Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov.

Although environmental DNA surveys improve our understanding of biodiversity, interpretation of unidentified lineages is limited by the absence of associated morphological traits and living cultures. Unidentified lineages of marine stramenopiles are called “MAST clades”. Twenty‐five MAST clades have been recognized: MAST‐1 through MAST‐25; seven of these have been subsequently discarded because the sequences representing those clades were found to either (1) be chimeric or (2) affiliate within previously described taxonomic groups. Eighteen MAST clades remain without a cellular identity. Moreover, the discarded “MAST‐13” has been used in different studies to refer to two different environmental sequence clades. After establishing four cultures representing two different species of heterotrophic stramenopiles and then characterizing their morphology and molecular phylogenetic positions, we determined that the two different species represented the two different MAST‐13 clades: (1) a lorica‐bearing Bicosoeca kenaiensis and (2) a microaerophilic flagellate previously named “Cafeteria marsupialis”. Both species were previously described with only light microscopy; no cultures, ultrastructural data or DNA sequences were available from these species prior to this study. The molecular phylogenetic position of three different “C. marsupialis” isolates was not closely related to the type species of Cafeteria; therefore, we established a new genus for these isolates, Cantina gen. nov.     

Solenicola setigera is the first characterized member of the abundant and cosmopolitan uncultured marine stramenopile group MAST‐3

Culture‐independent molecular methods based on the amplification, cloning and sequencing of small‐subunit (SSU) rRNA genes are a powerful tool to study the diversity of prokaryotic and eukaryotic microorganisms for which morphological features are not conspicuous. In recent years, molecular data from environmental surveys have revealed several clades of protists lacking cultured and/or described members. Among them are various clades of marine stramenopiles (heterokonts), which are thought to play an essential ecological role as grazers, being abundant and distributed in oceans worldwide. In this work, we show that Solenicola setigera, a distinctive widespread colonial marine protist, is a member of the environmental clade MArine STramenopile 3 (MAST‐3). Solenicola is generally considered as a parasite or an epiphyte of the diatom Leptocylindrus mediterraneus. So far, the ultrastructural, morphological and ecological data available were insufficient to elucidate its phylogenetic position, even at the division or class level. We determined SSU rRNA gene sequences of S. setigera specimens sampled from different locations and seasons in the type locality, the Gulf of Lions, France. They were closely related, though not identical, which, together with morphological differences under electron microscopy, suggest the occurrence of several species. Solenicola sequences were well nested within the MAST‐3 clade in phylogenetic trees. Since Solenicola is the first identified member of this abundant marine clade, we propose the name Solenicolida for the MAST‐3 phylogenetic group.     

Morphology disentangles the systematics of a ubiquitous but elusive meiofaunal group (Kinorhyncha: Pycnophyidae)

Kinorhyncha is a group of benthic, microscopic animals distributed worldwide in marine sediments. The phylum is divided into two classes, Cyclorhagida and Allomalorhagida, congruent with the two major clades recovered in recent phylogenetic analyses. Allomalorhagida accommodates more than one‐third of the described species, most of them assigned to the family Pycnophyidae. All previous phylogenetic analyses of the phylum recovered the two genera within Pycnophyidae, Pycnophyes and Kinorhynchus, as paraphyletic and polyphyletic. A major problem in these studies was the lack of molecular data of most pycnophyids, due to the limited and highly localized distribution of most species, often in the Arctic and the deep‐sea. We here overcame the problem by adding a morphological partition with data for 79 Pycnophyidae species, 15 of them also represented by molecular data. Model‐based analyses yielded seven clades, which each was supported by several morphological apomorphies. Accordingly, Kinorhynchus is synonymized with Pycnophyes and six new genera are described for the remaining recovered clades: Leiocanthus gen. nov., Cristaphyes gen. nov., Higginsium gen. nov., Krakenella gen. nov., Setaphyes gen. nov. and Fujuriphyes gen. nov.     

Cryptic speciation along a bathymetric gradient

The deep ocean supports a highly diverse and mostly endemic fauna, yet little is known about how or where new species form in this remote ecosystem. How speciation occurs is especially intriguing in the deep sea because few obvious barriers exist that would disrupt gene flow. Geographic and bathymetric patterns of genetic variation can provide key insights into how and where new species form. We quantified the population genetic structure of a protobranch bivalve, Neilonella salicensis, along a depth gradient (2200–3800 m) in the western North Atlantic using both nuclear (28S and calmodulin intron) and mitochondrial (cytochrome c oxidase subunit I) loci. A sharp genetic break occurred for each locus between populations above 2800 m and below 3200 m, defining two distinct clades with no nuclear or mitochondrial haplotypes shared between depth regimes. Bayesian phylogenetic analyses provided strong support for two clades, separated by depth, within N. salicensis. Although no morphological divergence was apparent, we suggest that the depth‐related population genetic and phylogenetic divergence is indicative of a cryptic species. The frequent occurrence of various stages of divergence associated with species formation along bathymetric gradients suggests that depth, and the environmental gradients that attend changes in depth, probably play a fundamental role in the diversification of marine organisms, especially in deep water. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 897–913.     

Biogeographic and Quantitative Analyses of Abundant Uncultivated γ-Proteobacterial Clades from Marine Sediment

16S rRNA gene-based molecular analyses revealed the presence of several large and so far uncultivated clades within class γ-Proteobacteria, designated γ-proteobacterial marine sediment (GMS) clades 1 to 4, in marine sediment. The GMS clades appear only indigenous to marine sediment and so far have an unknown functionality. SYBR Green–based real-time PCR analyses using GMS clade-specific primers indicated GMS clades were a significant part of the bacterial community (0.3–8.7% of total 16S rRNA genes) in both polar and temperate marine sediment samples. Univariate statistical analyses indicated that GMS clade communities were indistinguishable in two temperate coastal sediment samples even though these possessed very different mean grain sizes, organic contents, and organic loading rates. GMS clade communities were slightly different (p < 0.05) between polar and temperate sites, suggesting that psychrophilic adaptation among GMS clade taxa corresponds only to subtle phylogenetic differences. Similar levels of difference were also observed through a sediment core reflecting that through the sediment core history, which spanned ∼3000 years, GMS clonal diversity shifted only marginally.     

Ecophysiological steps of marine adaptation in extant and extinct non-avian tetrapods

Marine reptiles and mammals are phylogenetically so distant from each other that their marine adaptations are rarely compared directly. We reviewed ecophysiological features in extant non-avian marine tetrapods representing 31 marine colonizations to test whether there is a common pattern across higher taxonomic groups, such as mammals and reptiles. Marine adaptations in tetrapods can be roughly divided into aquatic and haline adaptations, each of which seems to follow a sequence of three steps. In combination, these six categories exhibit five steps of marine adaptation that apply across all clades except snakes: Step M1, incipient use of marine resources; Step M2, direct feeding in the saline sea; Step M3, water balance maintenance without terrestrial fresh water; Step M4, minimized terrestrial travel and loss of terrestrial feeding; and Step M5, loss of terrestrial thermoregulation and fur/plumage. Acquisition of viviparity is not included because there is no known case where viviparity evolved after a tetrapod lineage colonized the sea. A similar sequence is found in snakes but with the haline adaptation step (Step M3) lagging behind aquatic adaptation (haline adaptation is Step S5 in snakes), most likely because their unique method of water balance maintenance requires a supply of fresh water. The same constraint may limit the maximum body size of fully marine snakes. Steps M4 and M5 in all taxa except snakes are associated with skeletal adaptations that are mechanistically linked to relevant ecophysiological features, allowing assessment of marine adaptation steps in some fossil marine tetrapods. We identified four fossil clades containing members that reached Step M5 outside of stem whales, pinnipeds, sea cows and sea turtles, namely Eosauropterygia, Ichthyosauromorpha, Mosasauroidea, and Thalattosuchia, while five other clades reached Step M4: Saurosphargidae, Placodontia, Dinocephalosaurus, Desmostylia, and Odontochelys. Clades reaching Steps M4 and M5, both extant and extinct, appear to have higher species diversity than those only reaching Steps M1 to M3, while the total number of clades is higher for the earlier steps. This suggests that marine colonizers only diversified greatly after they minimized their use of terrestrial resources, with many lineages not reaching these advanced steps. Historical patterns suggest that a clade does not advance to Steps M4 and M5 unless these steps are reached early in the evolution of the clade. Intermediate forms before a clade reached Steps M4 and M5 tend to become extinct without leaving extant descendants or fossil evidence. This makes it difficult to reconstruct the evolutionary history of marine adaptation in many clades. Clades that reached Steps M4 and M5 tend to last longer than other marine tetrapod clades, sometimes for more than 100 million years.     

Cichlid species‐area relationships are shaped by adaptive radiations that scale with area

A positive relationship between species richness and island size is thought to emerge from an equilibrium between immigration and extinction rates, but the influence of species diversification on the form of this relationship is poorly understood. Here, we show that within‐lake adaptive radiation strongly modifies the species‐area relationship for African cichlid fishes. The total number of species derived from in situ speciation increases with lake size, resulting in faunas orders of magnitude higher in species richness than faunas assembled by immigration alone. Multivariate models provide evidence for added influence of lake depth on the species‐area relationship. Diversity of clades representing within‐lake radiations show responses to lake area, depth and energy consistent with limitation by these factors, suggesting that ecological factors influence the species richness of radiating clades within these ecosystems. Together, these processes produce lake fish faunas with highly variable composition, but with diversities that are well predicted by environmental variables.     

A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column

Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra‐high‐pressure liquid chromatography coupled to high‐resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80–110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy‐GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME‐1b clades dominated. Correlation analyses suggest that the IPLs GDGT‐0, GDGT‐1, and GDGT‐2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME‐1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho‐dihexose and hexose‐glucuronic acid head groups.     

Copper toxicity response influences mesotrophic Synechococcus community structure

Picocyanobacteria from the genus Synechococcus are ubiquitous in ocean waters. Their phylogenetic and genomic diversity suggests ecological niche differentiation, but the selective forces influencing this are not well defined. Marine picocyanobacteria are sensitive to Cu toxicity, so adaptations to this stress could represent a selective force within, and between, ‘species’, also known as clades. Here, we compared Cu stress responses in cultures and natural populations of marine Synechococcus from two co‐occurring major mesotrophic clades (I and IV). Using custom microarrays and proteomics to characterize expression responses to Cu in the lab and field, we found evidence for a general stress regulon in marine Synechococcus. However, the two clades also exhibited distinct responses to copper. The Clade I representative induced expression of genomic island genes in cultures and Southern California Bight populations, while the Clade IV representative downregulated Fe‐limitation proteins. Copper incubation experiments suggest that Clade IV populations may harbour stress‐tolerant subgroups, and thus fitness tradeoffs may govern Cu‐tolerant strain distributions. This work demonstrates that Synechococcus has distinct adaptive strategies to deal with Cu toxicity at both the clade and subclade level, implying that metal toxicity and stress response adaptations represent an important selective force for influencing diversity within marine Synechococcus populations.     

ANALYSIS OF A PLASTID MULTIGENE DATA SET AND THE PHYLOGENETIC POSITION OF THE MARINE MACROALGA CAULERPA FILIFORMIS (CHLOROPHYTA)1

Molecular phylogenetic relationships within the Chlorophyta have relied heavily on rRNA data. These data have revolutionized our insight in green algal evolution, yet some class relationships have never been well resolved. A commonly used class within the Chlorophyta is the Ulvophyceae, although there is not much support for its monophyly. The relationships among the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae are also contentious. In recent years, chloroplast genome data have shown their utility in resolving relationships between the main green algal clades, but such studies have never included marine macroalgae. We provide partial chloroplast genome data (～30,000 bp, 23 genes) of the ulvophycean macroalga Caulerpa filiformis (Suhr) K. Herig. We show gene order conservation for some gene combinations and rearrangements in other regions compared to closely related taxa. Our data also revealed a pseudogene (ycf62) in Caulerpa species. Our phylogenetic results, based on analyses of a 23‐gene alignment, suggest that neither Ulvophyceae nor Trebouxiophyceae are monophyletic, with Caulerpa being more closely related to the trebouxiophyte Chlorella than to Oltmannsiellopsis and Pseudendoclonium.     

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda,Leptosomatidae)

Derycke, S., De Ley, P., De Ley, I.T., Holovachov, O., Rigaux, A. & Moens, T. (2010). Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae).—Zoologica Scripta, 39, 276–289. Recent taxonomic and population genetic studies have revealed the presence of substantial cryptic diversity through sequence analysis of nematode morphospecies classified in different major clades. Correct interpretations of intra‐ and interspecific genetic variation require certainty about the conspecificity of the sequenced specimens, which in turn must depend on appropriate protocols with built‐in verifiability procedures. In this study, we performed a population genetic study in the free‐living marine nematode Thoracostoma trachygaster, a member of one of the earliest major clades to diverge in nematode phylogeny. We collected 367 nematodes from 11 populations located in the Californian Bight, all of which were video captured before DNA extraction to document and verify their individual morphology. Sequences for the cytochrome c oxidase subunit 1 (COI), D2D3 and 18S genes showed eight deeply divergent clades, and using a reverse taxonomy approach, six of these clades proved to be other morphospecies than T. trachygaster. Phylogenetic analyses of COI, internal transcribed spacer and D2D3 showed evidence for two sympatrically distributed cryptic species within the morphospecies T. trachygaster. Population genetic analyses of the most widespread cryptic species showed a moderate genetic structuring (Φ_ST = 0.28), and 18% of this genetic variation was caused by differences between populations north and south of Point Conception. Within the southern Californian Bight, some genetic differentiation could be attributed to differences between populations north and south of Malibu, supporting the idea of a barrier to gene flow near Los Angeles region. The results for T. trachygaster support the contention that species diversity within free‐living nematodes is underestimated, and that dispersal of marine nematodes from tidal environments associated with kelp holdfasts is substantial at scales of a few 100 km.     

MITOCHONDRIAL DNA PHYLOGENY OF THE SYMBIOTIC DINOFLAGELLATES (SYMBIODINIUM,DINOPHYTA)1

Symbiotic dinoflagellates belonging to the genus Symbiodinium (Freudenthal) are found worldwide in association with shallow‐water tropical and subtropical marine invertebrates. Most phylogenetic studies of Symbiodinium have used nuclear rRNA (nrDNA) genes to infer relationships among members of the genus. In this report, we present the first phylogeny of Symbiodinium based on DNA sequences from a mitochondrial protein‐coding gene (cytochrome oxidase subunit I [cox1]). Two principal groups, one comprised of Symbiodinium clade A and the second encompassing Symbiodinium clades B/C/D/E/F, are strongly supported in the cox1 phylogeny. Relationships within Symbiodinium clades B/C/D/E/F, however, are less well resolved compared with phylogenies inferred from nrDNA and chloroplast large subunit (cp23S)‐rDNA genes. Statistical tests between alternative tree topologies verified, with an exception being the position of one controversial member of Symbiodinium clade D, that relationships inferred from cox1 are congruent with those inferred from nrDNA and cp23S‐rDNA. Taken together, the relationships between the major Symbiodinium clades are robust, and there appears to be no evidence of hybridization or differential introgression of nuclear and plastid genomes between clades.     

Evolutionary relationships among pollinators and repeated pollinator sharing in sexually deceptive orchids

The mechanism of pollinator attraction is predicted to strongly influence both plant diversification and the extent of pollinator sharing between species. Sexually deceptive orchids rely on mimicry of species‐specific sex pheromones to attract their insect pollinators. Given that sex pheromones tend to be conserved among related species, we predicted that in sexually deceptive orchids, (i) pollinator sharing is rare, (ii) closely related orchids use closely related pollinators and (iii) there is strong bias in the wasp lineages exploited by orchids. We focused on species that are pollinated by sexual deception of thynnine wasps in the distantly related genera Caladenia and Drakaea, including new field observations for 45 species of Caladenia. Specialization was extreme with most orchids using a single pollinator species. Unexpectedly, seven cases of pollinator sharing were found, including two between Caladenia and Drakaea, which exhibit strikingly different floral morphology. Phylogenetic analysis of pollinators using four nuclear sequence loci demonstrated that although orchids within major clades primarily use closely related pollinator species, up to 17% of orchids within these clades are pollinated by a member of a phylogenetically distant wasp genus. Further, compared to the total diversity of thynnine wasps within the study region, orchids show a strong bias towards exploiting certain genera. Although these patterns may arise through conservatism in the chemical classes used in sex pheromones, apparent switches between wasp clades suggest unexpected flexibility in floral semiochemical production. Alternatively, wasp sex pheromones within lineages may exhibit greater chemical diversity than currently appreciated.     

Molecular characterization of microbial communities in fault-bordered aquifers in the Miocene formation of northernmost Japan

We investigated the diversity and distribution of archaeal and bacterial 16S rRNA gene sequences in deep aquifers of mid‐ to late Miocene hard shale located in the northernmost region of the Japanese archipelago. A major fault in the north‐west–south‐east (NW–SE) direction runs across the studied area. We collected three groundwater samples from boreholes on the south‐west (SW) side of the fault at depths of 296, 374 and 625 m below ground level (m.b.g.l.) and one sample from the north‐east (NE) side of the fault at a depth of 458 m.b.g.l. The groundwater samples were observed to be neutral and weakly saline. The total microbial counts after staining with acridine orange were in the order 10⁵?10⁶ cells mL^?1 and 10³ cells mL^?1 in the aquifers to the SW and to the NE of the fault, respectively. A total of 407 archaeal and bacterial 16S rRNA gene sequences (204 and 203 sequences, respectively) were determined for clone libraries constructed from all groundwater samples. Phylogenetic analyses showed that the libraries constructed from the SW aquifers were generally coherent but considerably different from those constructed from the NE aquifer. All of the archaeal clone libraries from the SW aquifers were predominated by a single sequence closely related to the archaeon Methanoculleus chikugoensis, and the corresponding bacterial libraries were mostly predominated by the sequences related to Bacteroidetes, Firmicutes and δ‐Proteobacteria. In contrast, the libraries from the NE aquifer were dominated by uncultured environmental archaeal clones with no methanogen sequences and by β‐proteobacterial clones with no sequences related to Bacteroidetes and δ‐Proteobacteria. Hence, the possible coexistence of methanogens and sulphate reducers in Horonobe deep borehole (HDB) on the SW side is suggested, particularly in HDB‐6 (374 m.b.g.l.). Moreover, these organisms might play an important geochemical role in the groundwater obtained from the aquifers.     

Seasonal diversity and dynamics of haptophytes in the Skagerrak,Norway, explored by high‐throughput sequencing

Microalgae in the division Haptophyta play key roles in the marine ecosystem and in global biogeochemical processes. Despite their ecological importance, knowledge on seasonal dynamics, community composition and abundance at the species level is limited due to their small cell size and few morphological features visible under the light microscope. Here, we present unique data on haptophyte seasonal diversity and dynamics from two annual cycles, with the taxonomic resolution and sampling depth obtained with high‐throughput sequencing. From outer Oslofjorden, S Norway, nano‐ and picoplanktonic samples were collected monthly for 2 years, and the haptophytes targeted by amplification of RNA/cDNA with Haptophyta‐specific 18S rDNA V4 primers. We obtained 156 operational taxonomic units (OTUs), from c. 400.000 454 pyrosequencing reads, after rigorous bioinformatic filtering and clustering at 99.5%. Most OTUs represented uncultured and/or not yet 18S rDNA‐sequenced species. Haptophyte OTU richness and community composition exhibited high temporal variation and significant yearly periodicity. Richness was highest in September–October (autumn) and lowest in April–May (spring). Some taxa were detected all year, such as Chrysochromulina simplex, Emiliania huxleyi and Phaeocystis cordata, whereas most calcifying coccolithophores only appeared from summer to early winter. We also revealed the seasonal dynamics of OTUs representing putative novel classes (clades HAP‐3–5) or orders (clades D, E, F). Season, light and temperature accounted for 29% of the variation in OTU composition. Residual variation may be related to biotic factors, such as competition and viral infection. This study provides new, in‐depth knowledge on seasonal diversity and dynamics of haptophytes in North Atlantic coastal waters.     

Characterization of halotolerant Bicosoecida and Placididea (Stramenopila) that are distinct from marine forms,and the phylogenetic pattern of salinity preference in heterotrophic stramenopiles

Recent culture‐based studies demonstrate the distinctiveness of the microbial eukaryote biota of very hypersaline environments. In contrast, microscopy‐based faunistic studies suggest that the biota of habitats of more moderate hypersalinity (60–150‰) overlaps substantially with that of marine environments, but this has barely been studied with modern techniques. To investigate the diversity and salinity tolerance range of these organisms, eight cultures of heterotrophic stramenopiles were established from (or from nearby) moderately hypersaline locations. These isolates represent five independent groups; Groups A, B and C are bicosoecids; Groups D and E belong to Placididea. One isolate (Group A) is a strain of the widespread marine species Cafeteria roenbergensis, and cannot grow above 100‰ salinity. The other isolates – Groups B–E – can all grow at 150–175‰ salinities and are probably moderate halophiles. Groups B–E all represent previously unsequenced species or even genera, although Group B is the sister group of the borderline extreme halophile Halocafeteria. The high level of novelty en countered suggests that moderately hypersaline environments may harbour a heterotrophic stramenopile biota distinct from that of marine environments. Interestingly, our new isolates are all most closely related to marine or halophilic forms, and our phylogenies show large clades defined by saline/non‐saline habitats within bicosoecids, placidomonads and related lineages. In particular, most freshwater/soil bicosoecids form one well‐supported clade. The sole major exception is Bicosoeca, which is intermixed with marine environmental sequences originally referred to as ‘MAST‐13’, which are from brackish water, not typical seawater. It seems that the freshwater/marine barrier has been crossed very few times in the evolutionary history of these heterotrophic stramenopile flagellates.     

Historical biogeography of Australian Rhamnaceae, tribe Pomaderreae

Aim To discover the pattern of relationships of areas of endemism for Australian genera in the plant family Rhamnaceae tribe Pomaderreae for comparison with other taxa and interpretation of biogeographical history. Location Australian mainland, Tasmania and New Zealand. Methods A molecular phylogeny and geographic distribution of species within four clades of Pomaderreae are used as a basis for recognition of areas of endemism and analysis of area relationships using paralogy‐free subtrees. The taxon phylogeny is the strict consensus tree from a parsimony analysis of 54 taxa, in four clades, and sequence data for the internal transcribed spacer regions of ribosomal DNA (ITS1‐5.8S‐ITS2) and the plastid DNA region trnL‐F. Results The biogeographical analysis identified five subtrees, which, after parsimony analysis, resulted in a minimal tree with 100% consistency and seven resolved nodes. Three sets of area relationships were identified: the areas of Arnhem and Kimberley in tropical north Australia are related based on the phylogeny of taxa within Cryptandra; the moister South‐west of Western Australia, its sister area the coastal Geraldton Sandplains, the semi‐arid Interzone region and arid Western Desert are related, based on taxa within Cryptandra, Spyridium, Trymalium and Pomaderris; and the eastern regions of Queensland, McPherson‐Macleay, south‐eastern New South Wales (NSW), Victoria, southern Australia, Tasmania and New Zealand are related based on Cryptandra, Pomaderris and Spyridium. Tasmania and NSW are related based entirely on Cryptandra, but the position of New Zealand relative to the other south‐eastern Australian regions is unresolved. Main conclusions The method of paralogy‐free subtrees identified a general pattern of geographic area relationships based on Australian Pomaderreae. The widespread distribution of clades, the high level of endemicity and the age of fossils for the family, suggest that the Pomaderreae are an old group among the Australian flora. Their biogeographical history may date to the early Palaeogene with subsequent changes through to the Pleistocene.     

The evolution of Metriorhynchoidea (mesoeucrocodylia,thalattosuchia): an integrated approach using geometric morphometrics,analysis of disparity,and biomechanics

Metriorhynchoid crocodylians represent the pinnacle of marine specialization within Archosauria. Not only were they a major component of the Middle Jurassic–Early Cretaceous marine ecosystems, but they provide further examples that extinct crocodilians did not all resemble their modern extant relatives. Here, we use a varied toolkit of techniques, including phylogenetic reconstruction, geometric morphometrics, diversity counts, discrete character disparity analysis, and biomechanical finite‐element analysis (FEA), to examine the macroevolutionary history of this clade. All analyses demonstrate that this clade became more divergent, in terms of biodiversity, form, and function, up until the Jurassic–Cretaceous boundary, after which there is no evidence for recovery or further radiations. A clear evolutionary trend towards hypercarnivory in Dakosaurus is supported by phylogenetic character optimization, morphometrics, and FEA, which also support specialized piscivory within Rhacheosaurus and Cricosaurus. Within Metriorhynchoidea, there is a consistent trend towards increasing marine specialization, with the hypermarine Cricosaurus exhibiting numerous convergences with other Mesozoic marine reptiles (e.g. loss of the deltopectoral crest and retracted external nares). In addition, biomechanics, morphometrics, and character‐disparity analyses consistently distinguish the two newly erected metriorhynchid subfamilies. This study illustrates that together with phylogeny, quantitative assessment of diversity, form, and function help elucidate the macroevolutionary pattern of fossil clades. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 801–859.     

Tracking the history of an invasion: the freshwater croakers (Teleostei: Sciaenidae) in South America

In this study, the competing hypotheses of single vs. double colonisation events for freshwater Pachyurinae (Sciaenidae) in South America is tested and the historical biogeography of the expansion of this clade within the continent is reconstructed based on phylogenetic analysis. Parsimony and Bayesian inference (BI) for 19 marine and freshwater species assigned to Sciaenidae, Haemulidae and Polypteridae were determined based on partial sequences of the mitochondrial 16S and cytochrome b genes and fragments of the nuclear Tmo‐4C4 and rhodopsin genes. A parsimonious ancestral character reconstruction of euryhalinity was performed on a clade of families of closely related fishes to evaluate the role of ecological fitting in the colonisation of freshwater by a marine sciaenid. The parsimony and BI phylogenetic hypotheses for the concatenated sequences supported the monophyly of the freshwater Sciaenidae. Divergence of the two freshwater clades of Sciaenidae, Pachyurinae and Plagioscion, occurred within the Amazon Basin. Within Pachyurinae, two clades were recovered: one composed of species from the Amazon and the Paraná Basin and a second with representatives from the São Francisco and south‐eastern Atlantic basins. The results were compatible with the hypothesis of a single colonisation event of South American freshwater habitats by a marine lineage. The hypothesis of gradual adaptation to freshwater was rejected in favour of the hypothesis of ecological fitting. Sciaenidae, or a subordinate lineage within the family, is ancestrally capable of withstanding exposure to low‐salinity habitats, which putatively facilitated the colonisation of freshwater habitats. The subsequent diversification and expansion of Pachyurinae across South America followed this colonisation and replicated the general pattern of the area relationships of South American river basins for several other fish groups.     

Comparative experimental taphonomy of eight marine arthropods indicates distinct differences in preservation potential

Global biodiversity patterns in deep time can only be understood fully when the relative preservation potential of each clade is known. The relative preservation potential of marine arthropod clades, a diverse and ecologically important component of modern and past ecosystems, is poorly known. We tackled this issue by carrying out a 205‐day long comprehensive, comparative, taphonomic experiment in a laboratory by scoring up to ten taphonomic characters for multiple specimens of seven crustacean and one chelicerate species (two true crabs, one shrimp, one lobster, one hermit crab, one stomatopod, one barnacle and one horseshoe crab). Although the results are preliminary because we used a single experimental setup and algal growth partially hampered observations, some parts of hermit crabs, stomatopods, swimming crabs and barnacles decayed slowly relative to other parts, implying differential preservation potentials within species, largely consistent with the fossil record of these groups. An inferred parasitic isopod, manifested by a bopyriform swelling within a hermit crab carapace, decayed relatively fast. We found limited variation in the decay rate between conspecifics, and we did not observe size‐related trends in decay rate. Conversely, substantial differences in the decay rate between species were seen after c. 50 days, with shrimps and stomatopods decaying fastest, suggesting a relatively low preservation potential, whereas the lobster, calico crabs, horseshoe crabs and barnacles showed relatively slow decay rates, suggesting a higher preservation potential. These results are supported by two modern and fossil record‐based preservation potential metrics that are significantly correlated to decay rate ranks. Furthermore, we speculate that stemward slippage may not be ubiquitous in marine arthropods. Our results imply that diversity studies of true crabs, lobsters, horseshoe crabs and barnacles are more likely to yield patterns that are closer to their true biodiversity patterns than those for stomatopods, shrimps and hermit crabs.