Temporal genetic analysis of the endangered tidewater goby: extinction–colonization dynamics or drift in isolation?

Extinction and colonization dynamics are critical to understanding the evolution and conservation of metapopulations. However, traditional field studies of extinction–colonization are potentially fraught with detection bias and have rarely been validated. Here, we provide a comparison of molecular and field‐based approaches for assessment of the extinction–colonization dynamics of tidewater goby (Eucyclogobius newberryi) in northern California. Our analysis of temporal genetic variation across 14 northern California tidewater goby populations failed to recover genetic change expected with extinction–colonization cycles. Similarly, analysis of site occupancy data from field studies (94 sites) indicated that extinction and colonization are very infrequent for our study populations. Comparison of the approaches indicated field data were subject to imperfect detection, and falsely implied extinction–colonization cycles in several instances. For northern California populations of tidewater goby, we interpret the strong genetic differentiation between populations and high degree of within‐site temporal stability as consistent with a model of drift in the absence of migration, at least over the past 20–30 years. Our findings show that tidewater goby exhibit different population structures across their geographic range (extinction–colonization dynamics in the south vs. drift in isolation in the north). For northern populations, natural dispersal is too infrequent to be considered a viable approach for recolonizing extirpated populations, suggesting that species recovery will likely depend on artificial translocation in this region. More broadly, this work illustrates that temporal genetic analysis can be used in combination with field data to strengthen inference of extinction–colonization dynamics or as a stand‐alone tool when field data are lacking.     

Preying on invasives: the exotic New Zealand mudsnail in the diet of the endangered tidewater goby

This study documents predation by the endangered tidewater goby, Eucyclogobius newberryi, upon the invasive New Zealand mudsnail, Potamopyrgus antipodarum, in Big Lagoon, California, USA. To estimate the prevalence of NZ mudsnails in the diet of tidewater goby, the gastric contents of 411 individuals, collected monthly from April 2009 to August 2010, were examined. NZ mudsnails were found in the digestive tract of tidewater goby that ranged in size from 14 to 52 mm total length, corresponding to post-settlement and nearly maximal sizes of this species. Unlike other native species which are unable to extract nutrition from these snails, tidewater goby fully digest this hard-shelled prey, as evidenced by the presence of shell fragments and complete absence of intact shells in the hind gut. The number of ingested NZ mudsnail ranged from 1 to 27 (mean 4.4), and ranged in length from 0.39 to 4.0 mm. The average size of ingested snails increased with fish length (r ² = 0.42, P < 0.001). NZ mudsnails were found in over 80% of individuals during the summer and fall of 2009, when the estimated population size of tidewater goby in Big Lagoon was greater than three million. This study documents the first instance of a native and endangered species that preys upon and utilizes the NZ mudsnail as a food source, and suggests that tidewater goby can exert substantial predation pressure upon NZ mudsnails and take advantage of these readily available novel prey items.     

Using occupancy modelling to compare environmental DNA to traditional field methods for regional‐scale monitoring of an endangered aquatic species

Environmental DNA (eDNA) monitoring approaches promise to greatly improve detection of rare, endangered and invasive species in comparison with traditional field approaches. Herein, eDNA approaches and traditional seining methods were applied at 29 research locations to compare method‐specific estimates of detection and occupancy probabilities for endangered tidewater goby (Eucyclogobius newberryi). At each location, multiple paired seine hauls and water samples for eDNA analysis were taken, ranging from two to 23 samples per site, depending upon habitat size. Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance. Compared to traditional field sampling, eDNA provided improved occupancy parameter estimates and can be applied to increase management efficiency across a broad spatial range and within a diversity of habitats.     

The ecology, behavior, and conservation of the tidewater goby, Eucyclogobius newberryi

Understanding the ecology and behavior of endangered species, such as the tidewater goby, Eucyclogobius newberryi, is important for identifying problems and formulating solutions for species recovery. The tidewater goby forms isolated populations in California's coastal lagoons, creeks, and marshes. Rapid declines in the number of populations led to its listing as an endangered species in 1994. This benthic fish prefers stillwater habitats and feeds on small invertebrates. It is an annual species with an extended breeding season. Fish are larger in marsh habitats than in lagoon or creek habitats. The male digs a spawning burrow, preferably in sand, where he provides care for a single clutch. The tidewater goby is sex-role reversed: females compete more intensely than males for access to mates. The tidewater goby is a species at risk, in part due to narrow habitat preferences, isolation of populations, short lifespan, lack of marine dispersal, and vulnerability to introduced predatory fishes. Attributes that favor its recovery include euryhaline tolerances, rapid reproductive rate, its potential for opportunistic feeding, and the possibility of natural recolonization under certain circumstances. Potential conservation measures include protecting coastal marshes that adjoin creeks and lagoons, maintaining natural hydrologic regimes, preventing artificial breaching of the sandbar at the estuary's mouth, and preventing introductions of predatory fishes. Captive breeding and reintroduction of tidewater gobies are potential tools for recovery, provided that underlying problems of habitat availability and suitability and issues of genetic integrity and disease transmission are addressed. Further research into the tidewater goby's utilization of marsh habitats, dispersal mechanisms, response to artificial breaching events, and metapopulation genetics would provide additional information for management.     

Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi)

Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300‐ km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30‐ km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522‐base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.     

Invasion Genetics of Ponto-Caspian Gobies in the Great Lakes: A ‘Cryptic’ Species, Absence of Founder Effects, and Comparative Risk Analysis

Genetic variability and structure of nonindigenous vs native populations are compared for the Eurasian round goby Neogobius melanostomus and the tubenose goby Proterorhinus marmoratus, which both invaded Lake St. Clair of the North American Great Lakes about 1990. The round goby spread rapidly to all of the Great Lakes and the tubenose goby largely has been restricted to Lake St. Clair, with some recent range extension into western Lake Erie. Risk analyses may indicate whether genetic variability of colonizers is predictive of their relative invasive and establishment successes. The present investigation examined DNA sequence variation across the left domain of the mitochondrial DNA cytochrome b gene in round and tubenose gobies from Eurasian and Great Lakes locations. We also sequenced six additional Neogobius species (including the monkey N.␣fluviatilis, racer N. gymnotrachelus, and bigheadN. kessleri gobies that have been ‘on the move’ in Europe) and the knout goby Mesogobius batrachocephalus from the Black Sea in order to develop diagnostic genetic characters to identify them in case of future and/or undetected invasions and to delineate their phylogenetic relationships. Results show that a diverse number of haplotypes characterize round and tubenose goby populations from both North America and Eurasian sites, fitting a risk analysis prediction of high genetic variability in their successful introductions. Phylogenetic results indicate that the current genus Neogobius is paraphyletic and that the subgenusApollonia thus should be elevated to the level of genus, containingApollonia (N.) melanostomus (the round goby) andA. (N.) fluviatilis (the monkey goby). In addition, there appear to be two separate species of Proterorhinus marmoratus, a marine P. marmoratus Pallas 1814 in the Black Sea (matching the original type locality), and a ‘cryptic’ freshwater species in the Danube and Dnieper Rivers and probably other Eurasian freshwater habitats, as well as invasive in the Great Lakes. We suggest resurrecting the name P. semilunaris Heckel 1837 for the freshwater species (a taxon that was originally described from rivers draining into the Aegean Sea and the Danube River, but was later placed in synonymy with P. marmoratus). An erratum to this article is available at .     

Parasite fauna of native and non‐native populations of Neogobius melanostomus (Pallas, 1814) (Gobiidae) in the longitudinal profile of the Danube River

Parasite fauna of round goby Neogobius melanostomus (Pallas, 1814) in the Danube River was investigated in both its native range (two sites in the Bulgarian stretch of the Danube) and non‐native range of distribution (Croatian, Slovak and Austrian stretches) during 2005 and 2006. The aim was to identify possible changes in parasite communities associated with the introduction of a host into the new environment. A total of 29 metazoan parasite species were found to parasitize round goby in the Danube River; twelve of these parasite species were found in both the native and non‐native range of distribution. Introduction of a novel parasite species to the non‐native range via the round goby was not found. Eight parasite species occurred only in the native range and nine species only in the non‐native range of the round goby distribution. Losses of native parasite species in non‐native round goby populations and/or acquiring of novel parasite species in a new environment were not significant. Thirteen parasite taxa were recorded for the first time in round gobies. Three parasite taxa (Diplostomum spp., Pomphorhynchus laevis and Raphidascaris acus) were found in high prevalence and abundance at each sampling site in both the native and non‐native range. Parasite species diversity was assessed for each sampling site and season using three diversity indices (the Shannon, Simpson and Equitability indices), with the highest same‐season values found in a non‐native site in Slovakia (1.38, 0.69 and 0.60, respectively) and the lowest in a native site in Bulgaria (0.28, 0.12 and 0.14, respectively). Species diversity was higher in both non‐native round goby populations (Slovak and Austrian) compared to native Bulgarian populations. However, diversity indices values varied among almost all sampling sites.     

Phylogeography of the tidewater goby, Eucyclogobius newberryi (Teleostei, Gobiidae), in coastal California

The tidewater goby, Eucyclogobius newberryi, inhabits discrete, seasonally closed estuaries and lagoons along approximately 1500 km of California coastline. This species is euryhaline but has no explicit marine stage, yet population extirpation and recolonization data suggest tidewater gobies disperse intermittently via the sea. Analyses of mitochondrial control region and cytochrome b sequences demonstrate a deep evolutionary bifurcation in the vicinity of Los Angeles that separates southern California populations from all more northerly populations. Shallower phylogeographic breaks, in the vicinities of Seacliff, Point Buchon, Big Sur, and Point Arena segregate the northerly populations into five groups in three geographic clusters: the Point Conception and Ventura groups between Los Angeles and Point Buchon, a lone Estero Bay group from central California, and San Francisco and Cape Mendocino groups from northern California. The phylogenetic relationships between and patterns of molecular diversity within the six groups are consistent with repeated, and sometimes rapid, northward and southward range expansions out of central California caused by Quaternary climate change. Plio-Pleistocene tectonism, Quaternary coastal geography and hydrography, and historical human activities probably also influenced the modern geographic and genetic structure of E. newberryi. The phylogeography of E. newberryi is concordant with phylogeographic patterns in several other coastal California taxa, suggesting common extrinsic factors have had similar effects on different species. However, there is no evidence of a phylogeographic break coincident with a biogeographic boundary at Point Conception.     

Discrimination between invasive Ponto‐Caspian gobies using a PCR‐RFLP method

Accurate identification of invaders, and especially their juveniles and eggs, is a difficult task if several morphologically similar species co‐occur. The aim of the study was to develop and test a rapid and cost‐effective procedure for identification of five species of invasive gobies occurring in the middle Danube basin, namely round goby Neogobius melanostomus, bighead goby Ponticola kessleri, monkey goby Neogobius fluviatilis, racer goby Babka gymnotrachelus and tubenose goby Proterorhinus semilunaris. First, a 708 bp fragment of the cytochrome oxidase I gene was amplified and sequenced for representative samples of these five species. Appropriate sequences of the five species available in public databases were used for in silico analysis. A digestion of the amplified fragment with the BfaI enzyme was found to be suitable for the species identification, as it showed unique restriction patterns for each species. The technique was also successfully applied for fish remains from burbot Lota lota stomachs. Thus the technique could be a useful tool in monitoring biological invasions, especially by identifying specimens that could not be determined on the basis of morphological features. The results demonstrate that the PCR‐RFLP method may in some cases be more reliable for species identification than a standard DNA sequencing.     

Sex-role reversal in the tidewater goby, Eucyclogobius newberryi

Species in which females compete more intensely than males for access to mates are uncommon. Sex-role reversal in fishes has been documented only in species in which males bear eggs, such as pipefish and a mouth brooding cardinalfish. I investigated the reproductive behavior of the tidewater goby, Eucyclogobius newberryi (Gobiidae), to determine whether and to what degree this species is sex-role reversed. Males constructed and defended burrows for spawning in sand. Both sexes initiated courtship, but the female's breeding coloration was more striking. The intensity of sexual aggression was greater among females than among males. The female laid her entire clutch with a single male, and the male accepted only one clutch per brooding cycle. Both sexes spawned repeatedly (up to 12 times in aquaria), but fish did not form permanent pairs. Males cared for eggs in the burrow 9–11 days until hatching, and rarely if ever emerged to feed. Many aspects of male behavior (nest construction and defense, courtship, and parental care) were typical of most gobiids. On the other hand, female behavior (black nuptial coloration and intense female-female competition) was unusual, not only for gobiids but for animals in general. I therefore concluded that the tidewater goby is moderately sex-role reversed. Its sexual behavior is apparently unique among fishes because it is the only reported case of sex-role reversal in teleost males that do not bear eggs or developing young. This revised version was published online in July 2006 with corrections to the Cover Date.     

Morphological divergence and diagnostic characters of ginger goby <Emphasis Type="Italic">Neogobius eurycephalus</Emphasis> (Kessler, 1874) and surman goby <Emphasis Type="Italic">N. cephalargoides</Emphasis> Pinchuk, 1976 (Perciformes,Gobiidae)

Comparative analysis of morphometric characters of surman goby Neogobius cephalargoides and of two subspecies of ginger goby N. eurycephalus is made. Characteristics liable to size variation and sex dimorphism are revealed. Independence of the investigated species and the diagnostic value of characters previously suggested for classification are confirmed. The obtained data confirm isolation of north-western populations of ginger goby as a separate subspecies N. eurycephalus odessicus and suitability of three meristic characters for differentiation of the subspecies: the number of rays in the second dorsal fin and anal fin and the number of transverse rows of scales.     

Relative abundance of Ponto‐Caspian gobiids in the lower Vistula River (Poland) 3‐ to 4 years after first appearance

In the years 2000–2001, specimens of two Ponto‐Caspian gobiids (racer goby Neogobius gymnotrachelus and monkey goby Apollonia fluviatilis) were recorded for the first time in the lower Vistula River, which is a part of the central inland corridor used by Ponto‐Caspian species to migrate in Europe. In 2004, seine net surveys were made in the river course to examine relative abundance of the non‐indigenous gobiids in the local small‐fish community. Altogether 4420 specimens with total lengths ranging from 10 to 340 mm (mostly <100 mm) belonging to 18 species were recorded in 70 hauls. Monkey goby was one of the subdominant species (18.1% of total number of fish captured; 64.3% frequency of occurrence in hauls) together with bleak Alburnus alburnus (21.0, 54.3), roach Rutilus rutilus (18.2, 67.1) and three‐spined stickleback Gasterosteus aculaetus (17.3, 37.1). Racer goby was less abundant but quite common (2.5, 32.9), similar to common bream/white bream Abramis brama/Blicca bjoerkna (6.4, 47.1), Eurasian perch Perca fluviatilis (5.7, 57.1), dace Leuciscus leuciscus (4.2, 40.0) and European bitterling Rhodeus sericeus amarus (3.4, 27.1). The study shows that Ponto‐Caspian gobiids dispersed successfully in the lower Vistula, becoming species common to its nearshore zone 3‐ to 4 years after their first appearance.     

Identification of expressed sequence tags of watermelon (Citrullus lanatus) leaf at the vegetative stage

A cDNA library was constructed using mRNA prepared from leaves of watermelon [Citrullus lanatus (Thunb.) Matsum&Nakai] at the vegetative stage. Randomly selected cDNA clones were sequenced in order to identify potentially informative genes. Database comparisons indicated that out of the 704 watermelon cDNA clones, 399 clones (56.7 %) revealed a high degree of sequence similarity to genes from other organisms. These expressed sequence tag clones were divided into ten categories depending upon gene function. Since this kind of experiment has not previously been carried out in this genome, random nucleotide sequencing of these cDNAs could contribute considerable information concerning the novel genes in this organism. Received: 10 July 1999 / Revision received: 20 December 1999 / Accepted: 11 January 2000     

Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the north‐west Pacific

Larval dispersal may have an important effect on genetic structure of benthic fishes. To examine the population genetic structure of spottedtail goby Synechogobius ommaturus, a 478 base pair (bp) fragment of the hypervariable portion of the mtDNA control region was sequenced and used to interpret life‐history characteristics and larval dispersal strategy. Individuals (n = 186) from 10 locations on the coasts of China and Korea were analysed and 44 haplotypes were obtained. The levels of haplotype and nucleotide diversity were higher in East China Sea populations than in other populations. Both the phylogenetic tree and the minimum spanning tree showed that no significant genealogical structures corresponding to sampling locations existed. AMOVA and pair‐wise F_ST revealed significant genetic differentiation between populations from Korea and China. A significant isolation by distance pattern was observed in this species (r = 0·53, P < 0·001). Both mismatch distribution analysis and neutrality tests showed S. ommaturus to have experienced a recent population expansion. These results suggest that the Pleistocene ice ages had a major effect on the phylogeographic pattern of S. ommaturus, that larvae might avoid offshore dispersal and that dispersal of larvae may maintain a migration–drift equilibrium.     

Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.)

We report the development of microsatellites or simple sequence repeats (SSRs) in the olive tree (Olea europaea L.). Forty three positive clones obtained by the screening of a GA-enriched genomic library were sequenced and primers were designed for 13 microsatellite loci. Five primer pairs amplified polymorphic products of the expected size range. SSR polymorphism was explored in a set of 46 olive cultivars. A total of 26 alleles were detected for the five loci. Heterozygosity ranged from 0.46 to 0.71. Ninety one per cent of the cultivars had unique multilocus genotypes. Microsatellite segregation was studied in a complex population from a cross between the commercial cultivars ’Leccino’ and ’Dolce Agogia’. Received: 3 February 2000 / Accepted: 21 March 2000     

EST-library construction using spore RNA of the arbuscular mycorrhizal fungus Gigaspora rosea

RNA was extracted from activated spores of the arbuscular mycorrhizal fungus Gigaspora rosea. Double-stranded cDNA was synthesised, digested and cloned into the vector lambda-ZAP express. Of the 1,500 clones obtained, 1.5% carried inserts of the rRNA gene cluster. After excision, inserts from 50 randomly selected clones were sequenced. Database searches revealed that 62% of the clones had similarities to already known sequences. These mainly code for proteins involved in translation and protein processing, replication and the cell cycle and cell signal transduction. One fragment probably belonged to a metallothionein-encoding gene which may be involved in heavy-metal binding. The method presented is an easy and rapid way to obtain short fragments of coding regions for expressed sequence tag libraries. Accepted: 28 November 2000     

Effects of changes in seagrass shoot density and leaf height on the abundance of juveniles of Acentrogobius pflaumii in a Zostera marina bed

The effects of changes in the structural complexity of a seagrass (Zostera marina) habitat on the density of juveniles of the streaked goby, Acentrogobius pflaumii, were investigated by field experimentation at Moroiso Bay, Miura Peninsula, Japan. The experimental design, which included seven treatments plus a control, included reduction of seagrass shoot densities and leaf heights as well as complete removal of seagrass. Throughout the study period, juvenile densities remained similar among the experimental quadrats, including the completely cleared quadrat. On the other hand, juveniles did not appear over the bare sandy substratum surrounding the experimental seagrass bed. Within the bed, prey densities were high, being similar among the experimental quadrats, whereas prey were relatively scarce over the surrounding bare substratum. This result suggested that streaked goby juveniles were not attracted to the structure of the Zostera bed per se and that their distribution patterns may be determined by other factors, such as prey availability. Received: September 25, 2000 / Revised: November 22, 2000 / Accepted: January 16, 2001     

Differential modes of selection on the rhodopsin gene in coastal Baltic and North Sea populations of the sand goby,Pomatoschistus minutus

An excellent model to elucidate the mechanisms and importance of evolution in the marine environment is the spectral tuning mechanism of the visual pigment in vertebrates. In the sand goby Pomatoschistus minutus (Teleostei; Gobiidae), a distribution‐wide study showed that spatial variation at the rhodopsin gene (RH1) matches the characteristics of specific light environments. This match suggests that populations are locally adapted to selective light regimes targeting the RH1 gene. If so, then the direction of selection should depend on the regional spatial and temporal stability of the light conditions. We tested this prediction by comparing goby populations from two regions: the Baltic Sea, characterized by divergent, but temporally stable light conditions, and the North Sea, characterized by locally heterogeneous and temporally variable light conditions. RH1 sequences of 491 Pomatoschistus minutus individuals from 15 locations were analysed. We found that variation at the RH1 gene in the Baltic populations showed signatures of diversifying selection, whereas the RH1 gene in the North Sea showed signatures of stabilizing selection. These different modes of selection are consistent with the regional light conditions and hence support our predictions, but may also be influenced by migration between the open sea and more turbid estuarine environments. An interesting observation is that within one gene, synonymous and non‐synonymous SNPs show a totally different pattern between populations. Population differentiation based on non‐synonymous SNPs of the RH1 gene correlated with spectral variation of the local environment of the sand goby populations. In contrast, the differentiation based on synonymous SNPs of RH1 reflects more the neutral historical pattern of the species.     

Bacteria Associated with the Bleached and Cave Coral Oculina patagonica

The relative abundance of bacteria in the mucus and tissues of Oculina patagonica taken from bleached and cave (azooxanthellae) corals was determined by analyses of the 16S rRNA genes from cloned libraries of extracted DNA and from isolated colonies. The results were compared to previously published data on healthy O. patagonica. The bacterial community of bleached, cave, and healthy corals were completely different from each other. A tight cluster (>99.5% identity) of bacteria, showing 100% identity to Acinetobacter species, dominated bleached corals, comprising 25% of the 316 clones sequenced. The dominant bacterial cluster found in cave corals, representing 29% of the 97 clones sequenced, showed 98% identity to an uncultured bacterium from the Great Barrier Reef. Vibrio splendidus was the most dominant species in healthy O. patagonica. The culturable bacteria represented 0.1–1.0% of the total bacteria (SYBR Gold staining) of the corals. The most abundant culturable bacteria in bleached, cave, and healthy corals were clusters that most closely matched Microbulbifer sp., an α-proteobacterium previously isolated from healthy corals and an α-protobacterium (AB026194), respectively. Three generalizations emerge from this study on O. patagonica: (1) More bacteria are associated with coral tissue than mucus; (2) tissue and mucus populations are different; (3) bacterial populations associated with corals change dramatically when corals lack their symbiotic zooxanthellae, either as a result of the bleaching disease or when growing in the absence of light.