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

Local adaptation of antipredator behaviors in populations of a temperate reef fish

The temperament of animals can vary among individuals and among populations, but it is often unclear whether spatial variation in temperament is the result of acclimation to local environmental conditions or genetic adaptation to spatial differences in natural selection. This study tested whether populations of a marine fish that experience different levels of mortality and fishing exhibited local adaptation in behaviors related to predator avoidance and evasion. First, we measured variation in reactivity to perceived risk in wild populations of black surfperch (Embiotoca jacksoni). We compared flight initiation distances (FID) between populations with significantly different mortality rates. After finding that FID values were substantially lower in the low-risk locations, we tested for local adaptation by rearing lab-born offspring from both high- and low-risk populations in a common environment before measuring their behavior. Lab-reared offspring from high- and low-risk populations exhibited significant differences in several behaviors related to reactivity. Between 23 and 43% of the total variation in behaviors we measured could be attributed to source population. These results thus suggest that a substantial amount of spatial variation in behaviors related to predator evasion may represent local adaptation. In addition, behaviors we measured had an average, broad-sense heritability of 0.24, suggesting that the behavioral tendencies of these populations have some capacity to evolve further in response to any changes in selection.

Population genomics reveals a mismatch between management and biological units in green abalone (Haliotis fulgens)

Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone (Haliotis fulgens) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units of H. fulgens fishery; hence, the stock assessment and management areas should be revised.

"A cleaner break": Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta)

Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.

Habitat Discontinuities Separate Genetically Divergent Populations of a Rocky Shore Marine Fish

Habitat fragmentation has been suggested to be responsible for major genetic differentiations in a range of marine organisms. In this study, we combined genetic data and environmental information to unravel the relative role of geography and habitat heterogeneity on patterns of genetic population structure of corkwing wrasse (Symphodus melops), a rocky shore species at the northern limit of its distribution range in Scandinavia. Our results revealed a major genetic break separating populations inhabiting the western and southern coasts of Norway. This genetic break coincides with the longest stretch of sand in the whole study area, suggesting habitat fragmentation as a major driver of genetic differentiation of this obligate rocky shore benthic fish in Scandinavia. The complex fjords systems extending along the western coast of Norway appeared responsible for further regional genetic structuring. Our findings indicate that habitat discontinuities may lead to significant genetic fragmentation over short geographical distances, even for marine species with a pelagic larval phase, as for this rocky shore fish.

The effect of biogeographic and phylogeographic barriers on gene flow in the brown smoothhound shark, Mustelus henlei, in the northeastern Pacific

We assessed the effects of the prominent biogeographic (Point Conception and the Peninsula of Baja California) and phylogeographic barriers (Los Angeles Region) of the northeastern Pacific on the population connectivity of the brown smoothhound shark, Mustelus henlei (Triakidae). Data from the mitochondrial control region and six nuclear microsatellite loci revealed significant population structure among three populations: northern (San Francisco), central (Santa Barbara, Santa Catalina, Punta Lobos, and San Felipe), and southern (Costa Rica). Patterns of long-term and contemporary migration were incongruent, with long-term migration being asymmetric and occurring in a north to south direction and a lack of significant contemporary migration observed between localities with the exception of Punta Lobos that contributed migrants to all localities within the central population. Our findings indicate that Point Conception may be restricting gene flow between the northern and central populations whereas barriers to gene flow within the central population would seem to be ineffective; additionally, a contemporary expansion of tropical M. henlei into subtropical and temperate waters may have been observed.

Multiple paternity is a shared reproductive strategy in the live-bearing surfperches (Embiotocidae) that may be associated with female fitness

According to Bateman's principle, female fecundity is limited relative to males, setting the expectation that males should be promiscuous, while females should be choosy and select fewer mates. However, several surfperches (Embiotocidae) exhibit multiple paternity within broods indicating that females mate with multiple males throughout the mating season. Previous studies found no correlation between mating success and reproductive success (i.e., a Bateman gradient). However, by including samples from a broader range of reproductive size classes, we found evidence of a Bateman gradient in two surfperch species from distinct embiotocid clades. Using microsatellite analyses, we found that 100% of the spotfin surfperch families sampled exhibit multiple paternity (Hyperprosopon anale, the basal taxon from the only clade that has not previously been investigated) indicating that this tactic is a shared reproductive strategy among surfperches. Further, we detected evidence for a Bateman gradient in H. anale; however, this result was not significant after correction for biases. Similarly, we found evidence for multiple paternity in 83% of the shiner surfperch families (Cymatogaster aggregata) sampled. When we combine these data with a previous study on the same species, representing a larger range of reproductive size classes and associated brood sizes, we detect a Bateman gradient in shiner surfperch for the first time that remains significant after several conservative tests for bias correction. These results indicate that sexual selection is likely complex in this system, with the potential for conflicting optima between sexes, and imply a positive shift in fertility (i.e., increasing number) and reproductive tactic with respect to the mating system and number of sires throughout the reproductive life history of females. We argue that the complex reproductive natural history of surfperches is characterized by several traits that may be associated with cryptic female choice, including protracted oogenesis, uterine sac complexity, and sperm storage.

Phylogeography of the California sheephead, Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation.

Connectivity of the habitat-forming kelp, Ecklonia radiata within and among estuaries and open coast

With marine protected areas being established worldwide there is a pressing need to understand how the physical setting in which these areas are placed influences patterns of dispersal and connectivity of important marine organisms. This is particularly critical for dynamic and complex nearshore marine environments where patterns of genetic structure of organisms are often chaotic and uncoupled from broad scale physical processes. This study determines the influence of habitat heterogeneity (presence of estuaries) on patterns of genetic structure and connectivity of the common kelp, Ecklonia radiata. There was no genetic differentiation of kelp between estuaries and the open coast and the presence of estuaries did not increase genetic differentiation among open coast populations. Similarly, there were no differences in level of inbreeding or genetic diversity between estuarine and open coast populations. The presence of large estuaries along rocky coastlines does not appear to influence genetic structure of this kelp and factors other than physical heterogeneity of habitat are likely more important determinants of regional connectivity. Marine reserves are currently lacking in this bioregion and may be designated in the future. Knowledge of the factors that influence important habitat forming organisms such as kelp contribute to informed and effective marine protected area design and conservation initiatives to maintain resilience of important marine habitats.

Complex genetic patterns in closely related colonizing invasive species

Anthropogenic activities frequently result in both rapidly changing environments and translocation of species from their native ranges (i.e., biological invasions). Empirical studies suggest that many factors associated with these changes can lead to complex genetic patterns, particularly among invasive populations. However, genetic complexities and factors responsible for them remain uncharacterized in many cases. Here, we explore these issues in the vase tunicate Ciona intestinalis (Ascidiacea: Enterogona: Cionidae), a model species complex, of which spA and spB are rapidly spreading worldwide. We intensively sampled 26 sites (N = 873) from both coasts of North America, and performed phylogenetic and population genetics analyses based on one mitochondrial fragment (cytochrome c oxidase subunit 3–NADH dehydrogenase subunit I, COX3-ND1) and eight nuclear microsatellites. Our analyses revealed extremely complex genetic patterns in both species on both coasts. We detected a contrasting pattern based on the mitochondrial marker: two major genetic groups in C. intestinalis spA on the west coast versus no significant geographic structure in C. intestinalis spB on the east coast. For both species, geo-graphically distant populations often showed high microsatellite-based genetic affinities whereas neighboring ones often did not. In addition, mitochondrial and nuclear markers provided largely inconsistent genetic patterns. Multiple factors, including random genetic drift associated with demographic changes, rapid selection due to strong local adaptation, and varying propensity for human-mediated propagule dispersal could be responsible for the observed genetic complexities.

Phylogeography of two moray eels indicates high dispersal throughout the indo-pacific

Reef fishes disperse primarily as oceanic "pelagic" larvae, and debate continues over the extent of this dispersal, with recent evidence for geographically restricted (closed) populations in some species. In contrast, moray eels have the longest pelagic larval stages among reef fishes, possibly providing opportunities to disperse over great distances. We test this prediction by measuring mitochondrial DNA (mtDNA) and nuclear DNA variation in 2 species of moray eels, Gymnothorax undulatus (N = 165) and G. flavimarginatus (N = 124), sampled at 14-15 locations across the Indo-Pacific. The mtDNA data comprise 632 bp of cytochrome b and 596 bp of cytochrome oxidase I. Nuclear markers include 2 recombination-activating loci (421 bp of RAG-1 and 754 bp of RAG-2). Analyses of molecular variance and Mantel tests indicate little or no genetic differentiation, and no isolation by distance, across 22 000 km of the Indo-Pacific. We estimate that mitochondrial genetic variation coalesces within the past about 2.3 million years (My) for G. flavimarginatus and within the past about 5.9 My for G. undulatus. Permutation tests of geographic distance on the mitochondrial haplotype networks indicate recent range expansions for some younger haplotypes (estimated within approximately 600 000 years) and episodic fragmentation of populations at times of low sea level. Our results support the predictions that the extended larval durations of moray eels enable ocean-wide genetic continuity of populations. This is the first phylogeographic survey of the moray eels, and morays are the first reef fishes known to be genetically homogeneous across the entire Indo-Pacific.

Post-glacial redistribution and shifts in productivity of giant kelp forests

Quaternary glacial-interglacial cycles create lasting biogeographic, demographic and genetic effects on ecosystems, yet the ecological effects of ice ages on benthic marine communities are unknown. We analysed long-term datasets to develop a niche-based model of southern Californian giant kelp (Macrocystis pyrifera) forest distribution as a function of oceanography and geomorphology, and synthesized palaeo-oceanographic records to show that late Quaternary climate change probably drove high millennial variability in the distribution and productivity of this foundation species. Our predictions suggest that kelp forest biomass increased up to threefold from the glacial maximum to the mid-Holocene, then rapidly declined by 40-70 per cent to present levels. The peak in kelp forest productivity would have coincided with the earliest coastal archaeological sites in the New World. Similar late Quaternary changes in kelp forest distribution and productivity probably occurred in coastal upwelling systems along active continental margins worldwide, which would have resulted in complex shifts in the relative productivity of terrestrial and marine components of coastal ecosystems.

Meta-population structure in a coral reef fish demonstrated by genetic data on patterns of migration, extinction and re-colonisation

Background

Management strategies for coral reefs are dependant on information about the spatial population structure and connectivity of reef organisms. Genetic tools can reveal important information about population structure, however, this information is lacking for many reef species. We used a mitochondrial molecular marker to examine the population genetic structure and the potential for meta-population dynamics in a direct developing coral reef fish using 283 individuals from 15 reefs on the Great Barrier Reef, Australia. We employed a hierarchical sampling design to test genetic models of population structure at multiple geographical scales including among regions, among shelf position and reefs within regions. Predictions from island, isolation-by-distance and meta-population models, including the potential for asymmetric migration, local extinction and patterns of re-colonisation were examined.

Results

Acanthochromis polyacanthus displayed strong genetic structure among regions (Φ_ST = 0.81, P < 0.0001) that supported an equilibrium isolation-by-distance model (r = 0.77, P = 0.001). Significant structuring across the continental shelf was only evident in the northern region (Φ_ST = 0.31, P < 0.001) and no evidence of isolation-by-distance was found within any region. Pairwise Φ_ST values indicated overall strong but variable genetic structure (mean Φ_ST among reefs within regions = 0.28, 0.38, 0.41), and asymmetric migration rates among reefs with low genetic structure. Genetic differentiation among younger reefs was greater than among older reefs supporting a meta-population propagule-pool colonisation model. Variation in genetic diversities, demographic expansion and population growth estimates indicated more frequent genetic bottlenecks/founder effects and subsequent population expansion in the central and southern regions compared to the northern one.

Conclusion

Our findings provide genetic evidence for meta-population dynamics in a direct developing coral reef fish and we reject the equilibrium island and isolation-by distance models at local spatial scales. Instead, strong non-equilibrium genetic structure appears to be generated by genetic bottlenecks/founder effects associated with population reductions/extinctions and asymmetric migration/(re)-colonisation of such populations. These meta-population dynamics varied across the geographical range examined with edge populations exhibiting lower genetic diversities and higher rates of population expansion than more central populations. Therefore, coral reef species may experience local population reductions/extinctions that promote overall meta-population genetic differentiation.

A biophysical perspective on dispersal and the geography of evolution in marine and terrestrial systems

The fluid mechanics of marine and terrestrial systems are surprisingly similar at many spatial and temporal scales. Not surprisingly, the dispersal of organisms that float, swim or fly is influenced by the fluid environments of air and seawater. Nonetheless, it has been argued repeatedly that the geography of evolution differs fundamentally between marine and terrestrial taxa. Might this view emanate from qualitative contrasts between the pelagic ocean and terrestrial land conflated by anthropocentric perception of within- and between-realm variation? We draw on recent advances in biogeography to identify two pairs of biophysically similar marine and terrestrial settings--(i) aerial and marine microplankton and (ii) true islands and brackish seawater lakes--which have similar geographies of evolution. Commonalities at these scales, the largest and smallest biogeographic scales, delimit the geographical extents that can possibly characterize evolution in the remaining majority of species. The geographies of evolution therefore differ statistically, not fundamentally, between marine and terrestrial systems. Comparing the geography of evolution in diverse non-microplanktonic and non-island species from a biophysical perspective is an essential next step for quantifying precisely how marine and terrestrial systems differ and is an important yet under-explored avenue of macroecology.

Smelling home can prevent dispersal of reef fish larvae

Many marine fish and invertebrates show a dual life history where settled adults produce dispersing larvae. The planktonic nature of the early larval stages suggests a passive dispersal model where ocean currents would quickly cause panmixis over large spatial scales and prevent isolation of populations, a prerequisite for speciation. However, high biodiversity and species abundance in coral reefs contradict this panmixis hypothesis. Although ocean currents are a major force in larval dispersal, recent studies show far greater retention than predicted by advection models. We investigated the role of animal behavior in retention and homing of coral reef fish larvae resulting in two important discoveries: (i) Settling larvae are capable of olfactory discrimination and prefer the odor of their home reef, thereby demonstrating to us that nearby reefs smell different. (ii) Whereas one species showed panmixis as predicted from our advection model, another species showed significant genetic population substructure suggestive of strong homing. Thus, the smell of reefs could allow larvae to choose currents that return them to reefs in general and natal reefs in particular. As a consequence, reef populations can develop genetic differences that might lead to reproductive isolation.

Vicariance and dispersal across Baja California in disjunct marine fish populations

Population disjunctions, as a first step toward complete allopatry, present an interesting situation to study incipient speciation. The geological formation of the Baja California Peninsula currently divides 19 species of fish into disjunct populations that are found on its Pacific Coast and in the northern part of the Gulf of California (also called the Sea of Cortez), but are absent from the Cape (Cabo San Lucas) region. We studied the genetic makeup of disjunct populations for 12 of these 19 fish species. Phylogeographic patterns for the 12 species can be separated into two major classes: a first group (eight species) showed reciprocal monophyly and high genetic divergence between disjunct populations. A second group (four species) displayed what appeared to be panmictic populations. Population structure between Pacific Coast populations, across the Punta Eugenia biogeographic boundary, was also evaluated. While dispersal potential (inferred by pelagic larval duration) was a poor predictor of population structure between Gulf of California and Pacific populations, we found that population genetic subdivision along the Pacific Coast at Punta Eugenia was always positively correlated with differentiation between Pacific and Gulf of California populations. Vicariant events, ongoing gene flow, and ecological characteristics played essential roles in shaping the population structures observed in this study.

Strong genetic divergence among populations of a marine fish with limited dispersal, Acanthochromis polyacanthus, within the Great Barrier Reef and the Coral Sea

Acanthochromis polyacanthus is an unusual tropical marine damselfish that uniquely lacks pelagic larvae and has lost the capacity for broad-scale dispersal among coral reefs. On the modern Great Barrier Reef (GBR), three color morphs meet and hydridize at two zones of secondary contact. Allozyme electrophoreses revealed strong differences between morphs from the southern zone but few differences between morphs from the northern counterpart, thus suggesting different contact histories. We explore the phylogeography of Acanthochromis polyacanthus with mitochondrial cytochrome b region sequences (alignment of 565 positions) obtained from 126 individuals representing seven to 12 fish from 13 sites distributed over 12 reefs of the GBR and the Coral Sea. The samples revealed three major clades: (1) black fish collected from the southern GBR; (2) bicolored fish collected from the GBR and one reef (Osprey) from the northern Coral Sea; (3) black and white monomorphs collected from six reefs in the Coral Sea. All three clades were well supported (72-100%) by bootstrap analyses. Sequence divergences were very high between the major clades (mean = 7.6%) as well as within them (2.0-3.6%). Within clades, most reefs segregated as monophyletic assemblages. This was revealed both by phylogenetic analyses and AMOVAs that showed that 72-90% of the variance originated from differences among groups, whereas only 5-13% originated within populations. These patterns are discussed in relation to the known geological history of coral reefs of the GBR and the Coral Sea. Finally, we ask whether the monospecific status of Acanthochromis should be revisited because the sequence divergences found among our samples is substantially greater than those recorded among well-recognized species in other reef fishes.

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.