Ecological Speciation in Corals

Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia

Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.

Brazilian marine phylogeography: A literature synthesis and analysis of barriers

In the last 30 years a plethora of phylogeography studies have been published targeting Brazilian marine species. To date, several historical and extant physical and ecological processes have been identified as drivers of allopatric, sympatric and parapatric population genetic differentiation detected along the Brazilian coast. Examples of extant physical barriers include the split of the South Equatorial Current into the Brazil and North Brazil boundary currents, the mouth of major rivers (e.g., Amazon, São Francisco and Doce rivers) and coastal upwellings. Examples of historical barriers include the Vitória-Trindade seamount chain promoting genetic differentiation during periods of glacial maxima and lower sea levels. Examples of ecological speciation include adaptations to different substrata, resource use and reproductive biology. We used published data to build data sets and generalized additive models to identify patterns of spatial phylogeographical concordance across multiple taxa and markers. Our results identify Cape São Roque as the most dominant extant barrier to gene flow along the Brazilian coast, followed by the Vitória-Trindade seamount chain and Cape Santa Marta. Cape Santa Marta is the northern winter limit of the Rio da Plata plume and is intermittently influenced by the Malvinas Current. This study provides a novel explicit quantitative approach to comparative phylogeography that recognizes four Brazilian phylogeographical regions delimited by processes associated with barriers to gene flow.

Ecological speciation by sympatric host shifts in a clade of herbivorous sea slugs, with introgression and localized mitochondrial capture between species

Host shifting in insect-plant systems was historically important to the development of ecological speciation theory, yet surprisingly few studies have examined whether host shifting drives diversification of marine herbivores. When small-bodied consumers feed and also mate on a preferred host, disruptive selection can split a population into host races despite gene flow. Support for host shifts is notably lacking for invertebrates associated with macroalgae, where the scale of dispersal by planktonic larvae often far exceeds the grain of host patchiness, and adults are typically less specialized than terrestrial herbivores. Here, we present a candidate example of ecological speciation in a clade of sea slugs that primarily consume green algae in the genus Caulerpa, including highly invasive species. Ancestral character state reconstructions supported 'sea grapes' (C. racemosa, C. lentillifera) as the ancestral host for a tropical radiation of 12 Elysia spp., with one shift onto alternative Caulerpa spp. in the Indo-Pacific. A Caribbean radiation of three species included symaptric host shifts to Rhipocephalus brevicaulis in the ancestor of E. pratensis Ortea & Espinosa, 1996, and to C. prolifera in E. hamanni Krug, Vendetti & Valdes 2016, plus a niche expansion to a range of Caulerpa spp. in E. subornata Verrill, 1901. All three species are broadly sympatric across the Caribbean but are host-partitioned at a fine grain, and distinct by morphology and at nuclear loci. However, non-recombining mtDNA revealed a history of gene flow between E. pratensis and E. subornata: COI haplotypes from E. subornata were 10.4% divergent from E. pratensis haplotypes from four sites, but closely related to all E. pratensis haplotypes sampled from six Bahamian islands, indicating historical introgression and localized "mitochondrial capture." Disruptive selective likely fueled divergence and adaptation to distinct host environments, indicating ecological speciation may be an under-appreciated driver of diversification for marine herbivores as well as epibionts and other resource specialists.

Global diversification and evolutionary history of onchidiid slugs (Gastropoda, Pulmonata)

Many marine species are specialized to specific parts of a habitat. In a mangrove forest, for instance, species may be restricted to the mud surface, the roots and trunks of mangrove trees, or rotting logs, which can be regarded as distinct microhabitats. Shifts to new microhabitats may be an important driver of sympatric speciation. However, the evolutionary history of these shifts is still poorly understood in most groups of marine organisms, because it requires a well-supported phylogeny with relatively complete taxon sampling. Onchidiid slugs are an ideal case study for the evolutionary history of habitat and microhabitat shifts because onchidiid species are specialized to different tidal zones and microhabitats in mangrove forests and rocky shores, and the taxonomy of the family in the Indo-West Pacific has been recently revised in a series of monographs. Here, DNA sequences for onchidiid species from the North and East Pacific, the Caribbean, and the Atlantic are used to reconstruct phylogenetic relationships among Onchidella species, and are combined with new data for Indo-West Pacific species to reconstruct a global phylogeny of the family. The phylogenetic relationships of onchidiid slugs are reconstructed based on three mitochondrial markers (COI, 12S, 16S) and three nuclear markers (28S, ITS2, H3) and nearly complete taxon sampling (all 13 genera and 62 of the 67 species). The highly-supported phylogeny presented here suggests that ancestral onchidiids most likely lived in the rocky intertidal, and that a lineage restricted to the tropical Indo-West Pacific colonized new habitats, including mudflats, mangrove forests, and high-elevation rainforests. Many onchidiid species in the Indo-West Pacific diverged during the Miocene, around the same time that a high diversity of mangrove plants appears in the fossil record, while divergence among Onchidella species occurred earlier, likely beginning in the Eocene. It is demonstrated that ecological specialization to microhabitats underlies the divergence between onchidiid genera, as well as the diversification through sympatric speciation in the genera Wallaconchis and Platevindex. The geographic distributions of onchidiid species also indicate that allopatric speciation played a key role in the diversification of several genera, especially Onchidella and Peronia. The evolutionary history of several morphological traits (penial gland, rectal gland, dorsal eyes, intestinal loops) is examined in relation to habitat and microhabitat evolutionary transitions and that the rectal gland of onchidiids is an adaptation to high intertidal and terrestrial habitats.

Morphological stasis masks ecologically divergent coral species on tropical reefs

Coral reefs are the epitome of species diversity, yet the number of described scleractinian coral species, the framework-builders of coral reefs, remains moderate by comparison. DNA sequencing studies are rapidly challenging this notion by exposing a wealth of undescribed diversity, but the evolutionary and ecological significance of this diversity remains largely unclear. Here, we present an annotated genome for one of the most ubiquitous corals in the Indo-Pacific (Pachyseris speciosa) and uncover, through a comprehensive genomic and phenotypic assessment, that it comprises morphologically indistinguishable but ecologically divergent lineages. Demographic modeling based on whole-genome resequencing indicated that morphological crypsis (across micro- and macromorphological traits) was due to ancient morphological stasis rather than recent divergence. Although the lineages occur sympatrically across shallow and mesophotic habitats, extensive genotyping using a rapid molecular assay revealed differentiation of their ecological distributions. Leveraging "common garden" conditions facilitated by the overlapping distributions, we assessed physiological and quantitative skeletal traits and demonstrated concurrent phenotypic differentiation. Lastly, spawning observations of genotyped colonies highlighted the potential role of temporal reproductive isolation in the limited admixture, with consistent genomic signatures in genes related to morphogenesis and reproduction. Overall, our findings demonstrate the presence of ecologically and phenotypically divergent coral species without substantial morphological differentiation and provide new leads into the potential mechanisms facilitating such divergence. More broadly, they indicate that our current taxonomic framework for reef-building corals may be scratching the surface of the ecologically relevant diversity on coral reefs, consequently limiting our ability to protect or restore this diversity effectively.

Genomic signatures of host-associated divergence and adaptation in a coral-eating snail, Coralliophila violacea (Kiener, 1836)

The fluid nature of the ocean, combined with planktonic dispersal of marine larvae, lowers physical barriers to gene flow. However, divergence can still occur despite gene flow if strong selection acts on populations occupying different ecological niches. Here, we examined the population genomics of an ectoparasitic snail, Coralliophila violacea (Kiener 1836), that specializes on Porites corals in the Indo-Pacific. Previous genetic analyses revealed two sympatric lineages associated with different coral hosts. In this study, we examined the mechanisms promoting and maintaining the snails' adaptation to their coral hosts. Genome-wide single nucleotide polymorphism (SNP) data from type II restriction site-associated DNA (2b-RAD) sequencing revealed two differentiated clusters of C. violacea that were largely concordant with coral host, consistent with previous genetic results. However, the presence of some admixed genotypes indicates gene flow from one lineage to the other. Combined, these results suggest that differentiation between host-associated lineages of C. violacea is occurring in the face of ongoing gene flow, requiring strong selection. Indeed, 2.7% of all SNP loci were outlier loci (73/2,718), indicative of divergence with gene flow, driven by adaptation of each C. violacea lineage to their specific coral hosts.