Sexual selection, body mass and molecular evolution interact to predict diversification in birds

Combining Molecular, Macroevolutionary, and Macroecological Perspectives on the Generation of Diversity

Charles Darwin presented a unified process of diversification driven by the gradual accumulation of heritable variation. The growth in DNA databases and the increase in genomic sequencing, combined with advances in molecular phylogenetic analyses, gives us an opportunity to realize Darwin's vision, connecting the generation of variation to the diversification of lineages. The rate of molecular evolution is correlated with the rate of diversification across animals and plants, but the relationship between genome change and speciation is complex: Mutation rates evolve in response to life history and niche; substitution rates are influenced by mutation, selection, and population size; rates of acquisition of reproductive isolation vary between populations; and traits, niches, and distribution can influence diversification rates. The connection between mutation rate and diversification rate is one part of the complex and varied story of speciation, which has theoretical importance for understanding the generation of biodiversity and also practical impacts on the use of DNA to understand the dynamics of speciation over macroevolutionary timescales.

Sexual size dimorphism in mammals is associated with changes in the size of gene families related to brain development

In mammals, sexual size dimorphism often reflects the intensity of sexual selection, yet its connection to genomic evolution remains unexplored. Gene family size evolution can reflect shifts in the relative importance of different molecular functions. Here, we investigate the associate between brain development gene repertoire to sexual size dimorphism using 124 mammalian species. We reveal significant changes in gene family size associations with sexual size dimorphism. High levels of dimorphism correlate with an expansion of gene families enriched in olfactory sensory perception and a contraction of gene families associated with brain development functions, many of which exhibited particularly high expression in the human adult brain. These findings suggest a relationship between intense sexual selection and alterations in gene family size. These insights illustrate the complex interplay between sexual dimorphism, gene family size evolution, and their roles in mammalian brain development and function, offering a valuable understanding of mammalian genome evolution.

Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

Background

An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used methods rely on idealised models of rate variation, such as the uncorrelated and autocorrelated clocks, and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as current evidence suggests, they may have a significant influence on molecular dates.

Results

We simulate phylogenies and molecular sequences under three different realistic rate variation models—one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test three commonly used “relaxed clock” molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior using BEAST 2, to up to 91% when sequences evolved under the punctuated model are reconstructed under an autocorrelated prior using PAML.

Conclusions

We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02015-8.

Comparative Genomics and Evolution of Avian Specialized Traits

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.

Evolution by Sexual Selection

Charles Darwin published his second book “Sexual selection and the descent of man” in 1871 150 years ago, to try to explain, amongst other things, the evolution of the peacock’s train, something that he famously thought was problematic for his theory of evolution by natural selection. He proposed that the peacock’s train had evolved because females preferred to mate with males with more elaborate trains. This idea was very controversial at the time and it wasn’t until 1991 that a manuscript testing Darwin’s hypothesis was published. The idea that a character could arise as a result of a female preference is still controversial. Some argue that there is no need to distinguish sexual from natural selection and that natural selection can adequately explain the evolution of extravagant characteristics that are characteristic of sexually selected species. Here, I outline the reasons why I think that this is not the case and that Darwin was right to distinguish sexual selection as a distinct process. I present a simple verbal and mathematical model to expound the view that sexual selection is profoundly different from natural selection because, uniquely, it can simultaneously promote and maintain the genetic variation which fuels evolutionary change. Viewed in this way, sexual selection can help resolve other evolutionary conundrums, such as the evolution of sexual reproduction, that are characterised by having impossibly large costs and no obvious immediate benefits and which have baffled evolutionary biologists for a very long time. If sexual selection does indeed facilitate rapid adaptation to a changing environment as I have outlined, then it is very important that we understand the fundamentals of adaptive mate choice and guard against any disruption to this natural process.

Deep time diversity and the early radiations of birds

Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous-Paleogene (K-Pg) extinction.

Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds

Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict because many of the hypothesized effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.

Is Sexual Conflict a Driver of Speciation? A Case Study With a Tribe of Brush-footed Butterflies

Understanding the evolutionary mechanisms governing the uneven distribution of species richness across the tree of life is a great challenge in biology. Scientists have long argued that sexual conflict is a key driver of speciation. This hypothesis, however, has been highly debated in light of empirical evidence. Recent advances in the study of macroevolution make it possible to test this hypothesis with more data and increased accuracy. In the present study, we use phylogenomics combined with four different diversification rate analytical approaches to test whether sexual conflict is a driver of speciation in brush-footed butterflies of the tribe Acraeini. The presence of a sphragis, an external mating plug found in most species among Acraeini, was used as a proxy for sexual conflict. Diversification analyses statistically rejected the hypothesis that sexual conflict is associated with shifts in diversification rates in Acraeini. This result contrasts with earlier studies and suggests that the underlying mechanisms driving diversification are more complex than previously considered. In the case of butterflies, natural history traits acting in concert with abiotic factors possibly play a stronger role in triggering speciation than does sexual conflict. [Acraeini butterflies; arms race; exon capture phylogenomics; Lepidoptera macroevolution; sexual selection; sphragis.].

Sexual selection, body mass and molecular evolution interact to predict diversification in birds

Sexual selection is a powerful agent of evolution, driving microevolutionary changes in the genome and macroevolutionary rates of lineage diversification. The mechanisms by which sexual selection might influence macroevolution remain poorly understood. For example, sexual selection might drive positive selection for key adaptations that facilitate diversification. Furthermore, sexual selection might be a general driver of molecular evolutionary rate. We lay out some of the potential mechanisms that create a link between sexual selection and diversification, based on causal effects on other life-history traits such as body mass and the rate of molecular evolution. Birds are ideally suited for testing the importance of these relationships because of their diverse reproductive systems and the multiple evolutionary radiations that have produced their astounding modern diversity. We show that sexual selection (measured as the degree of polygyny) interacts with the rate of molecular evolution and with body mass to predict species richness at the genus level. A high degree of polygyny and rapid molecular evolution are positively associated with the net rate of diversification, with the two factors being especially important for explaining diversification in large-bodied taxa. Our findings further suggest that mutation rates underpin some of the macroevolutionary effects of sexual selection. We synthesize the existing theory on sexual selection as a force for diversity and propose avenues for exploring this association using genome data.