Combosch DJ, Giribet G. Clarifying phylogenetic relationships and the evolutionary history of the bivalve order Arcida (Mollusca: Bivalvia: Pteriomorphia). Molecular Phylogenetics and Evolution. 2016;94 (A) :298–312. Publisher's VersionAbstract

The systematics of the bivalve order Arcida constitutes an unresolved conundrum in bivalve systematics. The current definition of Arcida encompasses two superfamilies: Limopsoidea, which includes the recent families Philobryidae and Limopsidae, and Arcoidea, which encompasses the families Arcidae, Cucullaeidae, Noetiidae, Glycymerididae and Parallelodontidae. This classification, however, is controversial particularly with respect to the position and taxonomic status of Glycymerididae. Previous molecular phylogenies were limited either by the use of only a single molecular marker or by including only a few limopsoid and glycymeridid taxa. The challenging nature of Arcida taxonomy and the controversial results of some of the previous studies, prompted us to use a broad range of taxa (55 species), three nuclear markers (18S rRNA, 28S rRNA and histone H3) and a wide range of algorithmic approaches. This broad but stringent approach led to a number of results that differ significantly from previous studies. We provide the first molecular evidence that supports the separation of Arcoidea from Limopsoidea, although the exact position of Glycymerididae remains unresolved, and the monophyly of Limopsoidea is algorithm-dependent. In addition, we present the first time-calibrated evolutionary tree of Arcida relationships, indicating a significant increase in the diversification of arcidan lineages at the beginning of the Cretaceous, around 140 Ma. The monophyly of Arcida, which has been supported previously, was confirmed in all our analyses. Although relationships among families remain somehow unresolved we found support for the monophyly of most arcidan families, at least under some analytical conditions (i.e., Glycymerididae, Noetiidae, Philobryidae, and Limopsidae). However, Arcidae, and particularly Arcinae, remain a major source of inconsistency in the current system of Arcida classification and are in dire need of taxonomic revision.

Combosch DJ, Vollmer SV. Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Molecular Phylogenetics and Evolution. 2015;88 :154–162. Publisher's VersionAbstract

Discrepancies between morphology-based taxonomy and phylogenetic systematics are common in Scleractinian corals. In Pocillopora corals, nine recently identified genetic lineages disagree fundamentally with the 17 recognized Pocillopora species, including 5 major Indo-Pacific reef-builders. Pocillopora corals hybridize in the Tropical Eastern Pacific, so it is possible that some of the disagreement between the genetics and taxonomy may be due to introgressive hybridization. Here we used 6769 genome-wide SNPs from Restriction-site Associated DNA Sequencing (RAD-Seq) to conduct phylogenomic comparisons among three common, Indo-Pacific Pocillopora species – P. damicornis, P. eydouxi and P. elegans – within and between populations in the Tropical Eastern Pacific (TEP) and the Central Pacific. Genome-wide RAD- Seq comparisons of Central and TEP Pocillopora confirm that the morphospecies P. damicornis, P. eydouxi and P. elegans are not monophyletic, but instead fall into three distinct genetic groups. However, hybrid samples shared fixed alleles with their respective parental species and, even without strict monophyly, P. damicornis share a common set of 33 species-specific alleles across the Pacific. RAD-Seq data confirm the pattern of one-way introgressive hybridization among TEP Pocillopora, suggesting that introgression may play a role in generating shared, polyphyletic lineages among currently recognized Pocillopora spe- cies. Levels of population differentiation within genetic lineages indicate significantly higher levels of population differentiation in the Tropical Eastern Pacific than in the Central West Pacific.

Mixed asexual and sexual reproduction in the Indo-Pacific reef coral Pocillopora damicornis
Combosch DJ, Vollmer SV. Mixed asexual and sexual reproduction in the Indo-Pacific reef coral Pocillopora damicornis. Ecology and Evolution. 2013;3 (10) :3379–3387.Abstract
Keywords: Evolutionary significance; Minimal cryptic sex; Mixed reproduction; Parthenogenesis; Pseudogamy Abstract: Pocillopora damicornis is one of the best studied reef-building corals, yet it's somewhat unique reproductive strategy remains poorly understood. Genetic studies indicate that P. damicornis larvae are produced almost exclusively parthenogenetically, and yet population genetic surveys suggest frequent sexual reproduction. Using microsatellite data from over 580 larvae from 13 colonies, we demonstrate that P. damicornis displays a mixed reproductive strategy where sexual and asexual larvae are produced simultaneously within the same colony. The majority of larvae were parthenogenetic (94%), but most colonies (10 of the 13) produced a subset of their larvae sexually. Logistic regression indicates that the proportion of sexual larvae varied significantly with colony size, cycle day, and calendar day. In particular, the decrease in sexual larvae with colony size suggests that the mixed reproductive strategy changes across the life of the coral. This unique shift in reproductive strategy leads to increasingly asexual replications of successful genotypes, which (in contrast to exclusive parthenogens) have already contributed to the recombinant gene pool.
ENSO Drove 2500-Year Collapse of Eastern Pacific Coral Reefs
Toth LT, Aronson RB, Vollmer SV, Hobbs JW, Urrego DH, Cheng H, Enochs IC, Combosch DJ, van Woesik R, Macintyre IG. ENSO Drove 2500-Year Collapse of Eastern Pacific Coral Reefs. Science. 2012;337 (6090) :81-84 . PublicationAbstract
Cores of coral reef frameworks along an upwelling gradient in Panamá show that reef ecosystems in the tropical eastern Pacific collapsed for 2500 years, representing as much as 40% of their history, beginning about 4000 years ago. The principal cause of this millennial-scale hiatus in reef growth was increased variability of the El Niño–Southern Oscillation (ENSO) and its coupling with the Intertropical Convergence Zone. The hiatus was a Pacific-wide phenomenon with an underlying climatology similar to probable scenarios for the next century. Global climate change is probably driving eastern Pacific reefs toward another regional collapse.
Population Genetics of an Ecosystem-Defining Reef Coral Pocillopora damicornis in the Tropical Eastern Pacific
Combosch DJ, Vollmer SV. Population Genetics of an Ecosystem-Defining Reef Coral Pocillopora damicornis in the Tropical Eastern Pacific. PLoS ONE. 2011;6 :e21200. Publisher's VersionAbstract
Abstract Background Coral reefs in the Tropical Eastern Pacific (TEP) are amongst the most peripheral and geographically isolated in the world. This isolation has shaped the biology of TEP organisms and lead to the formation of numerous endemic species. For example, the coral Pocillopora damicornis is a minor reef-builder elsewhere in the Indo-West Pacific, but is the dominant reef-building coral in the TEP, where it forms large, mono-specific stands, covering many hectares of reef. Moreover, TEP P. damicornis reproduces by broadcast spawning, while it broods mostly parthenogenetic larvae throughout the rest of the Indo-West Pacific. Population genetic surveys for P. damicornis from across its Indo-Pacific range indicate that gene flow (i.e. larval dispersal) is generally limited over hundreds of kilometers or less. Little is known about the population genetic structure and the dispersal potential of P. damicornis in the TEP. Methodology Using multilocus microsatellite data, we analyzed the population structure of TEP P. damicornis among and within nine reefs and test for significant genetic structure across three geographically and ecologically distinct regions in Panama. Principal Findings/Conclusions We detected significant levels of population genetic structure (global RST = 0.162), indicating restricted gene flow (i.e. larvae dispersal), both among the three regions (RRT = 0.081) as well as within regions (RSR = 0.089). Limited gene flow across a distinct environmental cline, like the regional upwelling gradient in Panama, indicates a significant potential for differential adaptation and population differentiation. Individual reefs were characterized by unexpectedly high genet diversity (avg. 94%), relatively high inbreeding coefficients (global FIS = 0.183), and localized spatial genetic structure among individuals (i.e. unique genets) over 10 m intervals. These findings suggest that gene flow is limited in TEP P. damicornis populations, particularly among regions, but even over meter scales within populations.
Combosch DJ, Schuhmacher H. Biotische Korallenkrankheiten: Pathogene häufig unbekannt, Folgen verheerend, Therapien gesucht. Biologie in unserer Zeit. 2005;35 :178–185.