subfamilies each contain archaeal and eukaryotic members, suggesting that a gene duplication occurred before the archaea/eukaryote split. In the RADalpha subfamily, eukaryotic RAD51 and DMC1 genes formed two separate monophyletic groups when archaeal RADA genes were used as an outgroup. This result suggests that another duplication event occurred in the early stage of eukaryotic evolution, producing the DMC1 clade with meiosis-specific genes. The RADbeta subfamily has a basal archaeal clade and five eukaryotic clades, suggesting that four eukaryotic duplication events occurred before animals and plants diverged. The eukaryotic recA genes were detected in plants and protists and showed strikingly high levels of sequence similarity to recA genes from proteobacteria or cyanobacteria. These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes.

In animals that have separate sexes (gonochorists), many sperm are produced to fertilise a few eggs. As the male germline undergoes more mitoses, so the accumulated mutation frequency is elevated in sperm compared with ova, and evolution is 'male-driven'. In contrast, in many hermaphroditic animals, a single organ--the ovotestis--produces both ova and sperm. Since self-renewing cells in the ovotestis may give rise to both cell types throughout life, ova in hermaphrodites could in theory have undergone as many cell divisions as sperm. Here, I consider some possible effects of the ovotestis on evolution. In particular, I hypothesise that the accumulated mutation frequency of nuclear genes in hermaphrodites (including species that change sex) may reach twice that compared with gonochorists. There may be an even greater increase in the mitochondrial mutation frequency. Further developmental studies and the accumulation of comparative data should allow hypothesis testing. If the prediction is correct, then it may provide the most-straightforward explanation for the extraordinary diversity of mitochondrial DNA in some hermaphrodites, especially molluscs.

With over 1600 extant described species, the Muricidae are one of the most species-rich and morphologically diverse families of molluscs. As predators of molluscs, polychaetes, anthozoans barnacles and other invertebrates, they form an important component of many benthic communities. Traditionally, the classification of muricids at specific and generic levels has been based primarily on shells, while subfamilies have been defined largely by radular morphology, although the composition and relationships of suprageneric groups have never been studied exhaustively. Here we present the phylogenetic relationships of 77 muricid species belonging to nine of the ten currently recognized subfamilies, based on Bayesian inference and Maximum Likelihood analyses of partial sequences of three mitochondrial (12S, 16S and COI) and one nuclear (28S) genes. The resulting topologies are discussed with respect to traditional subfamilial arrangements, and previous anatomical and molecular findings. We confirm monophyly of each of the subfamilies Ergalataxinae, Rapaninae, Coralliophilinae, Haustrinae, Ocenebrinae and Typhinae as previously defined, but earlier concepts of Muricinae, Trophoninae and Muricopsinae are shown to be polyphyletic. Based on our phylogenetic hypothesis, a new arrangement of these subfamilies is proposed.

The genus Littoraria is one of very few molluscan groups that are closely associated with mangroves. We document its global evolutionary radiation and compare biogeographic patterns with those of mangrove plants, based on phylogenetic and fossil evidence. Using sequences from three genes (nuclear 28S rRNA, mitochondrial 12S rRNA and COI) we reconstruct a phylogeny of 37 of the 39 living morphospecies. Six monophyletic subgenera are defined (Bulimilittorina, Lamellilitorina, Littoraria, Palustorina, Protolittoraria, Littorinopsis) and we synonymize L. coccinea and L. glabrata. A deep division between Palustorina from the Indo-West Pacific and Littoraria from the Atlantic and Eastern Pacific is estimated by a Bayesian relaxed-clock method to be of Middle Eocene to Palaeocene age (43.2-62.7 Ma), which far predates the Early Miocene (18 Ma) closure of the Tethyan Seaway; this, as in mangrove plants, may reflect vicariance by climatic cooling, rather than tectonic processes. The age of Littoraria angulifera in the Atlantic is, however, consistent with Early Miocene vicariance of a Tethyan ancestor. We infer that speciation events are mainly of Miocene or older age, and that diversification has not been driven by depletion of mangrove habitats during recent glacial intervals. Parsimonious reconstruction of ancestral habitats suggests that the genus has inhabited mangrove or wood substrates since its origin, while the rock-dwelling habit of the four members of Protolittoraria is derived. Three species span the Eastern Pacific Barrier, and one is amphi-Atlantic, consistent with a long larval phase of up to 10 weeks. Allopatric speciation is inferred, but usually with subsequent range overlap. Ovoviviparity (interpreted as an adaptation to life in mangroves) has arisen twice.

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.'conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.

A phylogenetic approach to the origin and maintenance of species diversity ideally requires the sampling of all species within a clade, confirmation that they are evolutionarily distinct entities, and knowledge of their geographical distributions. In the marine tropics such studies have mostly been of fish and reef-associated organisms, usually with high dispersal. In contrast, snails of the genus Echinolittorina (Littorinidae) are restricted to rocky shores, have a four-week pelagic development (and recorded dispersal up to 1400 km), and show different evolutionary patterns. We present a complete molecular phylogeny of Echinolittorina, derived from Bayesian analysis of sequences from nuclear 28S rRNA and mitochondrial 12S rRNA and COI genes (nodal support indicated by posterior probabilities, maximum likelihood, and neighbor-joining bootstrap). This consists of 59 evolutionarily significant units (ESUs), including all 50 known taxonomic species. The 26 ESUs found in the Indo-West Pacific region form a single clade, whereas the eastern Pacific and Atlantic species are basal. The earliest fossil occurred in the Tethys during the middle Eocene and we suggest that the Indo-West Pacific clade has been isolated since closure of the Tethyan seaway in the early Miocene. The geographical distributions of all species (based on more than 3700 locality records) appear to be circumscribed by barriers of low temperature, unsuitable sedimentary habitat, stretches of open water exceeding about 1400 km, and differences in oceanographic conditions on the continuum between oceanic and continental. The geographical ranges of sister species show little or no overlap, indicating that the speciation mode is predominantly allopatric. Furthermore, range expansion following speciation appears to have been limited, because a high degree of allopatry is maintained through three to five branching points of the phylogeny. This may be explained by infrequent long-distance colonization, habitat specialization on the oceanic/continental gradient, and perhaps by interspecific competition. In the eastern Pacific plus Atlantic we identify five cases of divergence on either side of the Isthmus of Panama, but our estimates of their ages pre-date the emergence of the Isthmus. There are three examples of sister relationships between species in the western Atlantic and eastern Atlantic, all resulting from dispersal to the east. Within the Indo-West Pacific, we find no geographical pattern of speciation events; narrowly endemic species of recent origin are present in both peripheral and central parts of the region. Evidence from estimated divergence times of sister species, and from a plot of the number of lineages over time, suggest that there has been no acceleration of diversification during the glacio-eustatic cycles of the Plio-Pleistocene. In comparison with reefal organisms, species of Echinolittorina on rocky shores may be less susceptible to extinction or isolation during sea-level fluctuations. The species richness of Echinolittorina in the classical biogeographic provinces conforms to the common pattern of highest diversity (11 species) in the central "East Indies Triangle" of the Indo-West Pacific, with a subsidiary focus in the eastern Pacific and western Atlantic, and lowest diversity in the eastern Atlantic. The diversity focus in the East Indies Triangle is produced by a mosaic of restricted allopatric species and overlap of a few widespread ones, and is the result of habitat specialization rather than historical vicariance. This study emphasizes the plurality of biogeographic histories and speciation patterns in the marine tropics.

The construction of a stable phylogeny for the Cestoda, indicating the interrelationships of recognised orders and other major lineages, has proceeded iteratively since the group first received attention from phylogenetic systematists. Molecular analyses using nuclear ribosomal RNA gene fragments from the small (ssrDNA) and large (lsrDNA) subunits have been used to test competing evolutionary scenarios based on morphological data but could not arbitrate between some key conflicting hypotheses. To the ribosomal data, we have added a contiguous fragment of mitochondrial (mt) genome data (mtDNA) of partial nad1-trnN-trnP-trnI-trnK-nad3-trnS-trnW-cox1-trnT-rrnL-trnC-partial rrnS, spanning 4034-4447 bp, where new data for this region were generated for 18 species. Bayesian analysis of mtDNA and rDNA as nucleotides, and where appropriate as amino acids, demonstrated that these two classes of genes provide complementary signal across the phylogeny. In all analyses, except when using mt amino acids only, the Gyrocotylidea is sister group to all other Cestoda (Nephroposticophora), and Amphilinidea forms the sister group to the Eucestoda. However, an earliest-diverging position of Amphilinidea is strongly supported in the mt amino acid analysis. Amphilinidea exhibit a unique tRNA arrangement (nad1-trnI-trnL2-trnP-trnK-trnV-trnA-trnN-nad3), whereas Gyrocotylidea shares that of the derived lineages, providing additional evidence of the uniqueness of amphilinid genes and genomes. The addition of mtDNA to the rDNA genes supported the Caryophyllidea as the sister group to (Spathebothriidea+remaining Eucestoda), a hypothesis consistently supported by morphology. This relationship suggests a history of step-wise evolutionary transitions from simple monozoic, unsegmented tapeworms to the more familiar polyzoic, externally segmented (strobilate) forms. All our data partitions recovered Haplobothriidea as the sister group to Diphyllobothriidae. The sister-group relationship between Diphyllidea and Trypanorhyncha, as previously established using rDNA, is not supported by the mt data, although it is supported by the combined mt and rDNA analysis. With regards to the more derived taxa, in all except the mt amino acid analysis, the following topology is supported:(Bothriocephalidea (Litobothriidea (Lecanicephalidea (Rhinebothriidea (Tetraphyllidea,(Acanthobothrium, Proteocephalidea),(Nippotaeniidea, Mesocestoididae, Tetrabothriidea, Cyclophyllidea)))))), where the Tetraphyllidea are paraphyletic. Evidence from the mt data provides strong (nucleotides) to moderate (amino acids) support for Tetraphyllidea forming a group to the inclusion of Proteocephalidea, with the latter consistently forming the sister group to Acanthobothrium. The interrelationships among Nippotaeniidea, Mesocestoididae, Tetrabothriidea and Cyclophyllidea remain ambiguous and require further systematic attention. Mitochondrial and nuclear rDNA data provide conflicting signal for certain parts of the cestode tree. In some cases mt data offer results in line with morphological evidence, such as the interrelationships of the early divergent lineages. Also, Tetraphyllidea, although remaining paraphyletic with the inclusion of the Proteocephalidea, does not include the most derived cestodes; a result which has consistently been obtained with rDNA.

We present the most comprehensive molecular phylogeny of bryozoans to date. Our concatenated alignment of two nuclear ribosomal and five mitochondrial genes includes 95 taxa and 13,292 nucleotide sites, of which 8297 were included. The number of new sequences generated during this project are for each gene:ssrDNA (32), lsrDNA (22), rrnL (38), rrnS (35), cox1 (37), cox3 (34), and cytb (44). Our multi-gene analysis provides a largely stable topology across the phylum. The major groups were unambiguously resolved as (Phylactolaemata (Cyclostomata (Ctenostomata, Cheilostomata))), with Ctenostomata paraphyletic. Within Phylactolaemata,(Stephanellidae, Lophopodidae) form the earliest divergent clade. Fredericellidae is not resolved as a monophyletic family and forms a clade together with Plumatellidae, Cristatellidae and Pectinatellidae, with the latter two as sister taxa. Hyalinella and Gelatinella nest within the genus Plumatella. Cyclostome taxa fall into three major clades: i.(Favosipora (Plagioecia, Rectangulata)); ii.(Entalophoroecia ((Diplosolen, Cardioecia)(Frondipora, Cancellata))); and iii.(Articulata ((Annectocyma, Heteroporidae)(Tubulipora (Tennysonia, Idmidronea)))), with suborders Tubuliporina and Cerioporina, and family Plagioeciidae each being polyphyletic. Ctenostomata is composed of three paraphyletic clades to the inclusion of Cheilostomata:((Alcyonidium, Flustrellidra)(Paludicella (Anguinella, Triticella))(Hislopia (Bowerbankia, Amathia)) Cheilostomata); Flustrellidra nests within the genus Alcyonidium, and Amathia nests within the genus Bowerbankia. Suborders Carnosa and Stolonifera are not monophyletic. Within the cheilostomes, Malacostega is paraphyletic to the inclusion of all other cheilostomes. Conopeum is the most early divergent cheilostome, forming the sister group to ((Malacostega, Scrupariina, Inovicellina)((Hippothoomorpha, Flustrina)(Lepraliomorpha, Umbonulomorpha))); Flustrina is paraphyletic to the inclusion of the hippothoomorphs; neither Lepraliomorpha nor Umbonulomorpha is monophyletic. Ascophorans are polyphyletic, with hippothoomorphs grouping separately from lepraliomorphs and umbonulomorphs; no cribrimorphs were included in the analysis. Results are discussed in the light of molecular and morphological evidence. Ancestral state reconstruction of larval strategy in Gymnolaemata revealed planktotrophy and lecithotrophy as equally parsimonious solutions for the ancestral condition. More comprehensive taxon sampling is expected to clarify this result. We discuss the extent of non-bryozoan contaminant sequences deposited in GenBank and their impact on the reconstruction of metazoan phylogenies and those of bryozoan interrelationships.

Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.

Recent molecular data strongly support the monophyly of all extant Australian and New Guinean marsupials (Eomarsupialia) to the exclusion of extant South American marsupials. This, together with available geological and fossil evidence, has been used to argue that the presence of marsupials in Australia is simply the result of a single dispersal event from South America during the latest Cretaceous or Palaeocene, without subsequent dispersals between the two continents. Here, I describe an isolated ankle bone (calcaneus) of a metatherian from the early Eocene Tingamarra Local Fauna in northeastern Australia. Strikingly, this specimen, QM F30060, lacks the 'continuous lower ankle joint pattern'(CLAJP), presence of which is a highly distinctive apomorphy of the marsupial clade Australidelphia, which includes Eomarsupialia, the living South American microbiotherian Dromiciops and the Tingamarran fossil marsupial Djarthia. Comparisons with a range of marsupials and stem-metatherians strongly suggest that the absence of the CLAJP in QM F30060 is plesiomorphic, and that this specimen represents the first unequivocal non-australidelphian ('ameridelphian') metatherian known from Australia. This interpretation is confirmed by phylogenetic analyses that place QM F30060 within (crown-group) Marsupialia, but outside Australidelphia. Based on these results, the distribution of marsupials within Gondwana cannot be explained by simply a single dispersal event from South America and Australia. Either there were multiple dispersals by marsupials (and possibly also stem-metatherians) between South America and Australia, in one or both directions, or, alternatively, there was a broadly similar metatherian fauna stretching across southern South America, Antarctica and Australia during the Late Cretaceous-early Palaeogene.

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

Recent phylogenetic analyses have demonstrated the limits of traditional coral taxonomy based solely on skeletal morphology. In this phylogenetic context, Faviidae and Mussidae are ecologically dominant families comprising one third of scleractinian reef coral genera, but their phylogenies remain partially unresolved. Many of their taxa are scattered throughout most of the clades of the Robust group, and major systematic incongruences exist. Numerous genera and species remain unstudied, and the entire biogeographic area of the Indian Ocean remains largely unsampled. In this study, we analysed a portion of the mitochondrial cytochrome c oxidase subunit 1 gene and a portion of ribosomal DNA for 14 genera and 27 species of the Faviidae and Mussidae collected from the Indian Ocean and New Caledonia and this is the first analysis of five of these species. For some taxa, newly discovered evolutionary relationships were detected, such as the evolutionary distinctiveness of Acanthastrea maxima, the genetic overlap of Parasimplastrea omanensis and Blastomussa merleti, and the peculiar position of Favites peresi in clade XVII together with Echinopora and Montastrea salebrosa. Moreover, numerous cases of intraspecific divergences between Indian Ocean and Pacific Ocean populations were detected. The most striking cases involve the genera Favites and Favia, and in particular Favites complanata, Favites halicora, Favia favus, F. pallida, F. matthai, and F. rotumana, but divergence also is evident in Blastomussa merleti, Cyphastrea serailia, and Echinopora gemmacea. High morphological variability characterizes most of these taxa, thus traditional skeletal characteristics, such as corallite arrangement, seem to be evolutionary misleading and are plagued by convergence. Our results indicate that the systematics of Faviidae and Mussidae is far from being resolved and that the inclusion of conspecific populations of different geographical origin represents an unavoidable step when redescribing the taxonomy and systematics of scleractinian corals. More molecular phylogenies are needed to define the evolutionary lineages that could be corroborated by known and newly discovered micromorphological characters.

The diversification of Indo-Pacific marine fauna has long captivated the attention of evolutionary biologists. Previous studies have mainly focused on coral reef or shallow water-associated taxa. Here, we present the first attempt to reconstruct the evolutionary history--phylogeny, diversification, and biogeography--of a deep-water lineage. We sequenced the molecular markers 16S, COI, ND1, 18S, and 28S for nearly 80% of the nominal species of the squat lobster genus Paramunida. Analyses of the molecular phylogeny revealed an accelerated diversification in the late Oligocene-Miocene followed by a slowdown in the rate of lineage accumulation over time. A parametric biogeographical reconstruction showed the importance of the southwest Pacific area, specifically the island arc of Fiji, Tonga, Vanuatu, Wallis, and Futuna, for diversification of squat lobsters, probably associated with the global warming, high tectonic activity, and changes in oceanic currents that took place in this region during the Oligocene-Miocene period. These results add strong evidence to the hypothesis that the Neogene was a period of major diversification for marine organisms in both shallow and deep waters.

The Early Cretaceous fauna of Victoria, Australia, provides unique data on the composition of high latitude southern hemisphere dinosaurs. We describe and review theropod dinosaur postcranial remains from the Aptian-Albian Otway and Strzelecki groups, based on at least 37 isolated bones, and more than 90 teeth from the Flat Rocks locality. Several specimens of medium- and large-bodied individuals (estimated up to ~8.5 metres long) represent allosauroids. Tyrannosauroids are represented by elements indicating medium body sizes (~3 metres long), likely including the holotype femur of Timimus hermani, and a single cervical vertebra represents a juvenile spinosaurid. Single specimens representing medium- and small-bodied theropods may be referrable to Ceratosauria, Ornithomimosauria, a basal coelurosaur, and at least three taxa within Maniraptora. Thus, nine theropod taxa may have been present. Alternatively, four distinct dorsal vertebrae indicate a minimum of four taxa. However, because most taxa are known from single bones, it is likely that small-bodied theropod diversity remains underestimated. The high abundance of allosauroids and basal coelurosaurs (including tyrannosauroids and possibly ornithomimosaurs), and the relative rarity of ceratosaurs, is strikingly dissimilar to penecontemporaneous dinosaur faunas of Africa and South America, which represent an arid, lower-latitude biome. Similarities between dinosaur faunas of Victoria and the northern continents concern the proportional representatation of higher clades, and may result from the prevailing temperate-polar climate of Australia, especially at high latitudes in Victoria, which is similar to the predominant warm-temperate climate of Laurasia, but distinct from the arid climate zone that covered extensive areas of Gondwana. Most dinosaur groups probably attained a near-cosmopolitan distribution in the Jurassic, prior to fragmentation of the Pangaean supercontinent, and some aspects of the hallmark 'Gondwanan' fauna of South America and Africa may therefore reflect climate-driven provinciality, not vicariant evolution driven by continental fragmentation. However, vicariance may still be detected at lower phylogenetic levels.

The geobiotic history of landscapes can exhibit controls by tectonics over biotic evolution. This causal relationship positions ecologically specialized species as biotic indicators to decipher details of landscape evolution. Phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, including fishes, can reveal key events of drainage evolution, notably where geochronological resolution is insufficient. Where geochronological resolution is insufficient, phylogeographic statistics that reconstruct spatio-temporal details of evolutionary histories of aquatic species, notably fishes, can reveal key events of drainage evolution. This study evaluates paleo-environmental causes of mitochondrial DNA (mtDNA) based phylogeographic records of tigerfishes, genus Hydrocynus, in order to reconstruct their evolutionary history in relation to landscape evolution across Africa. Strong geographical structuring in a cytochrome b (cyt-b) gene phylogeny confirms the established morphological diversity of Hydrocynus and reveals the existence of five previously unknown lineages, with Hydrocynus tanzaniae sister to a clade comprising three previously unknown lineages (Groups B, C and D) and H. vittatus. The dated phylogeny constrains the principal cladogenic events that have structured Hydrocynus diversity from the late Miocene to the Plio-Pleistocene (ca. 0-16 Ma). Phylogeographic tests reveal that the diversity and distribution of Hydrocynus reflects a complex history of vicariance and dispersals, whereby range expansions in particular species testify to changes to drainage basins. Principal divergence events in Hydrocynus have interfaced closely with evolving drainage systems across tropical Africa. Tigerfish evolution is attributed to dominant control by pulses of geotectonism across the African plate. Phylogenetic relationships and divergence estimates among the ten mtDNA lineages illustrates where and when local tectonic events modified Africa's Neogene drainage. Haplotypes shared amongst extant Hydrocynus populations across northern Africa testify to recent dispersals that were facilitated by late Neogene connections across the Nilo-Sahelian drainage. These events in tigerfish evolution concur broadly with available geological evidence and reveal prominent control by the African Rift System, evident in the formative events archived in phylogeographic records of tigerfish.

BACKGROUND Understanding the processes driving speciation in marine ecosystems remained a challenge until recently, due to the unclear nature of dispersal boundaries. However, recent evidence for marine adaptive radiations and ecological speciation, as well as previously undetected patterns of cryptic speciation is overturning this view. Here, we use multi-gene phylogenetics to infer the family-level evolutionary history of Fucaceae (intertidal brown algae of the northern Pacific and Atlantic) in order to investigate recent and unique patterns of radiative speciation in the genus Fucus in the Atlantic, in contrast with the mainly monospecific extant genera. RESULTS We developed a set of markers from 13 protein coding genes based on polymorphic cDNA from EST libraries, which provided novel resolution allowing estimation of ancestral character states and a detailed reconstruction of the recent radiative history. Phylogenetic reconstructions yielded similar topologies and revealed four independent trans-Arctic colonization events by Fucaceae lineages, two of which also involved transitions from hermaphroditism to dioecy associated with Atlantic invasions. More recently, reversion of dioecious ancestral lineages towards hermaphroditism has occurred in the genus Fucus, particularly coinciding with colonization of more extreme habitats. Novel lineages in the genus Fucus were also revealed in association with southern habitats. These most recent speciation events occurred during the Pleistocene glaciations and coincided with a shift towards selfing mating systems, generally southward shifts in distribution, and invasion of novel habitats. CONCLUSIONS Diversification of the family occurred in the Late-Mid Miocene, with at least four independent trans-Artic lineage crossings coincident with two reproductive mode transitions. The genus Fucus arose in the Pliocene but radiated within a relatively short time frame about 2.5 million years ago. Current species distributions of Fucus suggest that climatic factors promoted differentiation between the two major clades, while the recent and rapid species radiation in the temperate clade during Pleistocene glacial cycles coincided with several potential speciation drivers.

There is a long-standing debate on the extent of vicariance and long-distance dispersal events to explain the current distribution of organisms, especially in those with small diaspores potentially prone to long-distance dispersal. Age estimates of clades play a crucial role in evaluating the impact of these processes. The aim of this study is to understand the evolutionary history of the largest clade of macrolichens, the parmelioid lichens (Parmeliaceae, Lecanoromycetes, Ascomycota) by dating the origin of the group and its major lineages. They have a worldwide distribution with centers of distribution in the Neo- and Paleotropics, and semi-arid subtropical regions of the Southern Hemisphere. Phylogenetic analyses were performed using DNA sequences of nuLSU and mtSSU rDNA, and the protein-coding RPB1 gene. The three DNA regions had different evolutionary rates: RPB1 gave a rate two to four times higher than nuLSU and mtSSU. Divergence times of the major clades were estimated with partitioned BEAST analyses allowing different rates for each DNA region and using a relaxed clock model. Three calibrations points were used to date the tree: an inferred age at the stem of Lecanoromycetes, and two dated fossils: Parmelia in the parmelioid group, and Alectoria. Palaeoclimatic conditions and the palaeogeological area cladogram were compared to the dated phylogeny of parmelioid. The parmelioid group diversified around the K/T boundary, and the major clades diverged during the Eocene and Oligocene. The radiation of the genera occurred through globally changing climatic condition of the early Oligocene, Miocene and early Pliocene. The estimated divergence times are consistent with long-distance dispersal events being the major factor to explain the biogeographical distribution patterns of Southern Hemisphere parmelioids, especially for Africa-Australia disjunctions, because the sequential break-up of Gondwana started much earlier than the origin of these clades. However, our data cannot reject vicariance to explain South America-Australia disjunctions.

Scapania is a northern temperate genus with a few disjunctions in the south. Despite receiving considerable attention, the supraspecific classification of this genus remains unsatisfactorily solved. We use three molecular markers (nrITS, cpDNA trnL-F region, atpB-rbcL spacer) and 175 accessions belonging to 50 species (plus eight outgroup taxa) to estimate the phylogeny and to test current classification systems. Our data support the classification of Scapania into six rather than three subgenera, rearrangements within numerous sections, and inclusion of Macrodiplophyllum microdontum. Scapania species with a plicate perianth form three early diverging lineages; the most speciose subgenus, Scapania s.str., represents a derived clade. Most morphological species concepts are supported by the molecular topologies but classification of sect. Curtae requires further study. Southern lineages are nested in northern hemispheric clades. Palearctic-Nearctic distribution ranges are supported for several species.

Dispersal can stimulate speciation by facilitating geographical expansion across barriers or inhibit speciation by maintaining gene flow among populations. Therefore, the relationship between dispersal ability and speciation rates can be positive or negative. Furthermore, an 'intermediate dispersal' model that combines positive and negative effects predicts a unimodal relationship between dispersal and diversification. Because both dispersal ability and speciation rates are difficult to quantify, empirical evidence for the relationship between dispersal and diversification remains scarce. Using a surrogate for flight performance and a species-level DNA-based phylogeny of a large South American bird radiation (the Furnariidae), we found that lineages with higher dispersal ability experienced lower speciation rates. We propose that the degree of fragmentation or permeability of the geographical setting together with the intermediate dispersal model are crucial in reconciling previous, often contradictory findings regarding the relationship between dispersal and diversification.