Michael E. Hellberg

Regionally isolated populations of an imperiled Caribbean coral, Acropora palmata.

The movements of larvae between marine populations are difficult to follow directly and have been the subject of much controversy, especially in the Caribbean. The debate centres on the degree to which populations are demographically open, such that depleted populations can be replenished by recruitment from distant healthy populations, or demographically closed and thus in need of local management. Given the depressed state of many tropical reef populations, the understanding of these movements now bears critically on the number, placement, and size of marine reserves. Most genetic analyses assume that dispersal patterns have been stable for thousands of generations, thus they commonly reflect past colonization histories more than ongoing dispersal. Recently developed multilocus genotyping approaches, however, have the demonstrated ability to detect both migration and population isolation over far shorter timescales. Previously, we developed five microsatellite markers and demonstrated them to be both Mendelian and coral‐specific. Using these markers and Bayesian analyses, we show here that populations of the imperiled reef‐building coral, Acropora palmata, have experienced little or no recent genetic exchange between the western and the eastern Caribbean. Puerto Rico is identified as an area of mixing between the two subregions. As a consequence of this regional isolation, populations in the western and eastern Caribbean should have the potential to adapt to local conditions and will require population‐specific management strategies.

No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

BackgroundThe mitochondrial DNA (mtDNA) of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin), by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans) known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea).ResultsThe mtDNA surveyed (630 bp of cytochrome oxidase subunit I) was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years) is similar to that in most plants, but 50–100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not.ConclusionSlow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes.

DEPENDENCE OF GENE FLOW ON GEOGRAPHIC DISTANCE IN TWO SOLITARY CORALS WITH DIFFERENT LARVAL DISPERSAL CAPABILITIES

When the level of gene flow among populations depends upon the geographic distance separating them, genetic differentiation is relatively enhanced. Although the larval dispersal capabilities of marine organisms generally correlate with inferred levels of average gene flow, the effect of different modes of larval development on the association between gene flow and geographic distance remains unknown. In this paper, I examined the relationship between gene flow and distance in two co‐occurring solitary corals. Balanophyllia elegans broods large, nonfeeding planulae that generally crawl only short distances from their place of birth before settling. In contrast, Paracyathus stearnsii free‐spawns and produces small planktonic larvae presumably capable of broad dispersal by oceanic currents. I calculated F‐statistics using genetic variation at six (P. stearnsii) or seven (B. elegans) polymorphic allozyme loci revealed by starch gel electrophoresis, and used these F‐statistics to infer levels of gene flow. Average levels of gene flow among twelve Californian localities agreed with previous studies: the species with planktonic, feeding larvae was less genetically subdivided than the brooding species. In addition, geographic isolation between populations appeared to affect gene flow between populations in very different ways in the two species. In the brooding B. elegans, gene flow declined with increasing separation, and distance explained 31% of the variation in gene flow. In the planktonically dispersed P. stearnsii distance of separation between populations at the scale studied (10–1000 km) explained only 1% of the variation in gene flow between populations. The mechanisms generating geographic genetic differentiation in species with different modes of larval development should vary fundamentally as a result of these qualitative differences in the dependence of gene flow on distance.

RELATIONSHIPS BETWEEN INFERRED LEVELS OF GENE FLOW AND GEOGRAPHIC DISTANCE IN A PHILOPATRIC CORAL, BALANOPHYLLIA ELEGANS

When the dispersal capability of a species is considerably less than its geographic range, genetic differences between populations should increase with the distance separating those populations. This pattern should be most evident in linearly distributed species. The sessile solitary cup coral Balanophyllia elegans lives along nearly the entire Pacific coast of North America, yet its crawling larvae usually settle within 40 cm of their birthplace. In this paper, I document geographic patterns of allozyme differentiation within and among populations of B. elegans and estimate the proportion of observed geographic pattern attributable to gene flow between adjacent populations. Genetic subdivision among localities separated by up to 3000 km was high (FST = 0.283, SE = 0.038). Inferred gene flow between pairs of localities ( M∘ , individuals per generation) correlated inversely with the geographic distance between those localities, consistent with the pattern expected for a species at equilibrium in which gene flow occurred exclusively between adjacent localities. Within localities, patches separated by 4 to 30 m were also significantly subdivided, but genetic differentiation between patches did not vary significantly with the distance separating them. Simulations revealed that the power to detect genetic pattern expected from gene flow between adjacent populations increased with both the number of loci used to infer gene flow and the heterozygosity of those loci. Simulations also verified that when geographic distance poorly approximated the number of steps between populations, reduced major‐axis regression more accurately portrayed the structural relationship between gene flow and separation than did ordinary least‐squares regression. Attenuation of gene flow with distance explained 15% of the between‐locality pattern of genetic differentiation in B. elegans. The remaining variation appeared to be due to neither natural selection nor a recent rangewide recolonization. Loci from the northern sampled localities, however, had fewer alleles than those from the remainder of the range, suggesting these localities had been recolonized recently following Pleistocene cooling.

MARINE RADIATIONS AT SMALL GEOGRAPHIC SCALES: SPECIATION IN NEOTROPICAL REEF GOBIES (ELACATINUS)

Abstract Studies of speciation in the marine environment have historically compared broad‐scale distributions and estimated larvel dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geography restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation<000 km) spatial scales could facilitate speciation by mechanisms otheer than the gradul accumulation of reproductive isolation during extended alopatry, such as ecological adaption to local environment codnitions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species‐rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species‐rich group of Neotropical reef fishes (Gobiidae: Elacatimus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large‐ and small ‐scale geographic isolation, ecological differentiation, and coloration twoard the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, Our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggest that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recuring adaptive radiations in stages taking place at small geographic scales.

Footprints on water: the genetic wake of dispersal among reefs

Analysis of genetic data can reveal past and ongoing demographic connections between reef populations. The history, extent, and geography of isolation and exchange help to determine which populations are evolutionarily distinct and how to manage threatened reefs. Here the genetic approaches undertaken to understand connectivity among reefs are reviewed, ranging from early allozyme studies on genetic subdivision, through the use of sequence data to infer population histories, to emerging analyses that pull the influences of the past connections away from the effects of ongoing dispersal. Critically, some of these new approaches can infer migration and isolation over recent generations, thus offering the opportunity to answer many questions about reef connectivity and to better collaborate with ecologists and oceanographers to address problems that remain.

SYMPATRIC SEA SHELLS ALONG THE SEA'S SHORE : THE GEOGRAPHY OF SPECIATION IN THE MARINE GASTROPOD TEGULA

Uncertainty and controversy surround the geographical and ecological circumstances that create genetic differences between populations that eventually lead to reproductive isolation. Two aspects of marine organisms further complicate this situation: (1) many species possess planktonic larvae capable of great dispersal; and (2) obvious barriers to movement between populations are rare. Past studies of speciation in the sea have focussed on identifying the effects of past land barriers and on biogeographical breakpoints. However, assessing the role such undeniable barriers actually play in the initial divergence leading to reproductive isolation requires phylogenetic studies of recent radiations living in varying degrees of sympatry and allopatry to see which barriers (if any) tend to separate sister species. Here I infer phylogenetic relationship between 23 species of the marine snail Tegula using DNA sequences from two regions of the mitochondrial genome: cytochrome c oxidase I (COI) and the small ribosomal subunit (12S) These snails possess planktonic larvae with moderate dispersal capabilities and have speciated rapidly with over 40 extant species arising since the genus first appeared in the mid‐Miocene (about 15 M.Y.B.P.). Trees constructed from the COI and 12S regions (which yielded 205 and 137 phylogenetically informative sites, respectively) were robust with respect to tree‐building method, bootstrapping, and the relative weightings of transitions, transversions, and gaps Within clades where all extant species have been sampled, five of six identified sister species pairs broadly coexist on the same side of biogeographical boundaries. These data suggest strong geographical barriers to gene flow may not always be required for speciation in the sea; transient allopatry or even ecological barriers may suffice. A survey of the geographic distributions of marine radiations suggests that coastal distributions may favor the sympatry of sister taxa more than island distributions do.

Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean

Geographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one‐fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long‐term biogeographic barrier for Caribbean animals.

Stepping-stone gene flow in the solitary coral Balanophyllia elegans: equilibrium and nonequilibrium at different spatial scales

Limited dispersal should result in genetic differences between populations proportional to geographic distances of separation. This association between gene flow and distance can be disrupted by (1) continuing genetic exchange among distant populations, (2) historical changes in gene flow, and (3) physical barriers or corridors to dispersal. The movements of larvae are thought to determine dispersal capability in benthic marine invertebrates. The solitary scleractinian Balanophyllia elegans Verrill possesses crawling larvae capable of only limited dispersal. Paradoxically, however, inferred levels of gene flow between pairs of localities spread over much of the 4000 km range of B. elegans exhibited a weaker relationship with geographical separation than that expected for a linear array of populations in which all genetic exchange takes place between adjacent populations. In this paper, I examined the pattern of gene flow (inferred from the frequencies of eight polymorphic allozyme loci) in B. elegans at a smaller (1 to 50 km) spatial scale to determine (1) whether gene flow at this spatial scale conformed to the expectations of the stepping-stone model, and (2) whether continuing long-distance gene flow or historical changes in gene flow were responsible for the weak relationship between gene flow and distance observed previously at the rangewide spatial scale. Between May and August 1992, I collected 75 adults from each of 18 localities along the coast of Sonoma County, California, USA. These populations of B. elegans were significantly subdivided both among localities separated by 1 to 50 km (FLT=0.053, Se=0.0075) and among patches separated by 4 to 8 m (FPL=0.026, SE=0.0023). The observed slope and correlation (r2=0.54) between inferred levels of gene flow and the geographic distance at the 1 to 50 km spatial scale conformed to equilibrium expectations (obtained by simulation) for a linear stepping-stone model, although those from the rangewide spatial scale did not. This implies that the mechanisms conferring patterns of inferred genetic differentiation between localities in B. elegans differ fundamentally with spatial scale. At a scale of 1 to 50 km, continuing gene flow and drift have equilibrated and the process of isolation-bydistance may facilitate local adaptive change. At a broader spatial scale, historical changes in gene flow, perhaps affected by late Pleistocene climatic fluctuations, disrupt the equilibration of gene flow and genetic drift, so that genetic differentiation may not increase continuously with separation between populations.

Cryptic species, cryptic endosymbionts, and geographical variation in chemical defences in the bryozoan Bugula neritina

Molecular markers often offer the only means to discriminate between species and to elucidate the specificity of many community interactions, both of which are key to the understanding of ecological patterns. Western Atlantic populations of the bryozoan Bugula neritina vary in the palatability of their larvae to predators: individuals south of Cape Hatteras produce chemical deterrents to fish predators that are absent in more northern individuals. We use mitochondrial cytochrome oxidase c subunit I (COI) sequences to show that the differences in palatability between populations correlate with the geographical distributions of two cryptic species within B. neritina. Furthermore, these cryptic species differ in their associations with bacteria that may confer chemical resistance to predation. Small subunit rRNA primers specific to a subset of γ‐proteobacteria amplified only the bacterium Endobugula sertula from the southern cryptic species. Endobugula sertula produces a family of chemical compounds (bryostatins) that may deter predators of its animal host. In contrast, the same primers amplified an array of γ‐proteobacteria from the unprotected northern cryptic bryozoan species, but never E. sertula. In combination, these findings suggest that the geographical variation in palatability observed in the larvae of B. neritina is not the result of local adaptation of a single species to regions of differing predation pressure, but rather results from the comparison of cryptic species that differ in the presence or absence of a bacterium that may provide protection against predators. The ability to identify the cryptic Bugula species and their differing relationships with bacterial associates provides an example of the important role molecular techniques may play in addressing ecological questions.