Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes,Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes

The partial sequences of 16S rRNA and cytochrome c oxidase subunit I (COI) mitochondrial genes were analyzed for species identification and phylogenetic relationships among the commercially important Indian sciaenids (Otolithes cuvieri, Otolithes ruber, Johnius dussumieri, Johnius elongatus, Johnieops vogleri, Otolithoides biauritus and Protonibea diacanthus). Sequence analysis of both genes revealed that the seven species fell into three distinct groups, which were genetically distant from each other and exhibited identical phylogenetic resolution. Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the seven sciaenids indicating the usefulness of mtDNA-based approach in species identification.     

Habitat segregation and cryptic adaptation of species of Periophthalmus (Gobioidei: Gobiidae)

A study was conducted on the habitat distribution of four sympatric species of Periophthalmus (the silver‐lined mudskipper Periophthalmus argentilineatus, the slender mudskipper Periophthalmus gracilis, the kalolo mudskipper Periophthalmus kalolo and the Malacca mudskipper Periophthalmus malaccensis) from northern Sulawesi. Molecular phylogenetic reconstructions based on one mtDNA marker (16S) were used to validate the morphological taxa, identifying five molecular clades. Periophthalmus argentilineatus includes two molecular species, which are named Periophthalmus argentilineatus clades F and K. Multivariate direct gradient analysis show that these species form three distinct ecological guilds, with the two molecular species occurring in different guilds. Periophthalmus clade F is ecologically eurytypic; Periophthalmus clade K and P. kalolo are prevalent in ecosystems isolated by strong oceanic currents and at shorter distances from the sea; P. gracilis plus P. malaccensis are prevalent in ecosystems connected by shallow coastal waters, in vegetated habitats at larger distances from the sea. This indicates for the first time that mudskipper species exhibit a range of adaptations to semiterrestrialism not only within genera, but even within morphospecies, delineating a much more complex adaptive scenario than previously assumed.     

First record of mudskipper Boleophthalmus dussumieri (Gobiidae: Oxudercinae) on the coast of Mozambique and evidence of two putative lineages along its known distribution range

Boleophthalmus dussumieri is one of the most widely distributed mudskippers and is native to the Persian Gulf in Iran down to the northeast of the Arabian Sea and the coast of India. Nonetheless, the present study is the first to confirm the presence of B. dussumieri in the marine areas of the Mozambique coast. In addition, molecular analysis revealed strong evidence for the existence of two lineages with a high level of nucleotide divergence along the sampled area, revealing a still-neglected taxonomic condition for this lineage/species.     

Morphological divergence in the Walton's Mudskipper,Periophthalmus waltoni Koumans, 1941, from the Persian Gulf and Gulf of Oman (Gobioidei: Gobiidae)

The body shape variation among 244 specimens of Periophthalmus waltoni Koumans, 1941, collected from seven stations in the Persian Gulf and Gulf of Oman, was analysed by utilising geometric morphometrics (GM) and truss-based morphometrics methods (TBM). Discriminant function analysis did not show significant differences between the shape of females and males. Canonical variate analysis and cluster analysis classified the specimens in two separate groups of stations: those in the Persian Gulf, and those in the Strait of Hormuz plus Gulf of Oman. Potential factors contributing to the observed variation include differences in physicochemical parameters between the Persian Gulf and the Gulf of Oman.     

Differentiation and adaptive radiation of amphibious gobies (Gobiidae: Oxudercinae) in semi-terrestrial habitats

During several surveys made in the region of the lower Fly River and delta, Papua New Guinea, nine species of oxudercine gobies (Gobiidae: Oxudercinae) were recorded: Boleophthalmus caeruleomaculatus, Oxuderces wirzi, Periophthalmodon freycineti, Periophthalmus darwini, Periophthalmus novaeguineaensis, Periophthalmus takita, Periophthalmus weberi, Scartelaos histophorus and Zappa confluentus. An exploratory multivariate analysis of their habitat conditions discriminated five guilds, differentially distributed in habitats with different quantities of environmental water and three guilds corresponding to different levels of salinity. A partial correspondence between phylogenetic and ecological categories suggested the presence of parallel adaptive radiations within different genera. In particular, the species found in the most terrestrial habitats (P. weberi) was also found in the widest range of conditions, suggesting that colonization of extreme semi-terrestrial and freshwater habitats by this species was facilitated by eurytypy. It is proposed that these findings provide insight into convergent adaptations for the vertebrate eco-evolutionary transition from sea to land.     

Length–weight relationships for three species of mudskippers (Gobiidae: Oxudercinae) in the coastal areas of the Persian Gulf, Iran

Length–weight relationships, W  =  aL ^b , were calculated for three species of mudskippers: Scartelaos tenuis , Periophthalmus waltoni and Boleophthalmus dussumieri from the Iranian coast of the Persian Gulf. Values of b ranged from 2.10 to 2.86 for both sexes at seven sites for the three species.     

4种弹涂鱼鳃的形态度量学比较及其生态学意义

通过对背眼虎鱼亚科中薄氏大弹涂鱼(Boleophthalmus boddarti)、青弹涂鱼(Scartelaos histophorus)、新几内亚弹涂鱼(Periophthalmus novaeguineaensis)和点弹涂鱼(P.spilotus)3属4种弹涂鱼鳃参数的测定,比较了各种之间鳃的形态度量学差异。结果表明,4种弹涂鱼的鳃参数(Y)与其体重(W)均符合方程logY=log a+b logW,且各鳃参数与体重的相关性显著(R2=0.50～0.98,P0.05)。等体重的弹涂鱼相比较,青弹涂鱼的总鳃丝数、总鳃丝长(mm)、鳃丝一侧鳃小片数(/mm)、总鳃面积(mm2)和相对鳃面积(mm2/g)均最大,薄氏大弹涂鱼相应鳃参数次之,新几内亚弹涂鱼和点弹涂鱼相应鳃参数较小。弹涂鱼鳃结构的这种梯度退化,表明青弹涂鱼和薄氏大弹涂鱼水生性较强,而新几内亚弹涂鱼和点弹涂鱼陆生性较强。4种弹涂鱼的总鳃丝长和总鳃面积明显小于其他等体重水生鱼类,这与弹涂鱼的两栖生活特征相符。     

Evolutionary history of tree squirrels (Rodentia,Sciurini) based on multilocus phylogeny reconstruction

Pe?nerová, P. & Martínková, N. (2012). Evolutionary history of tree squirrels (Rodentia, Sciurini) based on multilocus phylogeny reconstruction. —Zoologica Scripta, 41, 211–219. Tree squirrels of the tribe Sciurini represent a group with unresolved phylogenetic relationships in gene trees. We used partial sequences of mitochondrial genes for 12S rRNA, 16S rRNA, cytochrome b and d‐loop, and nuclear irbp, c‐myc exon 2 and 3 and rag1 genes to reconstruct phylogenetic relationships within the tribe, maximizing the number of analysed species. Bayesian inference analysis of the concatenated sequences revealed common trends that were similar to those retrieved with supertree reconstruction. We confirmed congruence between phylogeny and zoogeography. The first group that diverged from a common ancestor was genus Tamiasciurus, followed by Palaearctic Sciurus and Indomalayan Rheithrosciurus macrotis. Nearctic and Neotropical Sciurus species formed a monophyletic group that included Microsciurus and Syntheosciurus. Neotropical Sciurini were monophyletic with a putative exception of Syntheosciurus brochus that was included in a polychotomy with Nearctic Sciurus in supertree analyses. Our data indicate that Sciurini tree squirrels originated in the northern hemisphere and ancestors of contemporary taxa attained their current distribution through overland colonization from the nearest continent rather than through trans‐Pacific dispersal.     

Length‐weight relationships of six fishes from intertidal and coastal waters in the northern Persian Gulf

The length–weight relationships (LWRs) for six little‐known fish species collected in the northern Persian Gulf (south of Iran) are presented, namely, Plicofollis dussumieri, Pseudotriacanthus strigilifer, Cynoglossus bilineatus, Cynoglossus arel, Solea elongata, and Pseudorhombus elevates.     

Benthic ctenophores (Platyctenida: Coeloplanidae) in South Florida: predator–prey interactions

The primary goal of this study was to demonstrate, from field observations and laboratory experiments, some key trophic roles of benthic ctenophores as predators and prey in subtropical communities. We examined individuals of two benthic platyctenid species: Coeloplana waltoni, a minute epibiont on octocorals in exposed, open‐water settings; and Vallicula multiformis, an associate of calm‐water biofouling communities and floating Sargassum spp. Laboratory observations of individuals of both ctenophore species revealed frequent capture and ingestion of diverse zooplankton taxa, especially crustaceans. Laboratory predation trials demonstrated the capture of dolphinfish (Coryphaena hippurus) eggs and larvae by both ctenophore species. Dolphinfish eggs and larvae larger than individuals of C. waltoni were captured but not ingested during 2‐h trial periods. These prey items were sometimes purloined and ingested by polyps of the ctenophore's octocoral host. Ingestion of dolphinfish eggs and larvae by individuals of C. waltoni was observed, however, after longer periods of exposure to prey. In predation trials, dolphinfish eggs and larvae were both captured and ingested by larger individuals of the ctenophore species V. multiformis. Field and laboratory observations revealed diverse invertebrate and fish taxa that prey on both ctenophore species. In the laboratory, the mean daily per capita consumption of individuals of C. waltoni by a pomacanthid fish ranged 0.5–2.8 individuals, and ranged 2.6–3.6 individuals for predation by an ovulid mollusc. Field population densities of these predators ranged 0.1–0.7 individuals per m² for the pomacanthid, and 0.2–1.1 individuals per m² for the mollusc. Laboratory feeding observations demonstrated frequent consumption of individuals of V. multiformis by a sea anemone, and by three species of brachyuran crabs. Field observations revealed eight fishes that probably feed incidentally on individuals of V. multiformis. These findings add to the limited knowledge base of predator–prey dynamics in both C. waltoni and V. multiformis.     

Benthic ctenophores (Platyctenida: Coeloplanidae) in south Florida: environmental conditions,habitats, abundances,and behaviors

Two benthic ctenophores, Coeloplana waltoni and Vallicula multiformis, are contrasted in terms of their coastal environments, habitats, abundances, seasonal occurrences, and behavior in south Florida. Coeloplana waltoni occurs as an epibiont on octocorals in open water settings, and V. multiformis is present in bio‐fouling communities, associated with macroalgae, bryozoans, and inanimate substrates in protected, back‐water habitats. In our study, individuals of C. waltoni were found under moderate to strong current flow and relatively constant temperature and salinity (T/S) conditions, whereas individuals of V. multiformis occurred at sites of low current flow and more variable T/S conditions. In C. waltoni, individuals generally adhered tightly to host colony surfaces, whereas in V. multiformis, individuals often disassociated from substrates and floated free. Mean population densities of C. waltoni ranged ~500–850 individuals 100 mL^?1 (measured as the displacement volume of the octocoral habitat), and densities of V. multiformis ranged 5–360 individuals 100 mL^?1 (measured as the displacement volume of the biofouling habitat). Abundance of C. waltoni was significantly highest in the 2014 warm season (June–October) when numerous minute (≤0.5 mm body length) juveniles were present. Vallicula multiformis was abundant in the 2015 and 2016 warm seasons (July–October), and also relatively abundant in the 2016 cool season (March–April). Ctenophore abundance and surface seawater temperature indicate a significant positive response to warm‐season conditions in C. waltoni, whereas numbers of V. multiformis did not show any effect of seawater temperature. Recently settled individuals of V. multiformis (≤1.0 mm) occurred throughout the year. Individuals of V. multiformis recruited to fiber‐coated sponges during warm and cool periods, with mean body sizes increasing in one cohort from 1.41 to 6.46 mm over a 39‐d period, suggesting a growth rate of ~4% d^?1. Feeding in both species involves tentacle capture of water‐borne zooplankton and particulate organic matter. Individuals of C. waltoni were also observed inserting tentacles into octocoral polyps, possibly pilfering food. Chlorophyll a was detected in extracts of both ctenophore species. The high abundances and feeding behavior of benthic ctenophores could have a strong influence on octocoral and biofouling communities.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint,cleaner, and semi‐terrestrial shrimps (Caridea: Lysmata,Exhippolysmata, and Merguia)

Of paramount importance to studies that profit from molecular trees is the accuracy and robustness of the reconstructed phylogenies. Causes of systematic error that can mislead phylogenetic methods include nuclear copies of mitochondrial DNA (numts) and low phylogenetic informativeness (PI). Herein, numts and PI were explored in three mitochondrial genes commonly used for phylogenetic reconstruction: 16S, 12S, and cytochrome c oxidase I (COI). Shrimps from the genera Lysmata, Exhippolysmata, and Merguia were used as a model system. The existence of: (1) multiple bands on gels of COI and 12S polymerase chain reaction (PCR) products from various species; (2) double peaks, background noise, and ambiguity in sequence chromatograms of COI and 12S PCR products that produced a single clear band in other species; and (3) indels, stop codons, and considerable composition bias in COI‐like cloned sequences of one problematic species (Lysmata seticaudata), was interpreted as evidence of pervasive non‐functional nuclear copies of mitochondrial DNA (numts) of the targeted COI (and probably 12S) mtDNA fragment. The information content of the three mtDNA markers studied was investigated using PI profiling, spectral analysis, and neighbour‐nets. Marker‐specific PI profiles suggested that the COI marker has the highest information content and greatest power for resolving both shallow and deep nodes in trees depicting the phylogenetic relationship among the species studied. Nonetheless, spectral analysis of splits and neighbour‐nets suggested that the 16S and 12S markers were equally or even more powerful than the COI marker for resolving nodes at all phylogenetic levels. Altogether, these analyses suggest that all three mtDNA markers are equally useful for resolving phylogenetic relationships in the shrimps studied, and that PI profiling is not necessarily useful to estimate overall gene utility. A ‘total‐evidence’ phylogenetic analysis that included 34 species and used a concatenated data set of 1403 characters (from reliable 16S, 12S and COI sequences), demonstrated that the genus Lysmata is paraphyletic, and that the monophyletic clade comprising species of Lysmata and Exhippolysmata can be divided into four well‐supported subclades (Neotropical, Cleaner, Cosmopolitan, and Morphovariable). © 2013 The Linnean Society of London     

Phylogeography of Walton’s Mudskipper,Periophthalmus waltoni Koumans, 1941 (Perciformes: Gobiidae), from the Persian Gulf and Gulf of Oman

Mudskippers are amphibious air breathing fish with terrestrial adaptations in contrast to entirely aquatic fish. They are adapted to living on mudflats and show morphological, physiological, and behavioural features that could affect their phylogeny and phylogeography. A comparative genetic analysis was carried out on 100 specimens of the mudskipper Periophthalmus waltoni Koumans, 1941 from eight different sites along the coast of the Persian Gulf and Gulf of Oman. Phylogeographic inference based on two mitochondrial markers (Cyt b and D-loop) suggests that P. waltoni populations are divided into two well-divergent clades western and eastern. This is likely related to the geohydrological history of the area during the last Pleistocene glaciations. The regional phylogeographies are apparently also influenced by ecological and geographical barriers such as salinity, water current, and the geographic position of the Strait of Hormuz.     

Phylogenetic analysis of six species of pacific abalone (Haliotidae) based on DNA sequences of 16s rRNA and cytochrome c oxidase subunit I mitochondrial genes

Six species of abalones (Haliotidae) are found on the Korean coasts. Identification and characterization of these abalones are usually based on morphologic characters. In this research we compared the partial sequences of the mitochondrial 16S ribosomal RNA and cytochrome c oxidase subunit I genes to identify species using molecular data and to determine their phylogenetic relationships. Sequence alignments and phylogenetic analysis revealed that the 6 species fell into 2 distinct groups which were genetically distant from each other and exhibited little internal phylogenetic resolution. One group included Haliotis discus hannai, H. discus discus, H. madaka, and H. gigantea, while the other group contained H. diversicolor supertexta and H. diversicolor diversicolor. The 16S rRNA sequences were relatively more conserved than to the COI sequences, but both gene sequences provided sufficient phylogenetic information to distinguish among the 6 species of Pacific abalone, and thus could be valuable molecular characters for species identification.     

Length–weight and length–length relationships and seasonal condition factors for two mudskippers,Periophthalmus modestus (Cantor, 1842) and P. magnuspinnatus (Lee,Choi & Ryu, 1995) (Gobiidae), on tidal flats of Korea

Presented are the length–weight and length–length relationships and condition factors for two mudskippers, Periophthalmus modestus and Periophthalmus magnuspinnatus, on the tidal flats of Korea. Values of the exponent b, estimated by nonlinear least squares from weight and length data, were 3.031 for P. modestus and 3.044 for P. magnuspinnatus. All relationships between total and standard length were linear (r² > 0.974). The condition factors were significantly higher during the post‐spawning season than at other times for both species.     

Microstructural morphology in early dermal denticles of hammerhead sharks (Elasmobranchii: Sphyrnidae) and related taxa

Mello, W.C., de Carvalho, J.J., Brito, P.M.M. 2011. Microstructural morphology in early dermal denticles of hammerhead sharks (Elasmobranchii: Sphyrnidae) and related taxa. —Acta Zoologica (Stockholm) 00 : 1–7. This study uses scanning electron microscopies to investigate and describe the microstructural diversity of dermal denticles in the family Sphyrnidae, which comprises all living hammerhead shark species, comparing them to other related taxa (i.e. Carcharhinus dussumieri, Carcharhinus plumbeus, Carcharhinus acronotus, Rhizoprionodon acutus, Negaprion brevirostris and Hemigaleus microstoma). The results reveal that sphyrnids present noticeable microstructures in the dermal denticles, distinguishing them from the other related species investigated. Additionally, scale patterns are the same in three distinct body regions (i.e. cephalic, branchial and dorsal fin). Species of Sphyrnidae that reach bigger total lengths and that are widely distributed (i.e. Sphyrna lewini and Sphyrna mokarran) presented more, smaller and nearly hexagonal microstructures that do not cover the entire scale surface, unlike species reaching smaller sizes and restricted to coastal habits (i.e. Sphyrna tiburo, Sphyrna tudes, Sphyrna media and Eusphyra blochii). The sphyrnid scales are similar to R. acutus and C. dussumieri rather than to the other species, but it is not possible to identify the sphyrnid species only by scale features. It is clear that a similar morphology of scales is not necessarily related to similar life habits, and that they are candidates to provide new characters in phylogenetical studies among sphyrnids.     

Monophyly,candidate species and vicariance in Biomphalaria snails (Mollusca: Planorbidae) from the Southern Andean Altiplano

Collado, G. A., Vila, I. & Méndez, M. A. (2011). Monophyly, candidate species and vicariance in Biomphalaria snails (Mollusca: Planorbidae) from the Southern Andean Altiplano. —Zoologica Scripta, 40, 613–622. The landscape of the Neotropical southern Andean Altiplano is characterized by a succession of closed basins originated from the Miocene to the Holocene. In this region, the number of species and phylogenetic relationships among freshwater snails of the genus Biomphalaria are uncertain. Here we obtained sequences of the mitochondrial gene cytochrome oxidase subunit I from 17 Altiplano populations, including topotypes of three nominal species, which were analyzed together with published sequences of the genus using different methods of phylogenetic reconstruction and a species of Helisoma as outgroup. The Altiplano populations conform a monophyletic group whose sister group is the Neotropical species Biomphalaria peregrina. Within this clade we recovered four main lineages well supported and congruent with geographical distributions. One clade includes topotypes restricted exclusively to the Ascotán basin, the type locality of the nominal species Biomphalaria crequii. A second clade includes sequences that correspond to topotypes restricted to the Isluga and Carcote basins, the type localities of the nominal species Biomphalaria aymara and Biomphalaria costata, respectively. Two monophyletic groups clustered snails restricted to several aquatic systems within the Caquena and Lauca basins, which may represent candidate species. The branching pattern of the sequences suggests that in the diversification of these snails, events of vicariance inferred in the Pleistocene have predominated over dispersal phenomena.