Diversification of body shape in Sebastes rockfishes of the north‐east Pacific

Body shape variation is integrally related to many aspects of fish ecology, including locomotion and foraging, and can indicate the functional diversity of fish assemblages. Few studies have thoroughly characterized body shape in a diverse marine fish clade, or investigated both temporal and spatial patterns of variation in body shape disparity. Here, I use digital photographs to measure geometric body shape in 66 species of north‐east Pacific rockfish (Sebastes spp.), including a correction for error introduced by arching of specimens. Different components of interspecific shape variation show associations with fish size, depth habitat, trophic niche and phylogenetic relationships. Overall, the accumulation of body shape disparity appears to have been near‐constant over time, and shows little variation across the latitudinal range of rockfish.     

Otolith shape lends support to the sensory drive hypothesis in rockfishes

The sensory drive hypothesis proposes that environmental factors affect both signalling dynamics and the evolution of signals and receivers. Sound detection and equilibrium in marine fishes are senses dependent on the sagittae otoliths, whose morphological variability appears intrinsically linked to the environment. The aim of this study was to understand if and which environmental factors could be conditioning the evolution of this sensory structure, therefore lending support to the sensory drive hypothesis. Thus, we analysed the otolith shape of 42 rockfish species (Sebastes spp.) to test the potential associations with the phylogeny, biological (age), ecological (feeding habit and depth distribution) and biogeographical factors. The results showed strong differences in the otolith shapes of some species, noticeably influenced by ecological and biogeographical factors. Moreover, otolith shape was clearly conditioned by phylogeny, but with a strong environmental effect, cautioning about the use of this structure for the systematics of rockfishes or other marine fishes. However, our most relevant finding is that the data supported the sensory drive hypothesis as a force promoting the radiation of the genus Sebastes. This hypothesis holds that adaptive divergence in communication has significant influence relative to other life history traits. It has already been established in Sebastes for visual characters and organs; our results showed that it applies to otolith transformations as well (despite the clear influence of feeding and depth), expanding the scope of the hypothesis to other sensory structures.     

Speciation along a depth gradient in a marine adaptive radiation

Oceans are home to much of the world''s biodiversity, but we know little about the processes driving speciation in marine ecosystems with few geographical barriers to gene flow. Ecological speciation resulting from divergent natural selection between ecological niches can occur in the face of gene flow. Sister species in the young and ecologically diverse rockfish genus Sebastes coexist in the northeast Pacific, implying that speciation may not require geographical isolation. Here, I use a novel phylogenetic comparative analysis to show that rockfish speciation is instead associated with divergence in habitat depth and depth-associated morphology, consistent with models of parapatric speciation. Using the same analysis, I find no support for alternative hypotheses that speciation involves divergence in diet or life history, or that speciation involves geographic isolation by latitude. These findings support the hypothesis that rockfishes undergo ecological speciation on an environmental gradient.     

Investigating the complexities of sustainable fishing at a prehistoric village on western Vancouver Island, British Columbia, Canada

Zooarchaeological data provide direct evidence of long-term human resource utilization relevant to the modern study of sustainability and conservation. On the northwest coast of North America, prehistoric aboriginal communities relied heavily on nearshore marine fish species, many of which have life history characteristics that make them vulnerable to overexploitation. This study examines temporal trends in the abundance and distribution of nearshore fish from skeletal remains recovered from three separate areas of a prehistoric coastal village on the west coast of Vancouver Island (ca. 1800–250 yr BP). Over the course of 1500 years, site inhabitants from these contemporaneously occupied areas regularly utilized Sebastes spp. (rockfish), with varying impacts on abundance and total length. Contrasting temporal trends in Sebastes spp. total length in separate village areas suggest different consequences to prehistoric harvesting practices, differences that can be linked to ethnographic and archaeological evidence of lineage-based territories. These long-term zooarchaeological data provide unique insights into the context and challenges of sustainable resource use in prehistory and can inform contemporary conservation efforts focused on similar species in this modern-day marine protected area.     

Genetic Evidence of Postglacial Population Expansion in Puget Sound Rockfish (Sebastes emphaeus)

Several rockfish species (genus Sebastes) along the northeastern Pacific Ocean have rapidly declined in abundance owing in part to overfishing. A striking exception is the dwarf-like Puget Sound rockfish Sebastes emphaeus, whose densities have increased by several orders of magnitude over the last several decades. To describe their genetic structure, we sequenced 395 bp from the mitochondrial control region of 128 S. emphaeus adults from 5 locations spanning approximately 120 km of the Northwest Straits of Washington state. We detected no significant genetic differentiation among these populations and substantial genetic variation within populations, a pattern that may indicate high levels of ongoing gene flow. Preliminary data from 2 microsatellite loci are also consistent with panmixia. The mtDNA sequences also suggest that Puget Sound rockfish populations have expanded substantially since the retreat of Pleistocene glaciers made habitat in Puget Sound region available approximately 12,000 years ago.     

TESTS FOR ANCIENT SPECIES FLOCKS BASED ON MOLECULAR PHYLOGENETIC APPRAISALS OF SEBASTES ROCKFISHES AND OTHER MARINE FISHES

The concept of species flocks has been central to previous interpretations of patterns and processes of explosive species radiations within several groups of freshwater fishes. Here, molecular phytogenies of species-rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes. Similar appraisals were conducted using molecular data previously published for particular cichlid fishes in Africa that epitomize, by virtue of a rapid and recent radiation of species, the traditional concept of an intralacustrine “species flock.” As gauged by the magnitudes of genetic divergence in cytochrome b sequences from mitochondrial DNA, as well as in allozymes, most speciation events in the Sebastes complex were far more ancient than those in the cichlids. However, statistical tests of the nodal placements in the Sebastes phylogeny suggest that speciation events in the rockfishes were temporally nonrandom, with significant clustering of cladogenetic events in time. Similar conclusions also apply to an ancient complex of icefishes (within the Notothenioidei) analyzed in the same fashion. Thus, the rockfishes (and icefishes) may be interpreted as ancient species flocks in the marine realm. The analyses exemplified in this report introduce a conceptual and operational approach for extending the concept of species flocks to additional environmental settings and evolutionary timescales.     

Molecular phylogenetic perspective on speciation in the genus <Emphasis Type="Italic">Sebastes</Emphasis> (Scorpaenidae) from the Northwest Pacific and the position of <Emphasis Type="Italic">Sebastes</Emphasis> within the subfamily Sebastinae

In the Northeast and the Northwest Pacific, 26 and 68 species of Sebastes occur, respectively, the similar appearance of some pairs of shallow coastal water species in the two regions having been interpreted as evidence either for migration of ancestral species or of morphological convergence. To distinguish between these competing hypotheses, a portion of the mitochondrial DNA (mtDNA) cytochrome b gene was sequenced from 23 species of Sebastes from the Northwest Pacific and phylogenetic trees constructed so as to include the existing data from Northeastern species of Sebastes. The results clearly indicated separate origins for external morphology in Northeast and Northwest Pacific species. The shallow coastal water species in the Northwest Pacific are thought to have diverged from about 9.8MYA. Furthermore, the phylogenetic position of Sebastes was inferred among the subfamily Sebastinae, Helicolenus, Hozukius, Sebastes, and Sebastiscus, the results suggesting that Helicolenus and Hozukius are more closely related to Sebastes than Sebastiscus.     

Vicariance and dispersal across an intermittent barrier: population genetic structure of marine animals across the Torres Strait land bridge

Biogeographic barriers, some transitory in duration, are likely to have been important contributing factors to modern marine biodiversity in the Indo-Pacific region. One such barrier was the Torres Strait land bridge between continental Australia and New Guinea that persisted through much of the late Pleistocene and separated Indian and Pacific Ocean taxa. Here, we examine the patterns of mitochondrial DNA diversity for marine animals with present-day distributions spanning the Torres Strait. Specifically, we investigate whether there are concordant signatures across species, consistent with either vicariance or recent colonization from either ocean basin. We survey four species of reef fishes (Apogon doederleini, Pomacentrus coelestis, Dascyllus trimaculatus, and Acanthurus triostegus) for mtDNA cytochrome oxidase 1 and control region variation and contrast these results to previous mtDNA studies in diverse marine animals with similar distributions. We find substantial genetic partitioning (estimated from F-statistics and coalescent approaches) between Indian and Pacific Ocean populations for many species, consistent with regional persistence through the late Pleistocene in both ocean basins. The species-specific estimates of genetic divergence, however, vary greatly and for reef fishes we estimate substantially different divergence times among species. It is likely that Indian and Pacific Ocean populations have been isolated for multiple glacial cycles for some species, whereas for other species genetic connections have been more recent. Regional estimates of genetic diversity and directionality of gene flow also vary among species. Thus, there is no apparent consistency among historical patterns across the Torres Strait for these co-distributed marine animals.     

Assessing Genetic Diversity of Brazilian Reef Fishes by Chromosomal and DNA Markers

Little is known on genetics of Brazilian coral reef fish and most of this information is limited to chromosome characterization of major representative species. The diploid chromosome number in marine fish varies from 2n= 22–26 to 2n = 240–260. Despite of this apparent diversity, most studied marine species have a diploid complement with 48 acrocentric chromosomes. This latter trend is mostly observed among Perciformes, an important major taxon of coral reef fishes. Studies in the families Pomacentridae, Pomacanthidae and Chaetodontidae, for example, have shown a common karyotype pattern entirely formed by 48 uniarmed chromosomes. However, rare numerical and structural chromosome polymorphisms and cryptic chromosome rearrangements involving heterochromatin segments and/or nucleolar organizing sites have been reported among such fishes. Although new chromosome forms can contribute to the establishment of genetically isolated populations, their role in reef fish speciation at marine realm still is an open question. More recently, genomic DNA analyses using RAPD and microsatellites, and sequencing and RFLP of mitochondrial DNA have increasingly been used in Atlantic reef fish species. Genetic homogeneity over wide geographical ranges has been reported for different fish groups, in contrast to several cases of population substructuring related to environmental constraints or evolutionary history. Amazonas outflow and upwelling on the Southeastern coast of Brazil are believed to be strong barriers to dispersal of some reef species. Moreover, it is suggested that the pattern of speciation and population structure at South Atlantic is quite distinctive from Pacific Ocean, even when comparing closely related taxa. Further genetic studies are strongly encouraged in Brazilian reef fishes in order to provide a reliable scenario of the genetic structure in this important and diverse fish group.     

Use of Microsatellite Locus Flanking Regions for Phylogenetic Analysis? A Preliminary Study of Sebastes subgenera

The systematics of the species-rich genus of Sebastes rockfish has not been resolved, and is unlikely to be resolved using morphological criteria. Using an alternative approach based on DNA sequence variation, we sampled the genome for random, presumably neutral, nuclear DNA sequences, by sequencing microsatellite flanking regions of 15 Sebastes species (representing 15 of 22 extant subgenera) and Hozukius emblemarius. We aligned sequences of flanking regions of eight of the 13 loci that amplified, which presumably are homologous. In aggregate, the aligned sequences included 848 bp, 53 bp of which were polymorphic. The base changes among species included 27 transitions, 20 transversions, three multiple substitutions, and three deletions or insertions. The flanking regions at different loci had different base substitution rates. Nucleotide divergence among Sebastes species ranged from 0.0012 to 0.0216, whereas nucleotide divergence between Sebastes and Hozukius species ranged from 0.0095 to 0.0240. We used maximum parsimony, neighbor-joining, and maximum likelihood methods to examine relationships among the species. H. emblemariusformed a separate group, and five of the western Pacific Ocean species of rockfish clustered together, suggesting that they may have shared an evolutionary history distinct from many North American species. The flanking regions of some microsatellite loci contain DNA sequence variation that distinguishes rockfish species and may prove useful for clarifying relationships among rockfish, or other closely related species.     

Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean

Understanding how genetic diversity is maintained across patchy marine environments remains a fundamental problem in marine biology. The Coral Triangle, located in the Indo‐West Pacific, is the centre of marine biodiversity and has been proposed as an important source of genetic diversity for remote Pacific reefs. Several studies highlight Micronesia, a scattering of hundreds of small islands situated within the North Equatorial Counter Current, as a potentially important migration corridor. To test this hypothesis, we characterized the population genetic structure of two ecologically important congeneric species of reef‐building corals across greater Micronesia, from Palau to the Marshall Islands. Genetic divergences between islands followed an isolation‐by‐distance pattern, with Acropora hyacinthus exhibiting greater genetic divergences than A. digitifera, suggesting different migration capabilities or different effective population sizes for these closely related species. We inferred dispersal distance using a biophysical larval transport model, which explained an additional 15–21% of the observed genetic variation compared to between‐island geographical distance alone. For both species, genetic divergence accumulates and genetic diversity diminishes with distance from the Coral Triangle, supporting the hypothesis that Micronesian islands act as important stepping stones connecting the central Pacific with the species‐rich Coral Triangle. However, for A. hyacinthus, the species with lower genetic connectivity, immigration from the subequatorial Pacific begins to play a larger role in shaping diversity than input from the Coral Triangle. This work highlights the enormous dispersal potential of broadcast‐spawning corals and identifies the biological and physical drivers that influence coral genetic diversity on a regional scale.     

Mortalities of kelp-forest fishes associated with large oceanic waves off central California, 1982–1983

Synopsis Observations of three incidents of the mass mortality of nearshore fishes are reported; each corresponded to periods of high-amplitude, long-period swells during the 1982–1983 El Niño event along the coast of central California. Members of the nearshore kelp forest fish assemblage, primarily of the genusSebastes, accounted for 96% of the observed mortalities andS. mystinus (blue rockfish) alone accounted for 72%.     

Long‐term panmixia in a cosmopolitan Indo‐Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

Phylogeographical studies have shown that some shallow‐water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long‐term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long‐term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo‐Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two‐fold: first, to test for broad‐scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo‐Pacific and a range‐wide, long‐term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.     

Microsatellite markers for the heavily exploited canary (Sebastes pinniger) and other rockfish species

The isolation and characterization of nine polymorphic microsatellite loci (eight tetranucleotide and one dinucleotide) from the canary rockfish Sebastes pinniger are described. Polymorphism at these loci revealed from six to 28 alleles, with expected heterozygosities ranging between 0.42 and 0.88, enabling high‐resolution genetic population structure investigation for this overfished species in the northeastern Pacific. They also amplify in 13 other congeneric species, providing highly variable loci for research on other rockfishes.     

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish,Sebastes thompsoni (Pisces,Scorpaenoidei)

The goldeye rockfish, Sebastes thompsoni, commercial rockfish catch in the Northwest Pacific Ocean, may influence its population structure. To clarify the population genetic structure of Korean S. thompsoni and its degree of hybridization with the most close species, Sebastes joyneri, we analyzed a mitochondrial (mt) DNA control region and eleven polymorphic microsatellite (ms) loci. S. joyneri individuals were clearly distinguished from S. thompsoni by the mtDNA control region and ms loci results, with single interspecific hybridization between two species suggesting no impact on genetic structure of S. thompsoni. Analysis of mtDNA revealed no population structure within S. thompsoni, suggesting the survival of a single population in southern refugia during the glacial period. The ms loci results, in contrast, showed two genetically distinct clusters within S. thompsoni: One was predominant throughout Korean coasts (from the Yellow Sea, via the Korea Strait to the East Sea); the other was predominant at Dokdo Island in the East Sea; and both occurred in similar ratios at Wangdolcho Reef in the East Sea. A possible factor that restricts gene flow between Korean coastal and offshore populations in the East Sea may be related to the complex oceanic current patterns such as eddies and upwelling, which represent impermeable barriers to population connectivity for this species. Our findings highlight that these two populations might be representative of two separate stock within Korean waters and maintain their geographically related genetic structure.     

Multilocus phylogeography of the sea snake Hydrophis curtus reveals historical vicariance and cryptic lineage diversity

The Indo‐Australian archipelago (IAA) supports the world's highest diversity of marine fish, invertebrates and reptiles. Many of the marine fish and invertebrates show congruent phylogeographic patterns, supporting a view that the region's complex geo‐climatic history has played an important role in generating its exceptional biodiversity. Here, we examine population genetic structure of the viviparous sea snake, Hydrophis curtus, to assess how past and present barriers to gene flow in the IAA have contributed to genetic and species diversity in a fully marine reptile. Mitochondrial and anonymous nuclear sequences and ten microsatellite loci were used to identify patterns of historical genetic structure and population expansion, reconstruct dated genealogies and assess levels of recent gene flow. These markers revealed strong concordant geographic structure within H. curtus with a prominent genetic break between populations broadly distributed in the Indian Ocean and the West Pacific. These populations were estimated to have diverged in the late Pliocene or early Pleistocene, and microsatellite admixture analyses suggested limited recent gene flow between them despite the current lack of barriers to dispersal, indicating possible cryptic species. Subsequent divergence in the mid–late Pleistocene was detected within the West Pacific clade among the populations in the Phuket‐Thailand region, South‐East Asia and Australia, and two of these populations also showed genetic signals of recent range expansions. Our results show that climatic fluctuations during the Plio‐Pleistocene generated high levels of cryptic genetic diversity in H. curtus, and add to similar findings for diverse other marine groups in the IAA.     

Do abiotic and ontogenetic factors influence the diet of a generalist predator? Feeding ecology of the Pacific spiny dogfish (<Emphasis Type="Italic">Squalus suckleyi</Emphasis>) in the northeast Pacific Ocean

Stomach contents from 1221 Pacific spiny dogfish (Squalus suckleyi) were collected from the Gulf of Alaska over 2004–2006 and analyzed to determine predominant prey species. Pacific spiny dogfish in the Gulf of Alaska have a variable diet suggesting that they are generalist feeders. Of the 68.30% of stomachs with prey contents, the most important prey groups based on the percent prey-specific index of relative importance (%PSIRI) were shrimp (27.06%), cephalopods (17.16%), and forage fish (17.11%). Remaining components of the diet were inconsistent. Commercially valuable species, such as salmon, Oncorhynchus spp., and rockfish, Sebastes spp. constituted only 2.37% and 1.51% of the diet of Pacific spiny dogfish, respectively. Diet diversity was not significantly influenced by spatial, temporal or ontogenetic factors; however, trophic level of prey and average prey item weight varied both interannually and with ontogeny. With increasing size, Pacific spiny dogfish incorporate larger prey items into their diet, and diet composition may be driven more by seasonal availability and prey size than any other factors.     

Cloning and characterization of novel microsatellite DNA markers for the grass rockfish,Sebastes rastrelliger,and cross‐species amplification in 10 related Sebastes spp

Here we report development and characterization of seven polymorphic loci derived from grass rockfish (Sebastes rastrelliger) genomic DNA phagemid libraries enriched for microsatellite motifs. Within grass rockfish, average allelic diversity was 11.3 alleles per locus and average heterozygosity was 0.73. The seven loci also were surveyed in 10 related species of Sebastes, where allelic diversity ranged from highly polymorphic to monomorphic. Deviations from Hardy–Weinberg were nonsignificant in all but one species/locus combination suggesting low occurrence of null alleles. Significant linkage disequilibrium was detected among three loci, but these events were limited to a single species in each case.     

Evolution of a Mitochondrial CytochromebGene Sequence in the Species-Rich GenusSebastes(Teleostei, Scorpaenidae) and Its Utility in Testing the Monophyly of the SubgenusSebastomus

The ecologically diverse and species-rich rockfishes (Sebastes) are a useful group for the study of marine speciation. The monophyly of the genus is generally accepted, as is the validity of most of the numerous species found along the West Coast of North America. However, the subgeneric groupings that would help in the proposal and interpretation of various speciation schemes are poorly supported based on widely overlapping morphological characters. The use of genetic characters provides an alternative approach. In this study, we present the first quantitative analysis supporting the monophyly of all 14 species of the subgenusSebastomusamong 54 congeners. The structural features and evolution of the 750 bp of the cytochromebgene used to test the monophyly were similar to those of other vertebrates. Low levels of intrageneric sequence divergence (<10%) and incipient levels of saturation at third-codon positions were found in the gene. The monophyly ofSebastomuswas supported in extensive phylogenetic analyses using distance, cladistic, and likelihood methods. Further corroboration was obtained from permutation- and simulation-based statistical tests.     

Pelagic larval duration and population connectivity in New Zealand triplefin fishes (Tripterygiidae)

The relationship between pelagic larval duration (PLD) and population connectivity in marine fishes has been controversial, but most studies to date have focused on tropical taxa. Here, we examine PLD in 11 species of triplefin fishes from a temperate environment in the Hauraki Gulf, New Zealand, to describe daily increment patterns and settlement marks in the otoliths. The formation of daily increments was validated using larvae of known age and tetracycline marking of settled juveniles. Settlement mark identity was verified by comparing total increment counts from otoliths of recently settled fishes with PLD counts from post-settlement fishes. A similar pattern of three groups of increments across the otolith was found in all specimens examined. The settlement mark was similar in all species and occurred as a sharp drop in increment width within the area of transition in optical density. PLD was lengthy, compared to species of triplefins from elsewhere, and ranged between 54.4 ± 1.7 SE days in Bellapiscis lesleyae to 86.4 ± 2.6 SE days in Forsterygion malcolmi. Variation in PLD within species was high but did not mask interspecific differences. PLD was not phylogenetically constrained, as sister species differed significantly in PLD. PLD was compared with genetic population connectivity for eight of the study species using mitochondrial gene flow data from Hickey, Lavery, Hannan, Baker, Clements. Mol Ecol 18:680–696 (2009). The observed lack of correlation between PLD and gene flow suggests that dispersal is limited by other factors, such as larval behaviour and the availability of settlement habitat.