Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks

Comparing rates of molecular and morphological evolution identifies multiple speciation trajectories in a diverse radiation of skinks

There is increasing recognition that the process of species divergence is not uniform across the tree of life, and that newly diverged taxa may differ in their levels of phenotypic and genetic divergence. We investigate the relationship between phenotypic and genetic differentiation across the speciation continuum using sister pairs from a large ecologically diverse radiation of Australian skinks, the Tribe Eugongylini, a high-quality alignment of genomic sequence data, and morphometric data for 90 lineages across the radiation. Based on the framework proposed by Struck et al. (2018) for comparative study of species divergence, we used latent class regression to test for multiple speciation "trajectories." We found evidence for multiple relationships between genetic divergence and morphological disparity for recently diverged sister taxa, which we summarize into 2 broad patterns. One of these patterns is characterized by relatively rapid morphological differentiation for pairs with greater disparity in environmental variables, consistent with expectations of ecological speciation. The second pattern shows accumulation of both morphological and genetic differences in proportion to each other, consistent with gradual speciation. Our study shows how heterogeneity in speciation processes can be captured in a comparative framework.

Distinct latitudinal patterns of molecular rates across vertebrates

The latitudinal diversity gradient (LDG) is the most notable global biodiversity pattern, but its underlying mechanisms remain unresolved. The evolutionary speed hypothesis (ESH) posits that molecular rates play a crucial role in shaping the LDG, suggesting that higher temperatures accelerate molecular rates, thereby facilitating rapid speciation and accumulation of biodiversity in the tropics. However, whether ESH can explain the LDG across diverse taxonomic groups remains debated, and systematic examinations of its two key predictions using consistent datasets and methodologies across vertebrates are lacking. Here, we tested ESH using molecular rates from mitochondrial (5,424 species) and nuclear (1,512 species) genomes across major vertebrate groups, including fishes, amphibians, reptiles, mammals, and birds. Our findings revealed distinct latitudinal patterns in the absolute synonymous substitution rate (dS), which were influenced by thermoregulatory strategies. Specifically, the dS increases with ambient temperature and decreases with latitude in ectotherms but shows no correlation in most endotherms. These distinct patterns are likely attributed to different key predictors of dS between thermogroups, with temperature playing a major role only in ectotherms. For mitochondrial genes, absolute nonsynonymous substitution rates (dN) increase with temperature, likely driven by mutation rates in ectotherms and purifying selection in endotherms. However, neither mitochondrial dS nor dN correlates with diversification rates across vertebrates, contradicting the second prediction of ESH. For nuclear rates, the ESH was supported in reptiles and amphibians but not in mammals, birds, or fishes. In conclusion, our results provide limited support for ESH in vertebrates, underscoring the intricate processes that shape the LDG.

Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression-the exchange of genetic material through hybridization and backcrossing-are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report "ancient introgression"- referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violated as evolutionary divergence increases. To test the limitations of introgression detection methods when being applied to old systems, we simulated thousands of genomic datasets under a wide range of settings, with varying degrees of among-species rate variation and introgression. Using these simulated datasets, we showed that some commonly applied statistical methods, including the D-statistic and certain tests based on sets of local phylogenetic trees, can produce false-positive signals of introgression between divergent taxa that have different rates of evolution. These misleading signals are caused by the presence of homoplasies occurring at different rates in different lineages. To distinguish between the patterns caused by rate variation and genuine introgression, we developed a new test that is based on the expected clustering of introgressed sites along the genome and implemented this test in the program Dsuite.

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.

Sequence Capture From Historical Museum Specimens: Maximizing Value for Population and Phylogenomic Studies

The application of high-throughput, short-read sequencing to degraded DNA has greatly increased the feasibility of generating genomic data from historical museum specimens. While many published studies report successful sequencing results from historical specimens; in reality, success and quality of sequence data can be highly variable. To examine predictors of sequencing quality, and methodological approaches to improving data accuracy, we generated and analyzed genomic sequence data from 115 historically collected museum specimens up to 180 years old. Data span both population genomic and phylogenomic scales, including historically collected specimens from 34 specimens of four species of Australian rock-wallabies (genus Petrogale) and 92 samples from 79 specimens of Australo-Papuan murine rodents (subfamily Murinae). For historical rodent specimens, where the focus was sampling for phylogenomics, we found that regardless of specimen age, DNA sequence libraries prepared from toe pad or bone subsamples performed significantly better than those taken from the skin (in terms of proportion of reads on target, number of loci captured, and data accuracy). In total, 93% of DNA libraries from toe pad or bone subsamples resulted in reliable data for phylogenetic inference, compared to 63% of skin subsamples. For skin subsamples, proportion of reads on target weakly correlated with collection year. Then using population genomic data from rock-wallaby skins as a test case, we found substantial improvement in final data quality by mapping to a high-quality “closest sister” de novo assembly from fresh tissues, compared to mapping to a sample-specific historical de novo assembly. Choice of mapping approach also affected final estimates of the number of segregating sites and Watterson's θ, both important parameters for population genomic inference. The incorporation of accurate and reliable sequence data from historical specimens has important outcomes for evolutionary studies at both population and phylogenomic scales. By assessing the outcomes of different approaches to specimen subsampling, library preparation and bioinformatic processing, our results provide a framework for increasing sequencing success for irreplaceable historical specimens.

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlaying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental kinetic energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modelled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modelling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

Admixture of evolutionary rates across a butterfly hybrid zone

Hybridization is a major evolutionary force that can erode genetic differentiation between species, whereas reproductive isolation maintains such differentiation. In studying a hybrid zone between the swallowtail butterflies Papilio syfanius and Papilio maackii (Lepidoptera: Papilionidae), we made the unexpected discovery that genomic substitution rates are unequal between the parental species. This phenomenon creates a novel process in hybridization, where genomic regions most affected by gene flow evolve at similar rates between species, while genomic regions with strong reproductive isolation evolve at species-specific rates. Thus, hybridization mixes evolutionary rates in a way similar to its effect on genetic ancestry. Using coalescent theory, we show that the rate-mixing process provides distinct information about levels of gene flow across different parts of genomes, and the degree of rate-mixing can be predicted quantitatively from relative sequence divergence ([Formula: see text]) between the hybridizing species at equilibrium. Overall, we demonstrate that reproductive isolation maintains not only genomic differentiation, but also the rate at which differentiation accumulates. Thus, asymmetric rates of evolution provide an additional signature of loci involved in reproductive isolation.

Digest: Study associates squamate rates, traits, and climates. Evolution 2022;76:1094-1095. [PMID: 35266557 DOI: 10.1111/evo.14465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The large variation in evolutionary rates across species remains unexplained. A new many-species multivariate study of evolutionary rates in skinks found that environmental temperature explains 45% of rate variation. These results, together with previous studies highlighting different determinants in other organisms, urge a pluralistic understanding of the determinants of evolutionary rate, in contrast to reductive models.