Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes

Ecological transcriptomics reveals stress response pathways of a ground-herb species in a waterlogging gradient of Amazonian riparian forests

Environmental stress is a fundamental facet of life and a significant driver of natural selection in the wild. Gene expression diversity may facilitate adaptation to environmental changes, without necessary genetic change, but its role in adaptive divergence remains largely understudied in Neotropical systems. In Amazonian riparian forests, species distribution is predominantly influenced by species' waterlogging tolerance. The flooding gradient delineates distinct wetland forest types, shaping habitats and species characteristics. Here we investigated the molecular basis of environmental stress response in a tropical ground-herb species (Ischnosiphon puberulus) to environmental variation in Amazonian riparian forests. We compared environmental variables and gene expression profiles from individuals collected in two forest types: Igapó and Terra firme in the Amazonian riparian forests. Predictable seasonal flooding poses a significant challenge in Igapó compared to Terra firme environments, with the former presenting higher water column height and longer flooding duration. Our findings suggest that contrasting environmental conditions related to flooding regimes are important drivers of population genetic differentiation and differential gene expression in I. puberulus. Enriched gene ontology terms highlight associations with environmental stresses, such as defence response, water transport, phosphorylation, root development, response to auxin, salicylic acid and oxidative stress. By uncovering key environmental stress response pathways conserved across populations, I. puberulus offers novel genetic insights into the molecular basis of plant reactions to environmental constraints found in flooded areas of this highly biodiverse neotropical ecosystem.

Genetic basis of ecologically relevant body shape variation among four genera of cichlid fishes

Divergence in body shape is one of the most widespread and repeated patterns of morphological variation in fishes and is associated with habitat specification and swimming mechanics. Such ecological diversification is the first stage of the explosive adaptive radiation of cichlid fishes in the East African Rift Lakes. We use two hybrid crosses of cichlids (Metriaclima sp. × Aulonocara sp. and Labidochromis sp. × Labeotropheus sp., >975 animals total) to determine the genetic basis of body shape diversification that is similar to benthic-pelagic divergence across fishes. Using a series of both linear and geometric shape measurements, we identified 34 quantitative trait loci (QTL) that underlie various aspects of body shape variation. These QTL are spread throughout the genome, each explaining 3.2-8.6% of phenotypic variation, and are largely modular. Further, QTL are distinct both between these two crosses of Lake Malawi cichlids and compared to previously identified QTL for body shape in fishes such as sticklebacks. We find that body shape is controlled by many genes of small effect. In all, we find that convergent body shape phenotypes commonly observed across fish clades are most likely due to distinct genetic and molecular mechanisms.

No difference between critical and sprint swimming speeds for two galaxiid species

Researchers have used laboratory experiments to examine how fish might be affected by anthropogenic alterations and conclude how best to adjust fish passage and culvert remediation designs in response. A common way to document swimming performance for this purpose is measuring fish critical swimming speed (U_crit ). Nonetheless, the U_crit protocol as defined by Brett [(1964) Journal of the Fisheries Research Board of Canada, 21, 1183-1226] may be inappropriate for studying swimming performance and determining how it relates to upstream migration in benthic fish, as they may not actively swim throughout the entire U_crit test. An alternative method to estimate swimming performance is sprint swimming speed (U_sprint ), which is suggested to be a measure of the burst speed of fish rather than maximum sustained swimming speed. The authors conducted comparative swimming performance experiments to evaluate whether U_sprint can be used to compare swimming performance of benthic species to that of pelagic, actively swimming species. They measured individual swimming speeds of īnanga (Galaxias maculatus), an actively swimming pelagic species, and banded kōkopu (Galaxias fasciatus), a fish that exhibits benthic station-holding behaviour, using both the U_sprint and U_crit test. Experiments revealed that no significant statistical difference between swimming speeds was estimated using the U_crit and U_sprint test protocols for both G. maculatus and G. fasciatus. The result of this study suggests that fish swimming speeds obtained using these two methods are comparable for the species used in this study. By using U_sprint for benthic-associated fish and U_crit for pelagic fish, we may be able to compare a broader range of species' swimming abilities for use in a fish passage context.

Early stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes

Homoploid hybrid speciation (i.e., hybrid speciation without a change in ploidy) has traditionally been considered to be rare in animals. Only few accepted empirical examples of homoploid hybrid speciation in nature exist, and in only one previous case (insects) was it convincingly shown that this process occurred in complete sympatry. Here, we report an instance of sympatric homoploid hybrid speciation in Midas cichlid fishes in Crater Lake Xiloá, Nicaragua. The hybrid lineage, albeit at an early stage of speciation, has genomically and phenotypically diverged from both of its two parental species. Together with a distinct stable isotope signature this suggests that this hybrid lineages occupies a different trophic niche compared to the other sympatric Midas cichlid species in Crater Lake Xiloá.

Here, the authors present a rare example of sympatric homoploid hybrid speciation, without ploidy changes, in the Midas cichlid fishes from Nicaragua. Midas cichlid hybrids occupy a different ecological niche, likely facilitated by body shape adaptations.

Dual function and associated costs of a highly exaggerated trait in a cichlid fish

Exaggerated secondary sexual characteristics are apparently costly and seem to defy natural selection. This conundrum promoted the theory of sexual selection. Accordingly, exaggerated secondary sexual characteristics might be ornaments on which female choice is based and/or armaments used during male-male competition. Males of many cichlid fish species, including the adaptive radiation of Nicaraguan Midas cichlids, develop a highly exaggerated nuchal hump, which is thought to be a sexually selected trait. To test this hypothesis, we conducted a series of behavioral assays in F2 hybrids obtained from crossing a species with a relatively small hump and one with an exaggerated hump. Mate-choice experiments showed a clear female preference for males with large humps. In an open-choice experiment with limited territories, couples including large humped males were more successful in acquiring these territories. Therefore, nuchal humps appear to serve dual functions as an ornament for attracting mates and as an armament for direct contest with rivals. Although being beneficial in terms of sexual selection, this trait also imposes fitness costs on males possessing disproportionally large nuchal humps since they exhibit decreased endurance and increased energetic costs when swimming. We conclude that these costs illustrate trade-offs associated with large hump size between sexual and natural selection, which causes the latter to limit further exaggeration of this spectacular male trait.

Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina (Neritrema)

Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel-bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level-dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes

Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for 'molecular pre-adaptation' in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome-wide factors underlying the propensity for these cichlid fishes to adaptively radiate.

The physiology of rapid ecological specialization: A look at the Midas cichlids

Understanding the process of speciation is a primary goal of evolutionary biology, yet the question of whether speciation can reach completion in the presence of gene flow remains controversial. For more than 50 years, the cichlids of Africa, and more recently those in South and Central America, have served as model systems for the study of speciation in nature. Cichlids are distinguished by their enormous species richness, their diversity of behavioural and trophic adaptations, and their rapid rate of divergence. In both Africa and South and Central America, the repeated interaction of geology, new founder events and adaptive evolution has created a series of natural experiments with speciation occurring both within and between waterbodies of differing ages. In the "From the Cover" paper in this issue of the Journal of Molecular Ecology, Raffini, Schneider, Franchini, Kautt and Meyer move beyond the question of which mechanisms drive speciation, and instead show that divergent morphologies and physiologies translate into adaptive traits. They investigate differences in physiology and gene expression profiles in a benthic/limnetic species pair of Midas cichlidsin a 24,000-year-old Nicaraguan crater lake. While recently diverged, these two species demonstrate significant ecological, but limited genetic differentiation. The authors find that the distinct morphotypes translate into relevant differences in swimming performance and metabolic rates that correspond to differential gene expression profiles. Hence, the authors take an integrative approach examining the impacts of morphological differences on performance and niche partitioning: an approach that can advance our understanding of the drivers of morphological and physiological divergence during speciation.