Evolution最新文献

Ecological opportunity (EO) is an important catalyst for evolution. Whereas theory often centers around a lineage encountering a source of EO in isolation, in practice they experience numerous sources of opportunity, either concurrently or sequentially. Such multiplicity can obscure the macroevolutionary signature of EO. Here, we test the effects of elevation (a proxy of the "mountain effect") and an array of functional innovations on the evolutionary history of plethodontid salamanders, a diverse and charismatic radiation of lungless amphibians. Functional innovations unlock access to novel microhabitats, ultimately enabling sub-lineages to occupy a diverse range of ecological niches, particularly in lowland areas where those niches are more abundant. Consistent with expanded ecological opportunity, such transitions to lower elevation result in rapid phenotypic evolution. At high elevation, by contrast, rates of phenotypic evolution and phenotypic disparity decline, reflecting a loss of phenotypically extreme ecological specialists. Transitions in elevation and the origin of innovations appear largely coincident among lungless salamanders, suggesting myriad sources of EO. The magnitude of the "mountain effect" on evolutionary rates (∼10-fold) is on par or greatly exceeds that of islands, lakes, and coral reefs on other iconic vertebrate radiations. Therefore, we find that elevation acts as a major ecological moderator and, in concert with functional innovations, shapes the ecological and phenotypic diversity of lungless salamanders.

Contemporary evolution allows us to investigate how natural selection drives phenotypic and genotypic evolution in nature. Recent advances in molecular genetics have identified causative genes underlying adaptive traits, enabling estimation of selection coefficients at these loci. However, estimating selection is challenging when populations receive migrants from genetically and phenotypically distinct populations. With genome-wide data now allowing estimation of migration rates and effective population sizes, these demographic parameters can be integrated into models for measuring selection. In Lake Washington, USA, the frequency of the completely plated morph of the threespine stickleback (Gasterosteus aculeatus) increased from 1957 to 2005, plausibly due to increased trout predation pressure caused by enhanced water clarity. Here, we estimated the selection coefficient at a major locus responsible for the plate morph using historical data, taking migration and genetic drift into consideration. Model-based predictions of present allele frequencies were tested with samples collected in 2022. Consistent with directional selection, the completely plated morphs and the underlying allele have increased since 2005, but to higher frequencies than predicted, suggesting a recent increase in selection. Thus, integrating molecular genetics, population genomics, and simulations enables the estimation of selection strength while considering migration and drift, to reveal directional selection in nature.

In comparative evolutionary genomics, faster or slower evolution of a particular gene, site, or branch in a phylogenetic tree, when compared to the appropriate average, has been interpreted as evidence of conservation, functional importance, or adaptation. With large consortia generating hundreds of genomes, there is an opportunity to interrogate these datasets for evidence of accelerated or reduced evolutionary rates in protein-coding genes associated with the presence or absence of a given phenotype (e.g., marine vs terrestrial, nocturnal vs diurnal). Such rate shifts can reflect the molecular basis of convergent phenotypic adaptation when they occur repeatedly across independent lineages. Here we introduce an explicit phylogenetic rate test, MoleRate, for acceleration or reduction of nucleotide or protein evolutionary rates in focal lineages vs the rest of the phylogeny. Compared to existing methods, MoleRate offers execution, explicit likelihood-based hypothesis testing, and the ability to detect and filter out potentially aberrant signal from single lineages. We demonstrate MoleRate's performance on simulated and empirical data, and apply it to several mammalian phenotypes. We also highlight its visualization capabilities, which enable exploration and communication of results. These analyses show that MoleRate detects biologically significant enrichments in selective pressure on specific functions related to the given phenotype, and that enrichments in selective pressure related to the given phenotype, absent when random lineages are tested.

Allopatric speciation is the predominant mode of speciation in riverine fishes. However, the relative importance of genetic drift versus natural selection in the allopatric speciation of these fishes remain uncertain. Here, we present a case study that demonstrates the role of ecology in the diversification of a group of imperiled freshwater fishes from the central United States. We integrate a phylogenomic dataset with analyses of streamwise distance, environmental variables, meristic and morphological traits, and diet to investigate the ecological context and outcomes of allopatric speciation within a species complex comprising the Slenderhead Darter Percina phoxocephala (Nelson), Ouachita Darter Percina brucethompsoni (Robison, Cashner, and Near), and Longnose Darter Percina nasuta (Bailey). We find that two of the species traditionally delimited based on disparity in snout length, P. phoxocephala and P. nasuta, are polyphyletic, revealing three instances of the parallel evolution of snout length disparity. We propose a revised taxonomy including the delimitation of six new species based on disparity in phenotypic traits and phylogenomic analyses. We find that morphological differences are not correlated with genetic divergence but are congruent with with variations in diet and environmental niches, suggesting a role for ecological factors in allopatric speciation of riverine fishes.

Floral morphological variation has long shaped our understanding of evolution, with most studies focusing on how structural changes facilitate pollinator interactions. Less appreciated, however, is how floral morphology changes through time to sustain pollination under specific environmental conditions. We explored this topic by testing whether buzz-pollinated species occurring in humid areas and/or blooming during wet seasons have evolved mechanisms for water drainage, using acuminate petals in tribe Miconieae (Melastomataceae) as a study case. We analyzed petal shape and flower size in the context of phenologies and climatic niches for 502 species using a set of trait evolution models. We found that species with drip-tip (i.e., acuminate) petals are more likely to occur in more humid and less seasonal habitats, and that flower size and phenology significantly impacted the evolution of petal shape in the clade, with small flowered species that bloom during wet seasons being more likely to evolve drip-tip petals. We discuss how petals in which drip-tips evolved may have adapted from their primary function of pollinator attraction to additionally drain water. Our study offers a new perspective of how flower morphological evolution responds not only to pollinator interactions but also to climatic conditions where species live.

The storage effect is a plausible natural mechanism that generates balanced genetic polymorphism in temporally varying environments. Balanced polymorphism may facilitate evolutionary rescue, promoting the persistence of populations otherwise destined for extinction. However, it is unknown whether the storage effect can be established in small populations whose size is allowed to vary, and if so, whether it will lead to evolutionary rescue. In this study, we investigate whether the spatial storage effect emerges and facilitates evolutionary rescue across small populations of variable sizes that inhabit heterogeneous, temporally varying environments and exchange migrants. We use an eco-evolutionary model to examine the phenomenon under a wide set of conditions, including the magnitudes and periods of temporal variation, habitat harshness, migration rates, the degrees of spatial heterogeneity, and increasing fitness oscillations over time, all within the framework of the logistic population growth model. We find that the storage effect emerges and that it increases the persistence of populations in harsh, temporally varying habitats beyond levels expected in the absence of the mechanism. This mechanism demonstrates how rapid evolution broadens the known conditions for population persistence in the face of rapid and continuous environmental changes.

Ecological transitions can trigger rapid phenotypic evolution and novelty, yet the tempo and mode of such changes remain poorly understood in clades that diversify across broad geographic scales, such as continents and oceans. We analysed skull shape variation across 91 terrestrial, amphibious, and fully marine species of elapid snakes (Elapidae). We observed a significant increase in rates of skull shape evolution during the land-to-sea transition of viviparous sea snakes. This coincides with a shift into a new region of morphospace, defined by a higher frontoparietal region, more depressed snout, and a wider suspensorium. The acceleration of skull shape evolution in sea snakes was closely followed by a major dichotomy in the evolutionary trajectories of the Hydrophis and Aipysurus clades, which exhibit narrow and wide skulls, respectively. We suggest that narrow skulls in the Hydrophis group provided ecological opportunities that subsequently facilitated the rapid evolution of the axial skeleton (previously documented by Sherratt et al., 2022), with both morphological shifts preceding the increase in speciation rates in core Hydrophis. This study highlights the asynchronous nature of phenotypic and lineage diversification rates during the radiation of geographically widespread clades shaped by major ecological transitions.

Organisms can improve their fitness by modifying their environments-a process known as (positive) niche construction. Since niche construction is inherently costly, requiring time and energy to perform, niche constructors are vulnerable to displacement by non-niche-constructing invaders that exploit the constructed habitats. One way constructors could avoid such displacement is by adapting to withstand the invaders and thus undergoing evolutionary rescue. Here, we first analytically approximate the probability that a niche-constructing population-one building reproductive habitats-undergoes evolutionary rescue from habitat exploitation by an invading species. Then, we evaluate the approximation under two different fitness costs of construction: a fecundity cost and a mortality cost. We find that fecundity costs are not only less harmful than mortality costs but can even promote rescue compared with no costs by reducing the rate at which constructors attempt reproduction and thus construction. The resulting lower habitat density slows invasion, which then buys constructors more time to mutate. This invasion-slowing benefit can be stronger if the fecundity cost, instead of deriving from construction, stems from niche destruction, where organisms destroy their own habitats. Our results suggest that the same fitness costs rendering constructors vulnerable to habitat exploitation can help rescue constructors from such exploitation.

Fisher's fundamental theorem of natural selection continues to be widely cited in the literature but there is still misunderstanding about its interpretation and significance. Even though it is now recognized that the additive genetic variance in its statement captures only a partial rate of change in mean fitness, the original terms and arguments used to present it remain unclear, not to mention its real meaning. Here, we revisit the interpretation of this partial rate of change. Applying the properties of the additive genetic values and residual addends of a quantitative trait to the relative growth rate of genotype frequency in a diploid population, and comparing two reproductive systems, clonal reproduction and sexual reproduction with either random union of gametes or random mating with additive fecundities of mating types, we argue that this additive genetic rate of change corresponds to the change that is invariant under reshuffling of genes. We show that this is actually the case for the partial rate of change in the mean of any measurement given by the additive genetic covariance with fitness. We focus on the one-locus multiallele setting in continuous time without age effects for simplicity, but the conclusion can be extended to multilocus settings with age effects in continuous time as well as discrete time.

Rates of hybridization are increasing globally, but we lack an understanding of both the history and evolutionary outcomes of hybridization for most species. This makes it difficult to understand whether, and to what extent, humans are influencing hybridization. Integrating field studies with whole genome data is a critical next step for understanding hybridization and the extent of human influences on evolution. Here, we combine 3 years of population monitoring with 569 whole genomes to characterize the reproductive ecology of, and hybridization between, two common songbirds, black-capped (Poecile atricapillus) and mountain (P. gambeli) chickadees, for which hybridization is correlated with human habitat disturbance across North America. Working within a geographic region that we previously identified as a hotspot of contemporary chickadee hybridization we find that, despite geographic and temporal breeding overlap, few early generation hybrids are produced indicating that reproductive barriers typically prevent contemporary hybridization. Yet, every chickadee we sampled in sympatry possessed heterospecific ancestry, indicating that both contemporary and historical hybridization have occurred during the evolutionary history of chickadees in Colorado. Why contemporary hybridization continues to occur despite evidence for character displacement of chickadee song remains less clear, but urban forests may play a role.