With no gap to mind: a shallow genealogy within the world's most widespread small pelagic fish

Species‐delimitation studies across wide geographic ranges often reveal insights that ultimately improve our understanding of biogeographic and evolutionary processes. Here we investigated species delimitation and the global coastal pelagic population structures of the marine sardine species from the economically important subgenus Sardinella (Clupeidae). The main purpose of this study was to relate morphological and genetic discontinuities to biogeography, in a taxonomic and systematic context. Morphological examinations have first reduced the currently recognized five species of the subgenus to two distinct morphospecies with parapatric relationship. Genetic analyses further showed a remarkable shallow genealogy across a global scale, yet to be encountered among small pelagic fishes. Additional three species‐delimitation analyses have failed to delimit the five putative species, indicating the possible existence of only a single cosmopolitan species with two ecophenotypic variations, thus entitling Sardinella aurita as the world's most widespread small pelagic fish. Subsequent population‐structure investigations revealed distinct geographical intraspecific sub‐divisions, flagging the West Pacific Ocean through gene‐flow computations as the probable source of future speciation for the subgenus. Considering its utmost importance to fisheries, this finding of a remarkable global genetic homogeneity should attract future attention among population geneticists and fishery researchers.     

Extreme intraspecific mitochondrial DNA sequence divergence in Galaxias maculatus (Osteichthys: Galaxiidae), one of the world's most widespread freshwater fish

Biogeographic controversies surrounding the widespread freshwater fish, Galaxias maculatus, were addressed with DNA sequence data. Mitochondrial cytochrome b and 16S rRNA sequences were obtained from representatives of six populations of this species. Substantial levels of cytochrome b (maximum 14.6%) and 16S rRNA sequence divergence (maximum 6.0%) were detected between western Pacific (Tasmania-New Zealand) and South American (Chile-Falkland Islands) haplotypes. A considerable level of divergence was also detected between Tasmanian and New Zealand haplotypes (maximum 5.1%) and within and among Chilean and Falkland Island G. maculatus (maximum 3. 8%). The phylogenetic structure of haplotypes conflicts with the accepted pattern of continental fragmentation. Molecular clock calibrations suggest that haplotype divergences postdate the fragmentation of Gondwana. These findings point to marine dispersal rather than ancient vicariance as an explanation for the wide distribution. The phylogenetic structure of South American haplotypes was not consistent with their geographic distribution. We consider factors such as population divergence, population size, dispersal, secondary contact, and philopatry as potential causes of the high level of mtDNA nucleotide diversity in this species.     

Polymorphic microsatellite loci in the widespread amphidromous goby Sicyopterus lagocephalus and cross-genus amplification among Sicydiinae

Microsatellite DNA markers were isolated in an amphidromous goby (Sicyopterus lagocephalus) from a partial genomic library enriched for AC repeats. Eight microsatellites were highly polymorphic with six to 33 alleles per locus and expected heterozygosities ranging from 0.53 to 0.97. Cross-species amplifications were performed within the sub-family Sicydiinae by genotyping individuals from two species of the genus Cotylopus. Some of these loci were successfully amplified and showed polymorphism in the second genus.     

Breeding pattern and nest guarding in Sicyopterus lagocephalus, a widespread amphidromous Gobiidae

Amphidromous gobies are usually nest spawners. Females lay a large number of small eggs under stones or onto plant stems, leaves or roots while males take care of the clutch until hatching. This study investigates the breeding pattern and paternal investment of Sicyopterus lagocephalus in a stream on Reunion Island. In February 2007 and January 2010, a total of 170 nests were found and the presence of a goby was recorded at 61 of them. The number of eggs in the nests ranged from 5,424 to 112,000 with an average number of 28,629. We showed that males accepted a single female spawning in the nest and cared for the eggs until hatching. The probability for a nest to be guarded increased with the number of eggs within it, suggesting that paternal investment depends on a trade-off between the reproductive value of the current reproduction and future nesting events. We showed that large nest stones were occupied by large males (TL >80 mm), whereas smaller males (TL <50 mm) were found under smaller cobbles, probably because of male–male competition for available nests. Our results suggest that the male’s choice relies upon a similarity to the female size, while the female’s choice was based on both body and nest stone sizes.     

Coral—the world's most diverse symbiotic ecosystem

Zooxanthellate corals (i.e. those harbouring Symbiodinium) are the main builders of the world's shallow‐water marine coral reefs. They represent intimate diverse symbioses between coral animals, single‐celled photosynthetic dinoflagellates (Symbiodinium spp.), other microscopic eukaryotes, prokaryotes and viruses. Crabs and other crustaceans, worms, sponges, bivalves and hydrozoans, fishes, sea urchins, octopuses and sea stars are itinerant members of these ‘rainforests of the sea’. This review focuses on the biodiversity of scleractinian coral animals and their best studied microscopic epi‐ and endosymbionts. In relation to coral‐associated species diversity, Symbiodinium internal transcribed spacer region sequence types tally 10²–10³ or up to ~15 different operational taxonomic units (OTUs, or putative species at the 97% sequence identity level; this cut‐off was chosen based on intragenomic sequence diversity observed in monoclonal cultures) and prokaryotes (mostly bacterial) total 10²–10⁴ OTUs. We analysed all publically accessible 16S rRNA gene sequence data and found Gammaproteobacteria were extremely abundant, followed by Alphaproteobacteria. Notably, Archaea were poorly represented and ‘unassigned OTUs’ were abundant in data generated by high‐throughput DNA sequencing studies of corals. We outline and compare model systems that could be used in future studies of the coral holobiont. In our future directions, we recommend a global coral sampling effort including substantial attention being paid to method of coral tissue acquisition, which compartments (mucus, tissue, skeleton) to explore, broadening the holobiont members considered and linking biodiversity with functional investigations.     

Reef corals of Johnston Atoll: one of the world's most isolated reefs

Johnston Atoll lies 800 km southwest of the nearest reefs of Hawaii and over 1,500 km from other shallow reefs to the south and west. Only 33 species and 16 genera and subgenera of shallow water stony corals have been reported from the atoll. Endemic species are absent despite Johnston's great age and favorable environment. With few exceptions, only species with broad geographic distribution are represented. Factors contributing to the low number of species are remoteness, the atoll's small size, lack of favorable currents to transport larvae from the southwest Pacific, lack of reef stepping stones in the region since the Cretaceous, possible defaunation during eustatic sea-level rise and fall, and possible drowning from tectonic subsidence or tilting. The species list shows strongest affinity with that of Hawaii, but some unexpected discontinuities occur. Despite low species diversity, coral coverage is extremely high in most environments.     

Avian diversity and function across the world's most populous cities

Understanding the composition of urban wildlife communities is crucial to promote biodiversity, ecosystem function and links between nature and people. Using crowdsourced data from over five million eBird checklists, we examined the influence of urban characteristics on avian richness and function at 8443 sites within and across 137 global cities. Under half of the species from regional pools were recorded in cities, and we found a significant phylogenetic signal for urban tolerance. Site-level avian richness was positively influenced by the extent of open forest, cultivation and wetlands and avian functional diversity by wetlands. Functional diversity co-declined with richness, but groups including granivores and aquatic birds occurred even at species-poor sites. Cities in arid areas held a higher percentage of regional species richness. Our results indicate commonalities in the influence of habitat on richness and function, as well as lower niche availability, and phylogenetic diversity across the world's cities.     

Is Oithona the most important copepod in the world's oceans?

Oithona has been described as the most ubiquitous and abundantcopepod in the world's oceans. Most of our knowledge of zooplanktonabundance and distribution is derived from net samples whosemesh size is often 200 µm or greater, and researchershave commented on losses of smaller organisms such as Oithonaand Oncaea, as well as juvenile forms of larger copepods, fromthese nets. We review the literature on this subject over thelast 50 years, and note that such nets remain in common usefor estimating the abundance, biomass and productivity of mesozooplankton.We show that an important fraction of mesozooplankton between200 and 800 µm in length is significantly under-representedin many current and historical data sets. A 5 year study ofthe abundance and size distribution of zooplankton biomass onthe Atlantic Meridional Transect has produced a very large dataset covering a wide range of ecosystem types across the AtlanticOcean, from subtropical oligotrophic to areas of upwelling andvernal blooming. We use these data to derive estimates of meshselection effects for commonly used nets on measures of zooplanktonabundance, biomass and secondary production, and compare theseestimates to those derived from the literature. We estimatethat the conventionalWP-2 net with a 200 µm mesh may capture<10% of conventional mesozooplankton numbers, whilst underestimatingbiomass by one-third and leading to an underestimate of secondaryproduction by two-thirds. This has serious implications forestimates of zooplankton-mediated fluxes and for the modellingof ecosystem dynamics.     

Massive gene flow across the world's most potent marine biogeographic barrier

The ''Eastern Pacific Barrier'' (EPB), 5400 km of uninterrupted deep water between the central and eastern Pacific, constitutes the greatest marine obstacle to the dispersal of shallow-water organisms. However, some species are found on both sides of the EPB. These ''transpacific'' species are considered by ''dispersal'' biogeographers as evidence of invasions through the barrier. ''Vicariance'' biogeographers, on the other hand, think that transpacific species are morphologically conservative remnants of previously continuous distributions. We compared nucleotide sequences in a 642 bp region of mitochondrial DNA, and electrophoretically detected alleles in 17 enzymatic loci of central and eastern Pacific populations of Echinothrix diadema, an Indo-Pacific sea urchin recently reported from the eastern Pacific. Both types of molecules produced clear evidence of massive, recent gene flow across the EPB. Thus, rather than being isolated relicts of Tethyan distributions, conspecific populations from the eastern and central Pacific are genetically connected. Though the EPB is biogeographically important as a cause of speciation in many groups, it allows genetic connections in others, possibly through larval transport during El Niño events.     

Molecular and chemical characterization of the most widespread Ocimum species

DNA fingerprinting (AFLP) and chemical analyses of essential oils were utilized to define the extent of variation existing in the genus Ocimum. Research was carried out on 22 Ocimum accessions representing seven species. Concerning the essential oil composition of all investigated accessions, 115 compounds were identified. UPGMA cluster analysis, based on Euclidian distances of essential oil constituents between all pairs of accessions, showed four well-supported clusters (O. tenuiflorum, O. basilicum/O. africanum, O. basilicum, and O. americanum/O. africanum). Relating to the essential oil composition of all of the investigated accessions, 17 compounds were identified as the main ones, and according to them 13 chemotypes were determined. AFLP relationships were determined by neighbor-joining (NJ) cluster analysis based on Dice??s distance matrix and by maximum parsimony (MP) analysis. O. basilicum, O. americanum/O. africanum, O. tenuiflorum, and O. gratissimum represented four clusters supported with high bootstrap values. A neighbor-net diagram allowed the visualization of apparently conflicting data by revealing relationships between genotypes and chemotypes. Concerning the O. africanum species, two distinct chemotypes, geranial/neral (accession 11) and estragol (accession 10), have been established, while all the studied O. americanum accessions belong to the geranial/neral chemotype. This could be additional evidence that O. americanum is one of the parents of O. africanum. Furthermore, the fact that the O. africanum accession (10) as well as O. basilicum ??Purpurascens?? and O. basilicum ??Erevanskii?? accessions belong to the estragol chemotype supports the theory that O. africanum is one of the parents of these two O. basilicum accessions.     

Landforms predict phylogenetic structure on one of the world's most ancient surfaces

Background  

The iconic Pilbara in northwestern Australia is an ancient geological and biophysical region that is an important zone of biodiversity, endemism and refugia. It also is overlain by some of the oldest erosion surfaces on Earth, but very little is known about the patterns of biotic diversity within the Pilbara or how they relate to the landscape. We combined phylogenetic and spatial-autocorrelation genetic analyses of mitochondrial DNA data on populations of the gekkotan lizard Lucasium stenodactylum within the Pilbara with geological, distributional and habitat data to test the hypothesis that ancient surface geology predicts current clade-habitat associations in saxicoline animals.