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

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

The genomic basis of cichlid fish adaptation within the deepwater “twilight zone” of Lake Malawi

Deepwater environments are characterized by low levels of available light at narrow spectra, great hydrostatic pressure, and low levels of dissolved oxygen—conditions predicted to exert highly specific selection pressures. In Lake Malawi over 800 cichlid species have evolved, and this adaptive radiation extends into the “twilight zone” below 50 m. We use population-level RAD-seq data to investigate whether four endemic deepwater species (Diplotaxodon spp.) have experienced divergent selection within this environment. We identify candidate genes including regulators of photoreceptor function, photopigments, lens morphology, and haemoglobin, many not previously implicated in cichlid adaptive radiations. Colocalization of functionally linked genes suggests coadapted “supergene” complexes. Comparisons of Diplotaxodon to the broader Lake Malawi radiation using genome resequencing data revealed functional substitutions and signatures of positive selection in candidate genes. Our data provide unique insights into genomic adaptation within deepwater habitats, and suggest genome-level specialization for life at depth as an important process in cichlid radiation

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

Unravelling the Potamonautes lirrangensis (Rathbun, 1904) species complex (Potamoidea: Potamonautidae), with the description of two new species

The taxonomic status of the widely distributed freshwater crab Potamonautes lirrangensis (Rathbun, 1904) sensu lato is revised because morphological and molecular evidence indicates that this taxon is a complex comprising more than one species. Four taxa are now recognized: Potamonautes lirrangensis (Rathbun, 1904) s. str. and P. kisangani sp. nov. from the Middle Congo River in Central Africa, P. amosae sp. nov. from the drainages of Lakes Kivu and Tanganyika, and P. orbitospinus (Cunnington, 1907) from Lake Malawi which had been previously synonymised with P. lirrangensis s. lat. Diagnoses, illustrations and distribution maps are provided for each of these taxa and they are compared to similar species from Central and Southern Africa

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