Isolation and characterization of 12 microsatellites from the black surfperch, Embiotoca jacksoni, a reef fish that lacks a pelagic larval phase

A set of 12 microsatellite markers was developed from Embiotoca jacksoni genomic DNA and tested for polymorphism using 64 individuals from two populations. All loci were polymorphic with a number of alleles ranging from two to 19 with expected heterozygosities ranging from 0.17 to 0.89. There was no evidence of linkage disequilibrium and all loci were in Hardy-Weinberg equilibrium, except for four loci in one population. High numbers of private alleles were consistent with strong population structure, and very limited dispersal. Six microsatellite markers successfully cross amplified and were polymorphic in closely related species, Embiotoca lateralis and Hyspurus caryi.     

Seasonally fluctuating resources and temporal variability of interspecific competition

Summary The influence of seasonal availability of two critical resources (food and substrates from which food was harvested) on interspecific competition between striped surfperch (Embiotoca lateralis) and black surfperch (Embiotoca jacksoni) was examined. There was a strong depth-related gradient in density of prey and in cover of foliose algae; both declined with increasing bottom depth. Density of prey was reduced 5–10 fold during the winter season, but cover of substrates remained constant throughout the year. Although both fishes co-occurred throughout the same depth range, striped surfperch were more common in shallow habitats and black surfperch were more abundant deeper. Local abundance and distribution patterns of both surfperch species did not change seasonally. Stepwise regression analyses suggested that availability of favored substrates was a proximate influence on local patterns of surfperch distribution and abundance, and that interspecific competition depressed abundance of the two species to the same degree. Removal experiments conducted during the cold-water season revealed that interspecific competition influenced depth distribution of black surfperch but not striped surfperch. Seasonal change in density of prey was accompanied by marked changes in overlap in use of foraging substrates by the surfperches. The pattern of change in interspecific overlap suggested that surfperch competed for food only when prey were seasonally scarce. There was no difference in the agonistic tendencies of the two fishes, and the absolute and relative frequency of interspecific chases was independent of food level. These results have important implications regarding the impact of temporal variability of interspecific competition in natural communities. In the surfperch system, competition was characterized by constant and time-varying elements that had symmetrical and asymmetrical effects and involved both interference and exploitation mechanisms.     

Food acquisition by competing surfperch on a patchy environmental gradient

Synopsis Black surfperch, Embiotoca jacksoni, and striped surfperch, Embiotoca lateralis, coexisted along steep sloping rocky habitats at Santa Cruz Island, California. The range of depths occupied (to 15 m) was characterized by a strong gradient in abundance of prey and a changing mosaic of substrate types from which surfperch harvested food. Availability of prey and diversity of benthic substrates were greatest in shallowest areas and both declined with increasing depth. Individuals of both surfperch species were residential within a narrow range of depths, with the result that different segments of their populations were consistently exposed to different foraging environments. These two phenomena (residential behavior combined with a gradient in availability of resources) resulted in variation in foraging behaviors and diets among individuals that resided at different depths. The pattern of within-population variation differed between the surfperch species. Black surfperch individuals achieved similar taxonomic diets and expended similar foraging effort at all depths, but deep-water foragers captured much less prey biomass per unit effort. The taxonomic composition of striped surfperch diets differed among depths, and although similar amounts of prey biomass were captured everywhere, individuals in deep areas expended much greater effort to obtain that level of food return. For both species, habitat profitability (food return to foraging effort) declined with depth. The difference in habitat profitability appeared to influence fitness components of both surfperches. Individuals occupying deep habitats were about 5% shorter in standard length than conspecifics of the same chronological age living in shallow areas; the disparity in body size resulted in an estimated difference in clutch size of 10–18%.     

Phylogeography and demography of sympatric sister surfperch species, Embiotoca jacksoni and E. lateralis along the California coast: historical versus ecological factors

With 18 closely related endemic species that radiated in a diversity of ecological niches, the California surfperches (Embiotocidae) species flock is a good candidate for the study of sympatric speciation. Resource partitioning has been suggested as an important driving force in the radiation of the surfperch family. Within the family, two congeneric sister species, Embiotoca jacksoni and E. lateralis, are known to compete strongly for a preferred single food resource and may be used as a model of ecological interactions for the family. Along the California coast, the distribution of the two species differs. Embiotoca jacksoni has a continuous range, whereas E. lateralis shows a disjunction with a distribution gap in the Southern California Bight. Two hypotheses may explain this disjunct distribution. Ecological competition may have displaced E. lateralis in favor of E. jacksoni. Alternatively, a common vicariant event may have separated the species into northern and southern populations, followed by secondary contact in E. jacksoni but not in E. lateralis. The two hypotheses predict different phylogeographic and demographic signatures. Using a combined phylogeographic and coalescent approach based on mitochondrial control region data, we show that vicariance can only account for a portion of the observed divergences. Our results are compatible with a significant role played by ecological competition in the southern range of the species.     

The influence of plant cover on surfperch abundance at an offshore temperate reef

Synopsis At an offshore reef near Santa Barbara, southern California, young-of-year (young) of five surfperch species (Embiotocidae: Embiotoca jacksoni, E. lateralis, Hypsurus caryi, Rhacochilus toxotes, Damalichthys vacca) once thrived in a dense kelp understory of Pterygophora californica and Laminaria farlowii, but disappeared after a severe storm in February, 1980 deforested their habitat. Measurements of fish density and kelp cover made before deforestation indicated that the young surfperch appeared in the spring and disappeared in the fall as cover increased and declined. Adult surfperch and large kelp bass (Paralabrax clathratus), which can eat young but not adult surfperch, remained all year. We tested to see if kelp cover was an essential refuge for the young by pruning back (thinning) kelp blades from one of two transects. The thinning caused a significant redistribution of young which clearly avoided open spaces, but not of adults which are less vulnerable to predation. Measurements of fish density made after the storm-induced deforestation showed that adult surfperch and kelp bass still remained abundant even after the young surfperch were gone. Only after an abrupt reforestation in 1983, more than a year after the present study was terminated, were young once again seen on the reef. Although young surfperch may seek tiny prey living on kelp blades, most lines of evidence indicated that the distribution of the young is more a response to risk of predation. Hence the extent of kelp understory was probably the main determinant of the survival of young surfperch on the reef.     

Multiple paternity and competition in sympatric congeneric reef fishes, Embiotoca jacksoni and E. lateralis

The black surfperch Embiotoca jacksoni and the striped surfperch E. lateralis (Embiotocidae, Perciformes) are livebearing temperate reef fishes that live sympatrically over a large portion of their distribution range, where they exhibit strong ecological competition. In order to assess whether mating strategies reflect competition, we investigated multiple paternity in these two species in an area of sympatry. We sampled 24 pregnant females (12 for each species) in Monterey Bay, California, used microsatellite analysis and assessed paternity with the COLONY software. While broods are relatively small (12 to 36 offspring), they were always sired by multiple fathers (2 to 9), with no correlation between the size of a brood and the number of fathers. The number of sires for each brood was not significantly different between the two species (approximately 3.5 sires per brood). We tested the deviation from stochasticity of fathered offspring for each father in one brood. Results showed a significant deviation for both E. jacksoni and E. lateralis . However, this deviation was not found to be significant between species. The striking similarity in the dynamics of multiple paternity in these species, when sampled in sympatry, may result from several alternative scenarios, including phylogenetic inertia, reproductive behaviour, and ecological competition.     

Contrasting effects of giant kelp on dynamics of surfperch populations

Summary The effect of giant kelp, Macrocystis pyrifera, on the population dynamics of two temperate reef fishes, striped surfperch (Embiotoca lateralis) and black surfperch (E. jacksoni), was examined. Based on an understanding of how particular reef resources influence abundances of the surfperch and of the effect of giant kelp on those resources, we anticipated that Macrocystis would adversely affect populations of striped surfperch but would enhance those of black surfperch. The natural establishment of giant kelp at sites at Santa Cruz Island, California, resulted in the predicted dynamical responses of surfperch. Abundances of striped surfperch declined rapidly when and where dense forests of giant kelp appeared, but showed little change where Macrocystis was continuously absent over the 8 y period of study. Abundances of adult black surperch, which increased following the appearance of giant kelp, were lagged by >1 y because the dynamical response involved enhanced local recruitment. No change in abundance of black surfperch populations was evident at areas without giant kelp.The mechanism by which giant kelp altered the dynamics of the surfperch involved modification of the assemblage of understory algae used by surfperch as foraging microhabitat. Foliose algae (including Gelidium robustum) were much reduced and turf was greatly enhanced following the appearance of Macrocystis; these two benthic substrata are the favored foraging microhabitat for striped surfperch and black surfperch respectively. Populations of both surfperch species tracked temporal changes in the local availability of their favored foraging microhabitat. Thus, while neither species used Macrocystis directly, temporal and spatial variation in giant kelp indirectly influenced the dynamics of these fishes by altering their foraging base. These results indicate that the dynamics of striped surfperch and black surfperch were governed to a large degree by density-dependent consumer-resource interactions. The present work underscores the predictive value that arises from a knowledge of the mechanisms by which processes operate.     

Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants

A polyphasic taxonomic study was undertaken to establish the taxonomic position of six representative strains isolated from activated sewage sludge foam. The organisms were found to have chemical and morphological properties consistent with their assignment to the genus Tsukamurella. DNA:DNA relatedness studies showed that five out of the six isolates formed a distinct genomic species, the remaining strain was most closely associated with this taxon. The five isolates had a unique phenotypic profile that served to distinguish them from representatives of the validly described species of Tsukamurella. The combination of the genotypic and phenotypic data indicated that the five strains should be classified as a new species in the genus Tsukamurella. The name proposed for this taxon is Tsukamurella spumae, the type strain is N1171T (= DSM 44.113T = NCIMB 13947T). It was also shown that some of the reference strains were misclassified as Tsukamurella paurometabola.     

Molecular phylogeny of the subfamily Amphistichinae (Teleostei: Embiotocidae) reveals parallel divergent evolution of red pigmentation in two rapidly evolving lineages of sand-dwelling surfperch

Pigment evolution was reconstructed in the subfamily Amphistichinae, a six-species clade of the surfperches, family Embiotocidae. Assignment was confirmed for all species within the subfamily, but low levels of differentiation were found among species within the subfamily, suggesting a recent radiation. The new phylogeny differs from previous hypotheses by the placement of the spotfin surfperch Hyperprosopon anale at the base of the subfamily, while still preserving the calico surfperch Amphistichus koelzi and the redtailed surfperch Amphistichus rhodoterus as sister species. Phenotypically, A. rhodoterus, A. koelzi and the silver surfperch Hyperprosopon ellipticum express high levels of red pigmentation. The barred surfperch, Amphistichus argenteus and the walleye surfperch Hyperprosopon argenteum express little to no red pigment, while basal H. anale expresses an intermediate amount of red pigment. Red pigmentation is proposed to have experienced parallel divergent evolution in each genus within the subfamily.     

Functional design and prey capture dynamics in an ecologically generalized surfperch (Embiotocidae)

Kinematic and electromyographic analyses of prey capture in two species of surfperch (Embiotocidae) reveal differing abilities to modulate strike activity in response to different prey types. Both the black perch, Embiotoca jacksoni, and the shiner perch, Cymatogaster aggregata, demonstrate stereotyped and conserved neuromuscular and kinematic activity in suction feeding. A distinguishing anatomical trait in this family, the interopercular shelf, enhances the coupling of hyoid movement with mandibular depression. Analyses of variance suggest a preprogrammed motor output that is ballistically launched for suction generation, with the possibility of more plasticity in latter phases of the strike. While the trophically limited shiner perch displays a stereotyped repertoire of this one strike pattern, very small prey, larger conglomerates of these, and large distinct prey elicit three modulated patterns in the black perch. Functional characteristics that enable the ecologically generalized black perch to exploit a variety of prey types include energy–conserving modulatory ability, behavioural flexibility in utilizing a conserved suction–generating programme, and the addition of specialized winnowing and spitting activity.     

Revision of the systematics of the genus Calliptamus Serville 1831, (Orthoptera: Acrididae: Calliptaminae) in Algeria using morphological,chemical, and genetic data

Summary. The genus Calliptamus contains swarming orthopterans that cause serious damage in Algerian agricultural systems. However, it remains difficult to identify species within this genus; a thorough understanding of the group’s systematics and the utilization of novel taxonomic criteria are needed. We used morphological analysis along with two other methods of species identification – chemotaxonomy with cuticular compounds and DNA barcoding involving the COI gene – to classify 81 individual grasshoppers collected at two different sites in the Sétif region (northeastern Algeria). The chemotaxonomic analyses yielded ambiguous results, but DNA barcoding allowed us to differentiate two Calliptamus species found in Algeria: Calliptamus barbarus (Costa 1836), and Calliptamus wattenwylianus (Pantel 1896). Several morphological criteria used in identification keys appear to reflect differences among morphotypes rather than differences between species, and their taxonomic specificity is not supported by the barcoding data. The number of spines on the hind tibia is the only morphological criterion that reflected genetic differences between species; it is thus considered to be a taxonomically useful feature for identifying species in this genus.     

Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand

A polyphasic approach was used to establish the taxonomic position of two actinomycetes isolated from a Namibian soil and shown to utilise nitrile compounds as growth substrates. The organisms, strains NAM-BN063AT and NAM-BN063B, had chemical and morphological properties consistent with their assignment to the genus Gordonia. Direct 165 rRNA sequencing studies confirmed the taxonomic position of the strains following the generation of phylogenetic trees using four different algorithms. The strains consistently formed a distinct phylogenetic line within the evolutionary radiation occupied by gordoniae and were most closely related to Gordonia rubropertincta DSM 43197T. DNA:DNA relatedness studies indicated that the two organisms belonged to a genomic species that was readily distinguished from G. rubropertincta. The unique phenotypic profile of the strains sharply separated them from representatives of all of the validly described species of Gordonia. The combination of genotypic and phenotypic data indicates that the two strains should be classified in the genus Gordonia as a new species. The name proposed for this taxon is Gordonia namibiensis, the type strain is NAM-BN063AT (= DSM 44568T = NCIMB 13780T).     

When genes meet nomenclature: tortoise phylogeny and the shifting generic concepts of Testudo and Geochelone

We used a five-gene data set (mtDNA: 12S rRNA, 16S rRNA, cyt-b; nDNA: Cmos, Rag2) comprising approximately two-thirds of all extant testudinid species and, for the first time, including all five Testudo species to investigate the question of whether all western Palaearctic testudinids are monophyletic. Further, we examined whether the recently suggested allocation of the African Geochelone pardalis in the otherwise exclusively South African genus Psammobates and of the Malagasy G. yniphora in the monotypic genus Angonoka is justified in the face of considerable morphological evidence against such placements. Our phylogenetic analyses do not support the paraphyly and generic break-up of Testudo, as suggested by previous papers using a smaller taxon sampling and mtDNA data only. We propose a continued usage of the generic name Testudo for all five western Palaearctic tortoise species. Within Testudo, two monophyletic subclades are present, one containing T. hermanni+T. horsfieldii, and the other comprising (T. kleinmanni+T. marginata)+T. graeca. Nomenclaturally, we demonstrate that Eurotestudo Lapparent de Broin et al., 2006, which was recently erected with the type species T. hermanni, is an objective junior synonym of Chersine Merrem, 1820 and Medaestia Wussow, 1916. Recognition of a monotypic genus Angonoka for G. yniphora is unwarranted according to both our re-analysis of sequence data and morphological data. Acknowledging the strong morphological similarity between G. yniphora and G. radiata, we suggest placing both species into the genus Astrochelys. Although sequence data for only one of the three Psammobates species was available for analysis, there is currently no cause to challenge the monophyly of this genus as established on the basis of morphological evidence. Thus, we hypothesize that G. pardalis is sister to a monophyletic Psammobates. In light of the clear morphological gap between G. pardalis and Psammobates species, the recognition of a distinct genus Stigmochelys for the former seems justified.     

The evolution of growth-forms in the Macaronesian genus Aeonium (Crassulaceae) inferred from chloroplast DNA RFLPs and morphology

Phylogenetic relationships among species of Aeonium were studied using morphological characters and chloroplast DNA RFLPs. Cladistic analysis of weighted morphological data indicates that the small, herbaceous and least woody species are basal in the genus. Chloroplast DNA data gave similar results, supporting the separation of the herbaceous or small, woody species from the large, hapaxanth rosettes, rosette trees, and branched subshrubs with yellow, white or red flowers as well as the only (herbaceous) species with axillary inflorescences. The relationships among the species descending from a polytomy that comprises all species of the genus as well as a polytomy which comprises 18 of the 26 species studied, are only very incompletely resolved, except for two monophyletic clades that contain the branched subshrubs with yellow flowers ( A . sect. Aeonium ) and the branched subshrubs and rosette trees with white or red flowers ( A . sect. Leuconium ), respectively. Cladistic analysis of the combined morphological and chloroplast DNA data improved resolution considerably. Four monophyletic clades are distinguished, each of which, except for three species, comprises only one of the five main growth-form types. Although Aeonium is generally regarded as an outstanding example of adaptive radiation, this mode of speciation seems to have been of minor significance in the evolution of the genus, because each growth-form apparently evolved only once. Instead, island speciation in the absence of major ecological shifts, is probably more important in the evolution of the genus.     

Transfer of Kaempferia candida to Curcuma (Zingiberaceae) based on morphological and molecular data

Results of morphological studies supported by molecular analyses of chloroplast psbA‐trnH and partial petA‐psbJ DNA sequences indicate that Kaempferia candida cannot be retained in this genus. The species is here formally transferred to Curcuma and the name is typified. Notes on the species and colour plates are given.     

Combined multiple gene genealogies and phenotypic characters differentiate several species previously identified as Botryosphaeria dothidea

Botryosphaeria dothidea is one of the most commonly reported species in a genus of important pathogens of woody plants. This taxon generally is accepted to represent a species complex, and hence its identity remains unclear. Previous studies either have treated B. dothidea as the valid name for B. ribis and B. berengeriana or argued for them to be separate entities. To add to the confusion, no ex-type cultures are available for either B. dothidea or B. ribis. The aim of the present study, therefore, was to recollect and characterize these fungi and designate a set of reference cultures that can be used in future studies. To this end, morphological, cultural and multi-allelic DNA sequence datasets from the rDNA (ITS 1, 5.8S, and ITS 2), β-tubulin and EF1-α genes were used to fully characterize these species. Botryosphaeria dothidea was found to be distinct from B. ribis, while B. berengeriana was retained as synonym of the former name. Furthermore, Fusicoccum aesculi is accepted as anamorph of B. dothidea, while the anamorph of B. ribis is newly described as F. ribis sp. nov. Botryosphaeria ribis could be distinguished from B. parva based on β-tubulin and EF1-α sequence data. A combined phylogeny of the three gene regions used in this study also showed that the genus Botryosphaeria represents two distinct phylogenetic assemblages that correspond to species with Diplodia and Fusicoccum anamorphs.     

Transfer of the members of the genus Brachiola (microsporidia) to the genus Anncaliia based on ultrastructural and molecular data

Two microsporidian genera, AnncaliiaIssi, Krylova, & Nicolaeva 1993 and BrachiolaCali et al. 1998, possess a Nosema-type life cycle and unique cell surface ornamentations, which include precocious electron-dense coating of the plasmalemma and a variety of secretory structures deposited on the parasite surface and scattered in the host cell cytoplasm. Comparative analysis of ultrastructure of Anncaliia meligethi (the type species of the genus Anncaliia) and of B. vesicularum and B. algerae (the best-studied members of the genus Brachiola) clearly demonstrated that these microsporidia share many distinctive morphological features. The comparison of small subunit ribosomal DNA sequences showed high sequence identity of A. meligethi and B. algerae. Phylogenetic analyses indicated that the rDNA sequences of A. meligethi clustered with those of B. algerae suggesting a close relatedness of these microsporidia. The combination of molecular and morphological data provided clear evidence that these microsporidia belong to the same genus and therefore, warranted emendation of the genus Anncaliia and establishments of the following new combinations: Anncaliia vesicularum nov. comb., Anncaliia algerae nov. comb., Anncaliia connori nov. comb., and Anncaliia gambiae nov. comb. The generic name Brachiola is submerged according to the rule of priority.     

Barriers to gene flow in Embiotoca jacksoni, a marine fish lacking a pelagic larval stage

Abstract.— Marine species generally show high dispersal capabilities, which should be accompanied by high levels of gene flow and low speciation rates. However, studies that focused on the relationship between dispersal and gene flow in marine fishes have been inconclusive. This study focuses on the black surfperch, Embiotoca jacksoni , a temperate reef fish that lacks a pelagic larval stage and lives on almost continuous reefs along the California and Baja California coasts. Mitochondrial control-region sequences from 240 individuals were obtained, and phylogeographic patterns were analyzed. A major phylogeographic break was found at Santa Monica Bay, a sandy expanse that prevents adult dispersal. Deep water separating the southern California Channel Islands was also found to be a major barrier to gene flow. Minor phylogeographic breaks were also detected in the Big Sur/Morro Bay and in the Punta Eugenia/Guerrero Negro regions, but none in the Point Conception region. Gene flow levels in E. jacksoni were found to be almost identical to those of another species with limited dispersal, Acanthochromis polyacanthus , thus indicating that the lack of a pelagic larval stage combined with barriers to adult dispersal may have had similar effects on these two species.