ALBERT

Description: The data sheet contains the individual counts of seven hamlet species (Hypoplectrus spp.) observed within transects at Puerto Rican coral reefs. The data is based on a series of SCUBA based transects conducted during March 2017. Each row contains the hamlet counts of a single 400 m² transect.

Description: Transect surveys of hamlet communities (Hypoplectrus spp., Serranidae) covering 14 000 m2 across 16 reefs off La Parguera, Puerto Rico, are presented and compared with a previous survey conducted in the year 2000. The hamlet community has noticeably changed over 17 years, with a 〉 30% increase in relative abundance of the yellowtail hamlet Hypoplectrus chlorurus on the inner reefs at the expense of the other hamlet species. The data also suggest that the density of H. chlorurus has declined and that its distribution has shifted towards shallower depths. Considering that H. chlorurus has been previously identified as one of the few fish showing a positive association with seawater turbidity on the inner reefs of La Parguera and that sedimentation of terrestrial origin has increased over recent decades on these reefs, it is proposed that turbidity may constitute an important but so far overlooked ecological driver of hamlet communities.

Description: This git repository contains all the scripts needed to reproduce our results from the study "Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence" from raw data to figures. It contains all scripts referenced within the materials & methods section. Related datasets are deposited at ENA (raw sequencing data, acession nr. PRJEB27858) and dryad (genome annotation & genotypes, doi:10.5061/dryad.pg8q56g).

Description: Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.

Description: Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef System (MBRS). We use whole-genome analysis to infer the demographic history of the Maya hamlet and contrast it with the sympatric and pan-Caribbean black (H. nigricans), barred (H. puella) and butter (H. unicolor) hamlets, as well as the allopatric but phenotypically similar blue hamlet (H. gemma). We show that H. maya is indeed a distinct evolutionary lineage, with genomic signatures of inbreeding and a unique demographic history of continuous decrease in effective population size since it diverged from congeners just ~3,000 generations ago. We suggest that this case of microendemism may be driven by the combination of a narrow ecological niche and restrictive oceanographic conditions in the southern MBRS, which is consistent with the occurrence of an unusually high number of marine microendemics in this region. The restricted distribution of the Maya hamlet, its decline in both census and effective population sizes, and the degradation of its habitat place it at risk of extinction. We conclude that the evolution of marine microendemism can be a fast and dynamic process, with extinction possibly occurring before speciation is complete.

Description: The work within this doctoral thesis introduces the Caribbean reef fish genus Hypoplectrus (hamlets) into the field of speciation genomics. The overarching theme within this thesis is the investigation of the underlying evolutionary drivers that are acting at the origin of this marine radiation and facilitate rapid speciation within the ocean. Distributed over four separate manuscripts, this work addresses several aspects impacting the dynamics of the Hypoplectrus radiation. Within the first manuscript, the temporal stability of the hamlet community in a patch of reefs in Puerto Rico is investigated. The findings indicate that the hamlet community composition is dynamic and potentially impacted by ecological factors such as turbidity or the presence of specific coral species. Within the second manuscript the hamlet reference genome is introduced and whole genome resequencing is applied to investigate the signals of speciation within three of the most common hamlet species. The results show that, against a genome wide background of very low differentiation, a small number of color pattern and vision genes are highly differentiated between species and apparently co-selected for. The third manuscript explores the demographic history of a rare endemic hamlet species. It uses a coalescent approach to show the decline in population size of this particular species since the recent evolutionary split from the remaining genus. In the last manuscript, nine different hamlet species are sequenced to provide a cross section through the hamlet radiation. The results of population- and phylogenomics indicate ongoing inter-species gene flow throughout the majority of the genome with only a small set of putative barrier genes. Phylogenetic relationships through most of the genome are diffuse, yet the signal within the few differentiated genomic intervals is discordant, pointing to introgession events or differential lineage sorting at those major effect loci.