Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback fish population pair adapted to contiguous, ecologically different lake and stream habitats. Clinal whole-genome sequence data reveal numerous genome regions (nearly) fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center closely matches the habitat transition. Simulations confirm that such strong divergence can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from near the habitat transition before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

Larval breeding sites of the mosquito Aedes aegypti in forest and domestic habitats in Africa and the potential association with oviposition evolution

Adaptations to anthropogenic domestic habitats contribute to the success of mosquito Aedes aegypti as a major global vector of several arboviral diseases. The species inhabited African forests before expanding into domestic habitats and spreading to the rest of the world. Despite a well-studied evolutionary history, how this species initially moved into human settlements in Africa remains unclear. During this initial habitat transition, Ae. aegypti switched from using natural containers like tree holes as larval breeding sites to using artificial containers like clay pots. Little is known about how these natural versus artificial containers differ in their environments, or whether Ae. aegypti in forest versus domestic habitats evolved any corresponding incipient behavioral divergence, such as in oviposition. To address these gaps, we first characterized physical characteristics, larval density, microbial density, bacterial composition, and volatile profiles of natural versus artificial containers used as mosquito larval breeding sites. We focused on two localities in Africa, La Lopé, Gabon and Rabai, Kenya. In both localities, our data showed that the two habitat-specific container types had significantly different characteristics. We then examined whether such containers differed in their attractiveness for oviposition, a key behavior affecting larval distribution. Forest Ae. aegypti readily accepted artificial containers in our field experiments, and laboratory choice experiments did not find distinct oviposition preference between forest and village Ae. aegypti colonies. These results suggested that African Ae. aegypti were likely generalists in their oviposition site choice. This flexibility to accept different containers might play a vital role during the initial domestication of Ae. aegypti, allowing the mosquitoes to use human-stored water as fallback breeding sites during dry seasons. Although ovipositional changes were not present initially, after longer domestic habitat breeding, the mosquitoes did evolve divergence oviposition preference, as suggested by previous comparisons of African Ae. aegypti and human-specialized non-African Ae. aegypti.

Recreated Ancestral Opsin Associated with Marine to Freshwater Croaker Invasion Reveals Kinetic and Spectral Adaptation

Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim-light environments. Aquatic environments are particularly challenging for vision due to the spectrally dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine environments, croakers are known as highly visual benthic predators. In this study, we isolate rhodopsins from a diversity of freshwater and marine croakers and find that strong positive selection in rhodopsin is associated with a marine to freshwater transition in South American croakers. In order to determine if this is accompanied by significant shifts in visual abilities, we resurrected ancestral rhodopsin sequences and tested the experimental properties of ancestral pigments bracketing this transition using in vitro spectroscopic assays. We found the ancestral freshwater croaker rhodopsin is redshifted relative to its marine ancestor, with mutations that recapitulate ancestral amino acid changes along this transitional branch resulting in faster kinetics that are likely to be associated with more rapid dark adaptation. This could be advantageous in freshwater due to the redshifted spectrum and relatively narrow interface and frequent transitions between bright and dim-light environments. This study is the first to experimentally demonstrate that positively selected substitutions in ancestral visual pigments alter protein function to freshwater visual environments following a transition from an ancestrally marine state and provides insight into the molecular mechanisms underlying some of the physiological changes associated with this major habitat transition.

Clinal genomic analysis reveals strong reproductive isolation across a steep habitat transition in stickleback fish

How ecological divergence causes strong reproductive isolation between populations in close geographic contact remains poorly understood at the genomic level. We here study this question in a stickleback population pair adapted to contiguous, ecologically different lake and stream habitats. Dense clinal whole-genome sequence data reveal numerous regions fixed for alternative alleles over a distance of just a few hundred meters. This strong polygenic adaptive divergence must constitute a genome-wide barrier to gene flow because a steep cline in allele frequencies is observed across the entire genome, and because the cline center co-localizes with the habitat transition. Simulations confirm that such strong reproductive isolation can be maintained by polygenic selection despite high dispersal and small per-locus selection coefficients. Finally, comparing samples from the cline center before and after an unusual ecological perturbation demonstrates the fragility of the balance between gene flow and selection. Overall, our study highlights the efficacy of divergent selection in maintaining reproductive isolation without physical isolation, and the analytical power of studying speciation at a fine eco-geographic and genomic scale.

Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition

ABSTRACT Symbiotic bacteria use diverse strategies to compete for host colonization sites. However, little is known about the environmental cues that modulate interbacterial competition as they transition between free-living and host-associated lifestyles. We used the mutualistic relationship between Eupyrmna scolopes squid and Vibrio fischeri bacteria to investigate how intraspecific competition is regulated as symbionts move from the seawater to a host-like environment. We recently reported that V. fischeri uses a type VI secretion system (T6SS) for intraspecific competition during host colonization. Here, we investigated how environmental viscosity impacts T6SS-mediated competition by using a liquid hydrogel medium that mimics the viscous host environment. Our data demonstrate that although the T6SS is functionally inactive when cells are grown under low-viscosity liquid conditions similar to those found in seawater, exposure to a host-like high-viscosity hydrogel enhances T6SS expression and sheath formation, activates T6SS-mediated killing in as little as 30 min, and promotes the coaggregation of competing genotypes. Finally, the use of mass spectrometry-based proteomics revealed insights into how cells may prepare for T6SS competition during this habitat transition. These findings, which establish the use of a new hydrogel culture condition for studying T6SS interactions, indicate that V. fischeri rapidly responds to the physical environment to activate the competitive mechanisms used during host colonization. IMPORTANCE Bacteria often engage in interference competition to gain access to an ecological niche, such as a host. However, little is known about how the physical environment experienced by free-living or host-associated bacteria influences such competition. We used the bioluminescent squid symbiont Vibrio fischeri to study how environmental viscosity impacts bacterial competition. Our results suggest that upon transition from a planktonic environment to a host-like environment, V. fischeri cells activate their type VI secretion system, a contact-dependent interbacterial nanoweapon, to eliminate natural competitors. This work shows that competitor cells form aggregates under host-like conditions, thereby facilitating the contact required for killing, and reveals how V. fischeri regulates a key competitive mechanism in response to the physical environment.

Freshwater-to-marine transitions may explain the evolution of herbivory in the subgenus Mollienesia (genus Poecilia, mollies and guppies)

The ability of organisms to cross ecosystem boundaries is an important catalyst of evolutionary diversification. The genus Poecilia (mollies and guppies) is an excellent system for studying ecosystem transitions because species display a range of salinity and dietary preferences, with herbivory concentrated in the subgenus Mollienesia. We reconstructed ancestral habitats and diets across a phylogeny of the genus Poecilia, evaluated diversification rates and used phylogenetically independent contrasts to determine whether diet evolved in response to habitat transition in this group. The results suggest that ancestors of subgenus Mollienesia were exclusively herbivorous, whereas ancestral diets of other Poecilia included animals. We found that transitions across euryhaline boundaries occurred at least once in this group, probably after the divergence of the subgenus Mollienesia. Furthermore, increased salinity affiliation explained 24% of the decrease in animals in the gut, and jaw morphology was associated with the percentage of animals in the gut, but not with the percentage of species occupying saline habitats. These findings suggest that in the genus Poecilia, herbivory evolved in association with transitions from fresh to euryhaline habitats, and jaw morphology evolved in response to the appearance of herbivory. These results provide a rare example of increased diet diversification associated with the transition from freshwater to euryhaline habitats.

Evolution in action: Habitat-transition leads to genome-streamlining in Methylophilaceae (Betaproteobacteriales)

The most abundant aquatic microbes are small in cell and genome size. Genome-streamlining theory predicts gene loss caused by evolutionary selection driven by environmental factors, favouring superior competitors for limiting resources. However, evolutionary histories of such abundant, genome-streamlined microbes remain largely unknown. Here we reconstruct the series of steps in the evolution of some of the most abundant genome-streamlined microbes in freshwaters (‘Ca. Methylopumilus’) and oceans (marine lineage OM43). A broad genomic spectrum is visible in the family Methylophilaceae (Betaproteobacteriales), from sediment microbes with medium-sized genomes (2-3 Mbp genome size), an occasionally blooming pelagic intermediate (1.7 Mbp), and the most reduced pelagic forms (1.3 Mbp). We show that a habitat transition from freshwater sediment to the relatively oligotrophic pelagial was accompanied by progressive gene loss and adaptive gains. Gene loss has mainly affected functions not necessarily required or advantageous in the pelagial or are encoded by redundant pathways. Likewise, we identified genes providing adaptations to oligotrophic conditions that have been transmitted horizontally from pelagic freshwater microbes. Remarkably, the secondary transition from the pelagial of lakes to the oceans required only slight modifications, i.e., adaptations to higher salinity, gained via horizontal gene transfer from indigenous microbes. Our study provides first genomic evidence of genome-reduction taking place during habitat transitions. In this regard, the family Methylophilaceae is an exceptional model for tracing the evolutionary history of genome-streamlining as such a collection of evolutionarily related microbes from different habitats is practically unknown for other similarly abundant microbes (e.g., ‘Ca. Pelagibacterales’, ‘Ca. Nanopelagicales’).