THE PHYSIOLOGICAL BASIS OF NATURAL SELECTION AT THE LAP LOCUS

Local Adaptation in Marine Foundation Species at Microgeographic Scales

AbstractNearshore foundation species in coastal and estuarine systems (e.g., salt marsh grasses, mangroves, seagrasses, corals) drive the ecological functions of ecosystems and entire biomes by creating physical structure that alters local abiotic conditions and influences species interactions and composition. The resilience of foundation species and the ecosystem functions they provide depends on their phenotypic and genetic responses to spatial and temporal shifts in environmental conditions. In this review, we explore what is known about the causes and consequences of adaptive genetic differentiation in marine foundation species over spatial scales shorter than dispersal capabilities (i.e., microgeographic scales). We describe the strength of coupling field and laboratory experiments with population genetic techniques to illuminate patterns of local adaptation, and we illustrate this approach by using several foundation species. Among the major themes that emerge from our review include (1) adaptive differentiation of marine foundation species repeatedly evolves along vertical (i.e., elevation or depth) gradients, and (2) mating system and phenology may facilitate this differentiation. Microgeographic adaptation is an understudied mechanism potentially underpinning the resilience of many sessile marine species, and this evolutionary mechanism likely has particularly important consequences for the ecosystem functions provided by foundation species.

Functional Analysis of a Putative Target of Spatially Varying Selection in the Menin1 Gene of Drosophila melanogaster

While significant effort has been devoted to investigating the potential influence of spatially varying selection on genomic variation, relatively little effort has been devoted to experimental analysis of putative variants or genes experiencing such selection. Previous population genetic work identified an amino acid polymorphism in the Mnn1 gene as one of the most strongly latitudinally differentiated SNPs in the genome of Drosophila melanogaster in the United States and Australia. Here we report the results of our transgenic analysis of this amino acid polymorphism. Genotypes carrying alternative Mnn1 alleles differed in multiple phenotypes in a direction generally consistent with phenotypic differences previously observed along latitudinal clines. These results support inferences from earlier population genomic work that this variant influences fitness, and support the idea that the alleles exhibiting clines may be likely to have pleiotropic effects that are correlated along the axes favored by natural selection.

From population connectivity to the art of striping Russian dolls: the lessons from Pocillopora corals

Here, we examined the genetic variability in the coral genus Pocillopora, in particular within the Primary Species Hypothesis PSH09, identified by Gélin, Postaire, Fauvelot and Magalon (2017) using species delimitation methods [also named Pocillopora eydouxi/meandrina complex sensu, Schmidt-Roach, Miller, Lundgren, & Andreakis (2014)] and which was found to split into three secondary species hypotheses (SSH09a, SSH09b, and SSH09c) according to assignment tests using multi-locus genotypes (13 microsatellites). From a large sampling (2,507 colonies) achieved in three marine provinces [Western Indian Ocean (WIO), Tropical Southwestern Pacific (TSP), and Southeast Polynesia (SEP)], genetic structuring analysis conducted with two clustering analyses (structure and DAPC) using 13 microsatellites revealed that SSH09a was restricted to the WIO while SSH09b and SSH09c were almost exclusively in the TSP and SEP. More surprisingly, each SSH split into two to three genetically differentiated clusters, found in sympatry at the reef scale, leading to a pattern of nested hierarchical levels (PSH > SSH > cluster), each level hiding highly differentiated genetic groups. Thus, rather than structured populations within a single species, these three SSHs, and even the eight clusters, likely represent distinct genetic lineages engaged in a speciation process or real species. The issue is now to understand which hierarchical level (SSH, cluster, or even below) corresponds to the species one. Several hypotheses are discussed on the processes leading to this pattern of mixed clusters in sympatry, evoking formation of reproductive barriers, either by allopatric speciation or habitat selection.

Temperature, energy metabolism, and adaptive divergence in two oyster subspecies

Comparisons of related species that have diverse spatial distributions provide an efficient way to investigate adaptive evolution in face of increasing global warming. The oyster subjected to high environmental selections is a model species as sessile marine invertebrate. This study aimed to detect the adaptive divergence of energy metabolism in two oyster subspecies from the genus Crassostrea—C. gigas gigas and C. gigas angulata—which are broadly distributed along the northern and southern coasts of China, respectively. We examined the effects of acute thermal stress on energy metabolism in two oyster subspecies after being common gardened for one generation in identical conditions. Thermal responses were assessed by incorporating physiological, molecular, and genomic approaches. Southern oysters exhibited higher fluctuations in metabolic rate, activities of key energetic enzymes, and levels of thermally induced gene expression than northern oysters. For genes involved in energy metabolism, the former displayed higher basal levels of gene expression and a more pronounced downregulation of thermally induced expression, while the later exhibited lower basal levels and a less pronounced downregulation of gene expression. Contrary expression pattern was observed in oxidative stress gene. Besides, energy metabolic tradeoffs were detected in both subspecies. Furthermore, the genetic divergence of a nonsynonymous SNP (SOD‐132) and five synonymous SNPs in other genes was identified and validated in these two subspecies, which possibly affects downstream functions and explains the aforementioned phenotypic variations. Our study demonstrates that differentiations in energy metabolism underlie the plasticity of adaptive divergence in two oyster subspecies and suggest C. gigas angulata with moderate phenotypic plasticity has higher adaptive potential to cope with exacerbated global warming.

INTERTIDAL MICROHABITAT AND SELECTION AT MPI: INTERLOCUS CONTRASTS IN THE NORTHERN ACORN BARNACLE, SEMIBALANUS BALANOIDES

Barnacles were sampled from various microhabitats in the rocky intertidal at multiple sites in two years. At sites in which there were large differences among microhabitats in temperature profiles, Mpi genotype frequencies were consistently and significantly different. Genotype frequencies for another allozyme locus (Gpi) as well as a DNA marker shown to be neutral (the mtDNA control region) were statistically homogeneous among thermal microhabitats at all sites in both years. The data indicate that temperature and/or desiccation mediated selection is operating at Mpi or a linked locus and that Mpi genotypes experience differential mortality in the various habitat types. If the relative fitness of genotypes is dependent on habitat type, the Mpi polymorphism may be actively maintained by a Levene model of balancing selection (Levene 1953). Because barnacle larvae are produced in abundance each year and spend five to eight weeks dispersing in the water column, there is little opportunity for the accumulation of adaptive divergence over the environmental grain size relevant in intertidal habitats. The Mpi polymorphism may be an important component of a suite of traits involved in the adaptation of barnacles to heterogeneous environments. Due to the relatively high concentration of mannose in a variety of algal groups, the metabolism of mannose may substantially affect individual performance and fitness in this and other species that feed on algae and phytoplankton. Because the Mpi locus is one of the most strongly polymorphic in marine organisms, these findings may be relevant for a diversity of other such species.

GENETICS OF PHYSIOLOGICAL DIFFERENTIATION WITHIN THE MARINE MUSSEL GENUS MYTILUS

Two divergent taxa in the marine mussel genus Mytilus are largely isolated geographically and are routinely exposed to distinctly different thermal environments. We tested the hypothesis that the two taxa are physiologically differentiated with respect to temperature and examined the evolved adaptations allowing one of the taxa to exploit habitats where warm-temperate conditions prevail for prolonged periods. We first analyzed the physiological response to high temperature of mussels collected from a hybrid population containing members of both pure taxa, F, hybrids, and a variety of introgressed genotypes. The experimental temperature of 23°C was chosen to be permissive to the taxon that occurs in warm-temperate regions (Mytilus galloprovincialis) and restrictive to the cold-water taxon (Mytilus edulis). The results show that the two taxa are physiologically differentiated. Under the experimental conditions, M. galloprovincialis exhibited a threefold higher feeding rate and a slightly elevated metabolic rate compared with M. edulis. These differences did not result in a significant difference in net energy balance between the two taxa, probably because of an interaction between physiological response and food availability. However, M. galloprovincialis grew significantly faster in the field, indicating that the physiological differences observed in the laboratory also occur in nature. Numerous introgressed genotypes provided the opportunity to test for cosegregation between the physiological differences and four highly differentiated genetic markers. Two of the markers (esterase and octopine dehydrogenase) cosegregate with variation in feeding rate and shell growth and explained most of the physiological differences observed between taxa. A strong concordance existed between these two loci, suggesting that they may be linked and may mark segregation of the same linkage group. The results suggest that the physiological differentiation between these taxa may be controlled by a few genes (perhaps only one) each with large effect.

Does natural selection explain the fine scale genetic structure at the nuclear exon Glu-5' in blue mussels from Kerguelen?

The Kerguelen archipelago, isolated in the Southern Ocean, shelters a blue mussel Mytilus metapopulation far from any influence of continental populations or any known hybrid zone. The finely carved coast leads to a highly heterogeneous habitat. We investigated the impact of the environment on the genetic structure in those Kerguelen blue mussels by relating allele frequencies to habitat descriptors. A total sample comprising up to 2248 individuals from 35 locations was characterized using two nuclear markers, mac-1 and Glu-5', and a mitochondrial marker (COI). The frequency data from 9 allozyme loci in 9 of these locations were also reanalyzed. Two other nuclear markers (EFbis and EFprem's) were monomorphic. Compared to Northern Hemisphere populations, polymorphism in Kerguelen blue mussels was lower for all markers except for the exon Glu-5'. At Glu-5', genetic differences were observed between samples from distinct regions (F CT = 0.077), as well as within two regions, including between samples separated by <500 m. No significant differentiation was observed in the AMOVA analyses at the two other markers (mac-1 and COI). Like mac-1, all allozyme loci genotyped in a previous publication, displayed lower differentiation (Jost's D) and F ST values than Glu-5'. Power simulations and confidence intervals support that Glu-5' displays significantly higher differentiation than the other loci (except a single allozyme for which confidence intervals overlap). AMOVA analyses revealed significant effects of the giant kelp Macrocystis and wave exposure on this marker. We discuss the influence of hydrological conditions on the genetic differentiation among regions. In marine organisms with high fecundity and high dispersal potential, gene flow tends to erase differentiation, but this study showed significant differentiation at very small distance. This may be explained by the particular hydrology and the carved coastline of the Kerguelen archipelago, together with spatially variable selection at Glu-5'.

Physiological energetics and biogeographic range limits of three congeneric mussel species

Closely related species with different physiological tolerances and distributions make ideal systems for documenting range shifts in response to a changing climate. Mytilus edulis, M. trossulus, and M. galloprovincialis are sibling species of marine mussels with distinct biogeographical ranges that are correlated with sea surface temperatures. We determined the scope for growth of these three species at a range of temperatures to determine if energetics could predict their distributions. Scope for growth (SFG) represents energy available for growth and/or reproduction above that necessary for maintenance requirements. The SFG of M. galloprovincialis, the species known to inhabit the warmest habitats, was shifted towards warmer temperatures compared to the other two species, remaining positive until nearly 30 °C. M. edulis, a cold-temperate species, maintained a positive SFG up to 23 °C. M. trossulus, a boreal species, generally was not able to maintain a positive SFG above 17 °C. The warm end of each species' range correlated strongly with the point at which that species' SFG became negative in summer and fall. Energetics at cold temperatures did not predict the cold end of the species' ranges, as there was no clear SFG advantage to explain the dominance of M. trossulus in cold habitats. As sea surface temperatures continue to warm with climate change, the energetics of these three species provide a basis for developing mechanistic models predicting future distribution and productivity changes in mussel populations.

Genetic structure and the North American postglacial expansion of the barnacle, Semibalanus balanoides

Population genetic characteristics are shaped by the life-history traits of organisms and the geologic history of their habitat. This study provides a neutral framework for understanding the population dynamics and opportunities for selection in Semibalanus balanoides, a species that figures prominently in ecological and evolutionary studies in the Atlantic intertidal. We used mitochondrial DNA (mtDNA) control region (N = 131) and microsatellite markers (∼40 individuals/site/locus) to survey populations of the broadly dispersing acorn barnacle from 8 sites spanning 800 km of North American coast and 1 site in Europe. Patterns of mtDNA sequence evolution were consistent with larger population sizes in Europe and population expansion at the conclusion of the last ice age, approximately 20 000 years ago, in North America. A significant portion of mitochondrial diversity was partitioned between the continents (ϕ(ST) = 0.281), but there was only weak structure observed from mtDNA within North America. Microsatellites showed significant structuring between the continents (F(ST) = 0.021) as well as within North America (F(ST) = 0.013). Isolation by distance in North America was largely driven by a split between populations south of Cape Cod and all others (P < 10(-4)). The glacial events responsible for generating allelic diversity at mtDNA and microsatellites may also be responsible for generating selectable variation at metabolic enzymes in S. balanoides.

Modelling the ecological niche from functional traits

The niche concept is central to ecology but is often depicted descriptively through observing associations between organisms and habitats. Here, we argue for the importance of mechanistically modelling niches based on functional traits of organisms and explore the possibilities for achieving this through the integration of three theoretical frameworks: biophysical ecology (BE), the geometric framework for nutrition (GF) and dynamic energy budget (DEB) models. These three frameworks are fundamentally based on the conservation laws of thermodynamics, describing energy and mass balance at the level of the individual and capturing the prodigious predictive power of the concepts of 'homeostasis' and 'evolutionary fitness'. BE and the GF provide mechanistic multi-dimensional depictions of climatic and nutritional niches, respectively, providing a foundation for linking organismal traits (morphology, physiology, behaviour) with habitat characteristics. In turn, they provide driving inputs and cost functions for mass/energy allocation within the individual as determined by DEB models. We show how integration of the three frameworks permits calculation of activity constraints, vital rates (survival, development, growth, reproduction) and ultimately population growth rates and species distributions. When integrated with contemporary niche theory, functional trait niche models hold great promise for tackling major questions in ecology and evolutionary biology.

Mosaic microecological differential stress causes adaptive microsatellite divergence in wild barley, Hordeum spontaneum, at Neve Yaar, Israel

Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun-rock (11 genotypes), (ii) sun-soil (18 genotypes), (iii) shade-soil (11 genotypes), and (iv) shade-rock (14 genotypes). Fifty-four genotypes were tested for ecological-genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun-rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, G(ST) was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun-rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).

The effects of diet and physiological stress on the evolutionary dynamics of an enzyme polymorphism

In the northern acorn barnacle Semibalanus balanoides, polymorphism at the mannose-6-phosphate isomerase (Mpi) locus appears to be maintained by distinct selection regimes that vary between intertidal microhabitats. The goal of the present experiment was to elucidate the mechanism of selection at the Mpi locus by examining the relationship between genotype and fitness-related life-history traits in laboratory manipulations. When barnacles were cultured on a mannose-supplemented diet and exposed to thermal stress, different Mpi genotypes exhibited differences in the rate of growth that predicted survivorship. In contrast, no such relationship was observed in control or fructose-supplemented dietary treatments either in the presence or in the absence of stress. Similarly, the phenotype and survivorship of genotypes at another allozyme locus and a presumably neutral mitochondrial DNA marker were homogeneous across all treatments and unaffected by experimental manipulations. These results suggest that the differential survivorship of Mpi genotypes in the field and laboratory results from a differential ability to process mannose-6-phosphate through glycolysis. The widespread polymorphism at Mpi observed in marine taxa may reflect the interaction between dietary composition and environmental heterogeneity in intertidal habitats.

Do discrepancies between microsatellite and allozyme variation reveal differential selection between sea and lagoon in the sea bass (Dicentrarchus labrax)?

In the present study the genetic structure of Dicentrarchus labrax (14 samples from the Mediterranean) was analysed at six microsatellite loci, in order to test the hypothesis that some enzymatic loci undergo selection between marine and lagoon habitat. Eight of the 14 samples were analysed at both microsatellite and allozyme markers. The analysis of the genetic variation among the Mediterranean samples showed that (i) &Fcirc;ST values obtained with the six microsatellite loci were much smaller than those obtained with the 28 allozymes and (ii) microsatellite loci seemed to reflect more the geographical proximity than an ecological one. Thirteen enzymatic loci exhibited moderate to high values compared with microsatellites. This was interpreted as evidence that these allozymes are non-neutral. However, only six loci seemed to be implicated in differentiation between marine and lagoon samples, the causes of selection being unknown for the others. A possible scenario of population dynamics of the sea bass between marine and lagoon habitat is suggested.

Selective neutrality and enzyme kinetics

This article appeals to a recent theory of enzyme evolution to show that the properties, neutral or adaptive, which characterize the observed allelic variation in natural populations can be inferred from the functional parameters, substrate specificity, and reaction rate. This study delineates the following relations between activity variables, and the forces--adaptive or neutral--determining allelic variation: (1) Enzymes with broad substrate specificity: The observed polymorphism is adaptive; mutations in this class of enzymes can result in increased fitness of the organism and hence be relevant for positive selection. (2) Enzymes with absolute substrate specificity and diffusion-controlled rates: Observed allelic variation will be absolutely neutral; mutations in this class of enzymes will be either deleterious or have no effect on fitness. (3) Enzymes with absolute or group specificity and nondiffusion-controlled rates: Observed variation will be partially neutral; mutants which are selectively neutral may become advantageous under an appropriate environmental condition or different genetic background. We illustrate each of the relations between kinetic properties and evolutionary states with examples drawn from enzymes whose evolutionary dynamics have been intensively studied.

Molecular systematics in the acanthocephalan genus Echinorhynchus (sensu lato) in northern Europe

New biological species and high levels of inter- and intraspecific genetic divergence were discovered in an allozyme study of some North European members of the acanthocephalan genus Echinorhynchus (sensu lato), parasites of fish and malacostracan crustaceans. (i) A strong differentiation between the marine E. gadi and the fresh- and brackish-water E. salmonis (genetic identity I congruent to 0) supports a generic distinction between these taxa; however, the subdivision would not entirely concur with the concepts of Echinorhynchus (sensu stricto) and Metechinorhynchus suggested earlier. (ii) Samples of E. gadi from the Baltic, Norwegian and North Seas included three distinct, partially sympatric biological species (spp. I-III; I congruent to 0.5). (iii) E. bothniensis, previously only known from the northern Baltic Sea, represents a complex of freshwater taxa with an intermediate host relationship to the 'glacial relict' Mysis spp. and with a distributional and host analogy to the North American E. leidyi. A population in a northern lake in the Barents Sea basin is closely related to E. bothniensis of the Baltic area, but is probably specifically distinct; the divergence between these populations (I congruent to 0.6) is similar to that between their Mysis host species. (iv) Considerable intraspecific differentiation (FST = 0.25), probably reflecting post-glacial population bottlenecks, was found between Baltic and nearby lacustrine E. bothniensis, and between Atlantic and Baltic E. gadi sp. I.

Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs

Population genetic analyses that depend on the assumption of neutrality for allozyme markers are used widely. Restriction fragment length polymorphisms in nuclear DNA of the American oyster evidence a pronounced population subdivision concordant with mitochondrial DNA. This finding contrasts with a geographic uniformity in allozyme frequencies previously thought to reflect high gene flow mediated by the pelagic gametes and larvae. The discordance likely is due to selection on protein electrophoretic characters that balances allozyme frequencies in the face of severe constraints to gene flow. These results raise a cautionary note for studies that rely on assumptions of neutrality for allozyme markers.

The amylase gene-enzyme system of chickens. II. Biochemical characterization of allozymes

The chicken amylase allozymes, AmyF and AmyS, were extracted from pancreatic tissues of AmyF/F and AmyS/S individuals and purified. Activities were measured under various reaction conditions (= treatments) to assess whether the allozymes were functionally different. The amylases had properties typical of alpha-amylases, i.e., both were inhibited by ethylenediaminetetraacetate and alpha-amylase inhibitor from wheat, had pH optima between 7.0 and 8.0, and could utilize a variety of substrates containing alpha 1,4 linkages. The amylases were also found to be inhibited by potassium phosphate buffer and p-chloromercuribenzoate. In terms of substrate specificity, both amylases could utilize all of the substrates tested with activity observed in the following order: amylopectin greater than potato starch greater than dextrin greater than glycogen greater than amylose. Statistical analysis indicated significant functional differences between the two allozymes in terms of specific activities, substrate specificities, and inhibitor sensitivities. AmyF had a significantly lower specific activity than did AmyS. The amylases responded differently to the substrate amylose, with AmyF better able to digest this substrate. AmyS was less sensitive than AmyF to alpha-amylase inhibitor from wheat.

Historical effective size and the level of genetic diversity in Drosophila melanogaster and Drosophila pseudoobscura

We report the results of a sequential gel electrophoretic study of protein variation in Drosophila melanogaster and its comparison with D. pseudoobscura. The number of alleles and mean heterozygosity were lower in D. melanogaster than in D. pseudoobscura. On the other hand, geographical populations of Drosophila melanogaster have been shown to be much more differentiated than those of D. pseudoobscura. The results suggest that in D. melanogaster low-frequency alleles have been lost during the colonization process and that major alleles have become differentiated among populations. Population bottlenecks, due to various causes, appear to have played a significant role in the shaping of genetic variation in natural populations of many species. It is proposed that a comparison of genetic variation at homologous gene loci between related species can bring out effects of historical bottlenecks and provide an alternative approach for analyzing causes of genetic variation in natural populations.