Speciation-by-depth on coral reefs: Sympatric divergence with gene flow or cryptic transient isolation?

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data.

Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time.

Identifying how past environmental conditions shaped the evolution of corals and their skeletal traits provides a framework for predicting their persistence and that of their non-calcifying relatives under impending global warming and ocean acidification. Here we show that ocean geochemistry, particularly aragonite-calcite seas, drives patterns of morphological evolution in anthozoans (corals, sea anemones) by examining skeletal traits in the context of a robust, time-calibrated phylogeny. The lability of skeletal composition among octocorals suggests a greater ability to adapt to changes in ocean chemistry compared with the homogeneity of the aragonitic skeleton of scleractinian corals.

Host-targeted RAD-Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast.

Many organisms are expanding their ranges in response to changing environmental conditions. Understanding the patterns of genetic diversity and adaptation along an expansion front is crucial to assessing a species' long-term success. While next-generation sequencing techniques can reveal these changes in fine detail, ascribing them to a particular species can be difficult for organisms that live in close association with symbionts.

Switch between Morphospecies of Pocillopora Corals.

Pocillopora corals are the main reef builders in the eastern tropical Pacific. The validity of Pocillopora morphospecies remains under debate because of disagreements between morphological and genetic data. To evaluate the temporal stability of morphospecies in situ, we monitored the shapes of individual colonies in three communities in the southern Gulf of California for 44 months.

The invasive coral Oculina patagonica has not been recently introduced to the Mediterranean from the western Atlantic.

Background: Effective policies, management, and scientific research programs depend on the correct identification of invasive species as being either native or introduced. However, many species continue to be misidentified. Oculina patagonica, first recorded in the Mediterranean Sea in 1966, is believed to have been introduced in anthropogenic times and expanding in a west to east direction.

Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia.

Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach.

Morphological variation and different branch modularity across contrasting flow conditions in dominant Pocillopora reef-building corals.

Pocillopora corals, the dominant reef-builders in the Eastern Tropical Pacific, exhibit a high level of phenotypic plasticity, making the interpretation of morphological variation and the identification of species challenging. To test the hypothesis that different coral morphospecies represent phenotypes that develop in different flow conditions, we compared branch characters in three Pocillopora morphospecies (P. damicornis, P.

Historical and recent processes shaping the geographic range of a rocky intertidal gastropod: phylogeography, ecology, and habitat availability.

Factors shaping the geographic range of a species can be identified when phylogeographic patterns are combined with data on contemporary and historical geographic distribution, range-wide abundance, habitat/food availability, and through comparisons with codistributed taxa. Here, we evaluate range dynamism and phylogeography of the rocky intertidal gastropod Mexacanthina lugubris lugubris across its geographic range - the Pacific coast of the Baja peninsula and southern California. We sequenced mitochondrial DNA (CO1) from ten populations and compliment these data with museum records, habitat availability and range-wide field surveys of the distribution and abundance of M.

Strong natural selection on juveniles maintains a narrow adult hybrid zone in a broadcast spawner.

Natural selection can maintain and help form species across different habitats, even when dispersal is high. Selection against inferior migrants (immigrant inviability) acts when locally adapted populations suffer high mortality on dispersal to unsuitable habitats. Habitat-specific populations undergoing divergent selection via immigrant inviability should thus show (1) a change in the ratio of adapted to nonadapted individuals among age/size classes and (2) a cline (defined by the environmental gradient) as selection counterbalances migration.

Cryptic diversity hides host and habitat specialization in a gorgonian-algal symbiosis.

Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts co-evolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations.

Unrecognized coral species diversity masks differences in functional ecology.

Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P.

Evaluating summary statistics used to test for incomplete lineage sorting: mito-nuclear discordance in the reef sponge Callyspongia vaginalis.

Conflicting patterns of population differentiation between the mitochondrial and nuclear genomes (mito-nuclear discordance) have become increasingly evident as multilocus data sets have become easier to generate. Incomplete lineage sorting (ILS) of nucDNA is often implicated as the cause of such discordance, stemming from the large effective population size of nucDNA relative to mtDNA. However, selection, sex-biased dispersal and historical demography can also lead to mito-nuclear discordance.

Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral.

Long-lived corals, the foundation of modern reefs, often follow ecological gradients, so that populations or sister species segregate by habitat. Adaptive divergence maintains sympatric congeners after secondary contact or may even generate species by natural selection in the face of gene flow. Such ecological divergence, initially between alternative phenotypes within populations, may be aided by immigrant inviability, especially when a long period separates larval dispersal and the onset of reproduction, during which selection can sort lineages to match different habitats.

No gene flow across the Eastern Pacific Barrier in the reef-building coral Porites lobata.

The expanse of deep water between the central Pacific islands and the continental shelf of the Eastern Tropical Pacific is regarded as the world's most potent marine biogeographic barrier. During recurrent climatic fluctuations (ENSO, El Niño Southern Oscillation), however, changes in water temperature and the speed and direction of currents become favourable for trans-oceanic dispersal of larvae from central Pacific to marginal eastern Pacific reefs. Here, we investigate the population connectivity of the reef-building coral Porites lobata across the Eastern Pacific Barrier (EPB).

The Tegula tango: a coevolutionary dance of interacting, positively selected sperm and egg proteins.

Reproductive proteins commonly show signs of rapid divergence driven by positive selection. The mechanisms driving these changes have remained ambiguous in part because interacting male and female proteins have rarely been examined. We isolate an egg protein the vitelline envelope receptor for lysin (VERL) from Tegula, a genus of free-spawning marine snails.

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria).

Neotropical reef fish communities are species-poor compared to those of the Indo-West Pacific. An exception to that pattern is the blenny clade Chaenopsidae, one of only three rocky and coral reef fish families largely endemic to the Neotropics. Within the chaenopsids, the genus Acanthemblemaria is the most species-rich and is characterized by elaborate spinous processes on the skull.

A new lysozyme from the eastern oyster, Crassostrea virginica, and a possible evolutionary pathway for i-type lysozymes in bivalves from host defense to digestion.

Background: Lysozymes are enzymes that lyse bacterial cell walls, an activity widely used for host defense but also modified in some instances for digestion. The biochemical and evolutionary changes between these different functional forms has been well-studied in the c-type lysozymes of vertebrates, but less so in the i-type lysozymes prevalent in most invertebrate animals. Some bivalve molluscs possess both defensive and digestive lysozymes.

Ecological partitioning among parapatric cryptic species.

Geographic range differences among species may result from differences in their physiological tolerances. In the intertidal zone, marine and terrestrial environments intersect to create a unique habitat, across which physiological tolerance strongly influences range. Traits to cope with environmental extremes are particularly important here because many species live near their physiological limits and environmental gradients can be steep.

Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes.

Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa.

High amino acid diversity and positive selection at a putative coral immunity gene (tachylectin-2).

Background: Genes involved in immune functions, including pathogen recognition and the activation of innate defense pathways, are among the most genetically variable known, and the proteins that they encode are often characterized by high rates of amino acid substitutions, a hallmark of positive selection. The high levels of variation characteristic of immunity genes make them useful tools for conservation genetics. To date, highly variable immunity genes have yet to be found in corals, keystone organisms of the world's most diverse marine ecosystem, the coral reef.

Nuclear sequences reveal mid-range isolation of an imperilled deep-water coral population.

The mitochondrial DNA of corals and their anthozoan kin evolves slowly, with substitution rates about two orders of magnitude lower than in typical bilateral animals. This has impeded the delineation of closely related species and isolated populations in corals, compounding problems caused by high morphological plasticity. Here we characterize rates of divergence and levels of variation for three nuclear gene regions, then use these nuclear sequences as markers to test for population structure in Oculina, a taxonomically confused genus of corals.

A molecular phylogenetic analysis of strombid gastropod morphological diversity.

The shells of strombid gastropods show a wide variety of forms, ranging from small and fusiform to large and elaborately ornamented with a strongly flared outer lip. Here, we present the first species-level molecular phylogeny for strombids and use the resulting phylogenetic framework to explore relationships between species richness and morphological diversity. We use portions of one nuclear (325 bp of histone H3) and one mitochondrial (640 bp of cytochrome oxidase I, COI) gene to infer relationships within the two most species-rich genera in the Strombidae: Strombus and Lambis.

Positive selection on nucleotide substitutions and indels in accessory gland proteins of the Drosophila pseudoobscura subgroup.

Genes encoding reproductive proteins often diverge rapidly due to positive selection on nucleotide substitutions. While this general pattern is well established, the extent to which specific reproductive genes experience similar selection in different clades has been little explored, nor have possible targets of positive selection other than nucleotide substitutions, such as indels, received much attention. Here, we inspect for the signature of positive selection in the genes encoding five accessory gland proteins (Acps) (Acp26Aa, Acp32CD, Acp53Ea, Acp62F, and Acp70A) originally described from Drosophila melanogaster but with recognizable orthologues in the D.

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

Background: The 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.

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.