Length–weight relationships of cryptic reef fishes from the southwestern Gulf of California, Mèxico

Length–weight relationships of 33 cryptic reef fishes from the southwestern Gulf of California were estimated. The most common families were Gobiidae (seven species), Labrisomidae (four), Pomacentridae (three), and Tripterygiidae (three). These are the first length–weight parameters reported for 32 of these species. Specimens were sampled during a comparative ecological study of community structure of fish assemblages associated with coral heads, rocky walls, and artificial reefs in Bahía de La Paz, Baja California Sur. The b values varied between 2.63 and 3.61. New maximum length records for five of the species were established in the study.     

Phosphoglucose isomerase isozymes in teleostean fishes from the Arabian Gulf

Two phosphoglucose isomerases (PGI) with different electrophoretic mobilities have been found in all groups of teleostean fishes studied, with the exception of the Clupeomorpha. PGI proved to be a good taxonomic criterion to differentiate members of the Nemipteridae, Sciaenidae, Platycephalidae and Stromateidae from the other teleost families.     

Comparative electrophoretic studies of muscle, eye lens and heart protein in fishes from the Arabian Gulf

Muscle myogen, eye lens and heart protein have been studied in 31 species of fishes from Kuwait, Arabian Gulf. The electrophoretic analysis revealed that muscle myogen can be considered a good taxonomic criterion to differentiate the families Ariidae, Belonidae and Lutjanidae from the other fish families studied. Within the Lutjanidae and Pomadasyidae the muscle myogens can be used to differentiate Lutjanus kasmira and Pomadasys argenteus, respectively. The muscle myogens can also be used to differentiate Sardinella perforata, Platycephalus inducus, Drepane longemana and Psethodes erumei. Eye lens protein can be considered a good taxonomic criterion to differentiate between the fish species studied and especially among the families Belonidae, Lutjanidae, Pomadsyidae, Sparidae and Scaenidae. Within the Lutjanidae and Sparidae, the eye lens protein can be used to differentiate Lutjanus kasmira and Acanthopagrus berda, respectively. Heart protein is not considered a good taxonomic criterion to differentiate the species of fishes studied, but can distinguish Lutjanus coccineus from the remaining species studied.     

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo–West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes– Bayesian PTP (PTP–bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.     

Comparative phylogeography of Atlantic reef fishes indicates both origin and accumulation of diversity in the Caribbean

Background  

Two processes may contribute to the formation of global centers of biodiversity: elevated local speciation rates (the center of origin hypothesis), and greater accumulation of species formed elsewhere (the center of accumulation hypothesis). The relative importance of these processes has long intrigued marine biogeographers but rarely has been tested.     

Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages

Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l. elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l. elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted.     

Brachiopods from cryptic coral reef habitats in the northern Red Sea

In contrast to the Palaeozoic to Jurassic fossil record, modern tropical and subtropical shallow-water brachiopods are typically small-sized and mostly restricted to cryptic habitats in coral reefs, but information on microhabitat-composition is scant. At Dahab, northern Red Sea, living brachiopods of the genus Argyrotheca were only detected on massively encrusted coral colonies attached to encrusting foraminifers and coralline red algae. Three samples from autochthonous sediments underneath coral colonies are comparatively rich in the brachiopod genera Megerlia and Argyrotheca, and additionally show low numbers of Novocrania and Thecidellina. Based on a coarse-grain analysis including more than 16,000 components >1 mm, these brachiopod shells co-occur with skeletal components of 11 higher taxa. Decapods, fixosessile foraminifers, molluscs, scleractinians, and coralline red algae clearly dominate the assemblages. Brachiopods in this study always contribute less than 2% to the sediment composition. This confirms previous results that even in brachiopod habitats the contribution of brachiopod shells to the total sediment composition is almost negligible. Our study indicates that brachiopods co-occur with pteriomorph bivalves and other epifauna in the cryptic habitats with limited space for encrusters or epibionts on the undersides of scleractinians and it tentatively supports the hypothesis of brachiopods preferring habitats with low grazing pressure, because shelly components of grazers (polyplacophorans and regular echinoids) are rare in our samples.     

Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean

Geographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one-fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long-term biogeographic barrier for Caribbean animals.     

Comparative phylogeography of Nearctic and Palearctic fishes

Combining phylogeographic data from mitochondrial DNA (mtDNA) of Nearctic and Palearctic freshwater and anadromous fishes, we used a comparative approach to assess the influence of historical events on evolutionary patterns and processes in regional fish faunas. Specifically, we (i) determined whether regional faunas differentially affected by Pleistocene glaciations show predictable differences in phylogeographic patterns; (ii) evaluated how processes of divergence and speciation have been influenced by such differential responses; and (iii) assessed the general contribution of phylogeographic studies to conservation issues. Comparisons among case studies revealed fundamental differences in phylogeographic patterns among regional faunas. Tree topologies were typically deeper for species from nonglaciated regions compared to northern species, whereas species with partially glaciated ranges were intermediate in their characteristics. Phylogeographic patterns were strikingly similar among southern species, whereas species in glaciated areas showed reduced concordance. The extent and locations of secondary contact among mtDNA lineages varied greatly among northern species, resulting in reduced intraspecific concordance of genetic markers for some northern species. Regression analysis of phylogeographic data for 42 species revealed significant latitudinal shifts in intraspecific genetic diversity. Both relative nucleotide diversity and estimates of evolutionary effective population size showed significant breakpoints matching the median latitude for the southern limit of the Pleistocene glaciations. Similarly, analysis of clade depth of phylogenetically distinct lineages vs. area occupied showed that evolutionary dispersal rates of species from glaciated and nonglaciated regions differed by two orders of magnitude. A negative relationship was also found between sequence divergence among sister species as a function of their median distributional latitude, indicating that recent bursts of speciation events have occurred in deglaciated habitats. Phylogeographic evidence for parallel evolution of sympatric northern species pairs in postglacial times suggested that differentiation of cospecific morphotypes may be driven by ecological release. Altogether, these results demonstrate that comparative phylogeography can be used to evaluate not only phylogeographic patterns but also evolutionary processes. As well as having significant implications for conservation programs, this approach enables new avenues of research for examining the regional, historical, and ecological factors involved in shaping intraspecific genetic diversity.     

Comparative phylogeography of the western Indian Ocean reef fauna

Assessing patterns of connectivity at the community and population levels is relevant to marine resource management and conservation. The present study reviews this issue with a focus on the western Indian Ocean (WIO) biogeographic province. This part of the Indian Ocean holds more species than expected from current models of global reef fish species richness. In this study, checklists of reef fish species were examined to determine levels of endemism in each of 10 biogeographic provinces of the Indian Ocean. Results showed that the number of endemic species was higher in the WIO than in any other region of the Indian Ocean. Endemic species from the WIO on the average had a larger body size than elsewhere in the tropical Indian Ocean. This suggests an effect of peripheral speciation, as previously documented in the Hawaiian reef fish fauna, relative to other sites in the tropical western Pacific. To explore evolutionary dynamics of species across biogeographic provinces and infer mechanisms of speciation, we present and compare the results of phylogeographic surveys based on compilations of published and unpublished mitochondrial DNA sequences for 19 Indo-Pacific reef-associated fishes (rainbow grouper Cephalopholis argus, scrawled butterflyfish Chaetodon meyeri, bluespot mullet Crenimugil sp. A, humbug damselfish Dascyllus abudafur/Dascyllus aruanus, areolate grouper Epinephelus areolatus, blacktip grouper Epinephelus fasciatus, honeycomb grouper Epinephelus merra, bluespotted cornetfish Fistularia commersonii, cleaner wrasse Labroides sp. 1, longface emperor Lethrinus sp. A, bluestripe snapper Lutjanus kasmira, unicornfishes Naso brevirosris, Naso unicornis and Naso vlamingii, blue-spotted maskray Neotrygon kuhlii, largescale mullet Planiliza macrolepis, common parrotfish Scarus psicattus, crescent grunter Terapon jarbua, whitetip reef shark Triaenodon obesus) and three coastal Indo-West Pacific invertebrates (blue seastar Linckia laevigata, spiny lobster Panulirus homarus, small giant clam Tridacna maxima). Heterogeneous and often unbalanced sampling design, paucity of data in a number of cases, and among-species discrepancy in phylogeographic structure precluded any generalization regarding phylogeographic patterns. Nevertheless, the WIO might have been a source of haplotypes in some cases and it also harboured an endemic clade in at least one case. The present survey also highlighted likely cryptic species. This may eventually affect the accuracy of the current checklists of species, which form the basis of some of the recent advances in Indo-West Pacific marine ecology and biogeography.     

Visual census methods underestimate density and diversity of cryptic reef fishes

The diversity and density of small, benthic reef fishes were estimated using visual census and enclosed rotenone stations. Visual census underestimated the number of species present and the density of common species by up to 91%.     

Comparative phylogeography of two colonial ascidians reveals contrasting invasion histories in North America

Surveys of genetic structure of introduced populations of nonindigenous species may reveal the source(s) of introduction, the number of introduction events, and total inoculum size. Here we use the mitochondrial cytochrome c oxidase subunit 1 (COI) gene to explore genetic structure and contrast invasion histories of two ecologically similar and highly invasive colonial ascidians, the golden star tunicate Botryllus schlosseri and the violet tunicate Botrylloides violaceus, in their global and introduced North American ranges. Haplotype and nucleotide diversities for B. schlosseri were significantly higher than for B. violaceus both globally (h = 0.872; ?? = 0.054 and h = 0.461; ?? = 0.007, respectively) and in their overlapping North American ranges (h = 0.874; ?? = 0.012 and h = 0.384; ?? = 0.006, respectively). Comparative population genetics and phylogenetic analyses revealed clear differences in patterns of invasion for these two species. B. schlosseri populations on the west and east coasts of North America were seeded from the Pacific and Mediterranean regions, respectively, whereas all North American B. violaceus populations were founded by one or more introduction events from Japan. Differences in genetic structure of invasive populations for these species in North America are consistent with their contrasting probable introduction vectors. B. schlosseri invasions most likely resulted from vessel hull fouling, whereas B. violaceus was likely introduced as a ??fellow traveler?? in the shellfish aquaculture trade.     

Morphology and molecules reveal two new species of Porites (Scleractinia,Poritidae) from the Red Sea and the Gulf of Aden

Two new reef coral species, Porites farasani sp. nov. and Porites hadramauti sp. nov. (Scleractinia, Poritidae), are described from the Red Sea and the Gulf of Aden. Porites farasani sp. nov. only occurs in the Farasan Islands in the southern Red Sea, while P. hadramauti sp. nov. has been collected in the Yemen Hadramaut region in the Gulf of Aden. Both species presented striking in situ differences with respect to other Porites species, and were characterized by small encrusting colonies and unusual polyp colouration. In order to test the genetic distinctiveness of P. farasani sp. nov. and P. hadramauti sp. nov. between each other and with respect to other representatives in the genus Porites, we investigated their evolutionary relationships with eight other morphological species of Porites occurring in the Red Sea and in the Gulf of Aden. Two DNA loci, the mitochondrial putative control region and the nuclear ribosomal ITS region, were sequenced, and three species delimitation approaches based on barcoding threshold (Automated Barcoding Gap Discovery) and coalescence theory (Poisson-Tree process, Generalized Mixed Yule Coalescent) were applied. Phylogenetic and species delimitation analyses were overall concordant, resolving P. farasani sp. nov. and P. hadramauti sp. nov. as two divergent but closely related lineages. Of the other morphologically defined Porites species, three were genetically differentiated (P. rus, P. columnaris and P. fontanesii), but five were genetically indistinguishable. The discovery of two regional endemics confirms the importance of the Red Sea and the Gulf of Aden as regions of high biodiversity and suggests the need for an integration of genome-wide molecular data with the re-evaluation of skeletal structures in the systematics of Porites.     

Similar cryptic behaviour during the early juvenile phase of two unrelated reef fishes: Epinephelides armatus and Bodianus frenchii

The juveniles of many reef fishes behave cryptically during critical juvenile stages in their life history and thus the microhabitats they often occupy are not well known. Comprehensive surveys of reef fishes on the temperate mid-west coast of Australia identified that juveniles of the unrelated Epinephelides armatus (Epinephelidae) and Bodianus frenchii (Labridae) < 100 mm total length both exhibit cryptic behaviour by exclusively swimming upside down under cave roofs and ledges. These individuals swam among the sponges and small algae in this microhabitat which would provide refuge from predation and also supply the dietary requirements of these two carnivores. Occupying this microhabitat would also reduce intra-specific competition, as individuals > 150 mm were only observed swimming ventrally oriented to the substrate in caves, under ledges or on open reef. Identifying the nursery habitats of fishery species, such as E. armatus and B. frenchii, is critical for understanding their life histories, but would also inform survey designs aimed at determining recruitment strength or variation.