Lake level fluctuations and divergence of cichlid fish ecomorphs in Lake Tanganyika

Lake Tanganyika has undergone substantial climate-driven lake level fluctuations that have repeatedly changed the distribution and extent of habitat for endemic fishes. Here we consider whether patterns of population genetic structure and phenotypic divergence within the cichlid fish Telmatochromis temporalis have been affected by changing lake levels. The species has a large-bodied rock-living ecomorph and a small-bodied shell-living ecomorph, and both are found in close proximity in littoral habitats. Using mtDNA sequences we found that geographically distant ([50 km) populations within the southern lake region diverged approximately 130,000–230,000 years ago, suggesting that the regional genetic structure persisted through a low stand of over 400 m *106,000 years ago that ended with a rise to present levels *100,000 years ago. We also found signatures of large population expansions since this rise across the study region, suggesting that the populations positively responded to new habitat as lake levels rose to present levels. Finally, we found that geographically adjacent (\10 km) ecomorphs exhibit both significant genetic differentiation and signatures of gene flow after the lake level rise. The results suggest that local ecomorph divergence progressed with gene flow after the last major rise in lake level *100,000, potentially facilitated by new ecological opportunities

Pleistocene climate change promoted rapid diversification of aquatic invertebrates in Southeast Australia

Background: The Pleistocene Ice Ages were the most recent geohistorical event of major global impact, but their consequences for most parts of the Southern hemisphere remain poorly known. We investigate a radiation of ten species of Sternopriscus, the most species-rich genus of epigean Australian diving beetles. These species are distinct based on genital morphology but cannot be distinguished readily by mtDNA and nDNA because of genotype sharing caused by incomplete lineage sorting. Their genetic similarity suggests a Pleistocene origin. Results: We use a dataset of 3858 bp of mitochondrial and nuclear DNA to reconstruct a phylogeny of Sternopriscus using gene and species trees. Diversification analyses support the finding of a recent rapid speciation event with estimated speciation rates of up to 2.40 species per MY, which is considerably higher than the proposed average rate of 0.16 species per MY for insects. Additionally, we use ecological niche modeling and analyze data on habitat preferences to test for niche divergence between species of the recent Sternopriscus radiation. These analyses show that the species can be characterized by a set of ecological variables referring to habitat, climate and altitude. Conclusions: Our results suggest that the repeated isolation of populations in glacial refugia might have led to divergent ecological adaptations and the fixation of morphological traits supporting reproductive isolation and therefore may have promoted speciation. The recent Sternopriscus radiation fulfills many characteristics of a species flock and would be the first described example of an aquatic insect species flock. We argue that the species of this group may represent a stage in speciation past the species flock condition because of their mostly broad and often non-overlapping ranges and preferences for different habitat types.Organismic and Evolutionary Biolog

Hotshots, hot spots, and female preference: exploring lek formation models with a bower-building cichlid fish

In many animals, males congregate in leks that females visit for the sole purpose of mating. We observed male and female behavior on 3 different-sized leks of the bower-building cichlid fish Nyassachromis cf. microcephalus to test predictions of 3 prominent lek models: the "hotshot,” "hot spot,” and "female preference” models. In this system, we were able to refine these predictions by distinguishing between indirect mate choice, by which females restrict their set of potential mates in the absence of individual male assessment, and direct mate choice, by which females assess males and their territories through dyadic behavioral interactions. On no lek were males holding central territories favored by indirect or direct mate choice, contrary to the prediction of the hotshot model that leks form because inferior males establish territories surrounding hotshot males preferred by females. Average female encounter rate of males increased with lek size, a pattern typically interpreted as evidence that leks form through female preference for lekking males, rather than because males congregate in hot spots of high female density. Female propensity to engage in premating behavior once courted did not increase with lek size, suggesting female preference for males on larger leks operated through indirect choice rather than direct choice based on individual assessment. The frequency of male-male competitive interactions increased with lek size, whereas their foraging rate decreased, implying a cost to males maintaining territories on larger leks. Together these data most strongly support the female preference model, where females may benefit through indirect mate choice for males able to meet the competitive cost of occupying larger lek

Population genetic structure of Morelet’s and American crocodiles in Belize:Hybridization, connectivity and conservation

Hybridization can influence the evolutionary potential of wild species and can be especially detrimental where one species is abundant, and the other much rarer. In Belize, the Morelet’s crocodile (Crocodylus moreletii) primarily inhabits inland freshwater lagoons, lakes and rivers, whereas the less abundant American crocodile (Crocodylus acutus) is more prevalent among the offshore cayes and atolls. Both species are historically sympatric along the brackish coastline, but it is unclear if admixture between the two is affecting genetic integrity of the species. We investigated the extent of interspecific hybridization across Belize using genomic variants identified using double digest restriction-site associated DNA sequencing (ddRADseq). Five groups of genetically pure C. moreletii were identified, two of which were inland, including the protected Chiquibul National Park. Two groups of genetically pure C. acutus were identified, one on northern offshore islands, and a second along the southern coastline. Hybrids were only identified along the central-southern coastline and were in close geographic proximity to coastal purebreds. Based on these results, we suggest that the central-southern coastline represents a hybrid zone, while the inland areas and offshore islands that harbour only genetically pure populations may benefit from conservation prioritisation

Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here, we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700m diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet and trophic morphology. With whole genome sequences of 146 fish, we identify 98 clearly demarcated genomic ‘islands’ of high differentiation and demonstrate association of genotypes across these islands to divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight vision associated genes), hormone signaling and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.The work was funded by Royal Society-Leverhulme Trust Africa Awards AA100023 and AA130107 (M.J.G., B.P.N. and G.F.T.), a Wellcome Trust PhD studentship grant 097677/Z/11/Z (M.M.), Wellcome Trust grant WT098051 (S.S. and R.D.), Wellcome Trust and Cancer Research UK core support and a Wellcome Trust Senior Investigator Award (E.A.M.), a Leverhulme Trust Research Fellowship RF-2014-686 (M.J.G.), a University of Bristol Research Committee award (M.G.), a Bangor University Anniversary PhD studentship (to A.M.T.) and a Fisheries Society of the British Isles award (G.F.T.). Raw sequencing reads are in the SRA nucleotide archive: RAD sequencing (BioProject: PRJNA286304; accessions SAMN03768857 to SAMN03768912) and whole genome sequencing (BioProject PRJEB1254: sample accessions listed in Table S16). The RAD based phylogeny and alignments have been deposited in TreeBase (TB2:S18241). Whole genome variant calls in the VCF format, phylogenetic trees, and primer sequences for Sequenom genotyping are available from the Dryad Digital Repository (http://dx.doi.org/10.5061/dryad.770mc). RD declares his interests as a founder and non-executive director of Congenica Ltd., that he owns stock in Illumina from previous consulting, and is a scientific advisory board member of Dovetail Inc. We thank R. Schley for generating pharyngeal jaw data; S. Mzighani, J. Kihedu and staff of the Tanzanian Fisheries Research Institute for logistical support; A. Smith, H. Sungani, A. Shechonge, P. Parsons, J. Swanstrom, G. Cooke and J. Bridle for contributions to sampling and aquarium maintenance, the Sanger Institute sequencing core for DNA sequencing and Dr. H. Imai (Kyoto University) for the use of spectrometer in his laboratory.This is the author accepted manuscript. The final version is available from AAAS via http://dx.doi.org/10.1126/science.aac992

Secondary contact seeds morphological novelty in cichlid fishes

Theory proposes that genomic admixture between formerly reproductively isolated populations can generate phenotypic novelty for selection to act upon. Secondary contact may therefore be a significant promoter of phenotypic novelty that allows species to overcome environmental challenges and adapt to novel environments, including during adaptive radiation. To date, this has largely been considered from the perspective of interspecific hybridization at contact zones. However, it is also possible that this process occurs more commonly between natural populations of a single species, and thus its importance in adaptive evolution may have been underestimated. In this study, we tested the consequences of genomic introgression during apparent secondary contact between phenotypically similar lineages of the riverine cichlid fish Astatotilapia calliptera. We provide population genetic evidence of a secondary contact zone in the wild, and then demonstrate using mate-choice experiments that both lineages can reproduce together successfully in laboratory conditions. Finally, we show that genomically admixed individuals display extreme phenotypes not observed in the parental lineages. Collectively, the evidence shows that secondary contact can drive the evolution of phenotypic novelty, suggesting that pulses of secondary contact may repeatedly seed genetic novelty, which when coupled with ecological opportunity could promote rapid adaptive evolution in natural circumstances

Diel variation in insect-dominated temperate pond soundscapes and guidelines for survey design

The data and code accompanying 'Diel variation in insect-dominated temperate pond soundscapes and guidelines for survey design' published in Freshwater Biology