Alternate histories in macroevolution Pennell, Matt
Proceedings of the National Academy of Sciences - PNAS,
02/2023, Letnik:
120, Številka:
9
Journal Article
The processes that allow some lineages to diversify rapidly at a global scale remain poorly understood. Although earlier studies emphasized the importance of dispersal, global expansions expose ...populations to novel environments and may also require adaptation and diversification across new niches. In this study, we investigated the contributions of these processes to the global radiation of crows and ravens (genus Corvus). Combining a new phylogeny with comprehensive phenotypic and climatic data, we show that Corvus experienced a massive expansion of the climatic niche that was coupled with a substantial increase in the rates of species and phenotypic diversification. The initiation of these processes coincided with the evolution of traits that promoted dispersal and niche expansion. Our findings suggest that rapid global radiations may be better understood as processes in which high dispersal abilities synergise with traits that, like cognition, facilitate persistence in new environments.
A great deal of macroevolutionary research on extinction has focused on large-scale processes, particularly mass episodes. In contrast, many recent conservation studies focus on Anthropocene dynamics ...at the population level. We discuss three ways in which a synthesis between these perspectives might illuminate hidden assumptions of value and reveal promising agendas for conservation biology. First, some lineages may have been on extinction trajectories before global change commenced. While it may be difficult to quantify this directly, the potential for pre-existing net-negative diversification rates in lineages or terminal declines in species may have a strong impact on our ethical valuations of biodiversity and consequent management decisions. Second, it is worthwhile to quantify the shape and scale of the Sixth Extinction relative to previous mass extinctions and we outline and model several relevant parameters, including the initial magnitude and subsequent change in diversification rates contributing to recovery. Placing recent estimates of Anthropocene extinction rates into a historical macroevolutionary context may suggest more precise frameworks for interpreting and extrapolating present-day patterns. Third, focusing on recovery dynamics from previous mass extinctions may be valuable, as quantitative models of present-day extinction portend various scenarios for future re-diversification. In this context, “conservation” is less about preserving past or existing states, but rather creating and promoting novel starting points for the near-term function and future evolution of biodiversity, differing from pre-human trajectories. Integrating historical and present-day perspectives on extinction promises a synergistic research program holding potential insights for macroevolution, conservation, and environmental ethics.
•Macroevolutionary data, models, and theory can illuminate Anthropocene extinction.•Some species were going extinct prior to humans; others are declining prematurely.•Mass extinctions have different shapes and scales, which should be quantified.•Present-day conservation can be modeled for effects on future biodiversity recovery.•This synthesis offers novel research agendas, illuminating potential hidden values.
Mutualisms are associations in which interacting species provide services or resources to each other. It has been suggested that being party to a mutualism can spur the diversification of the ...interacting species due to several potential hypothesized mechanisms. There is empirical evidence to both support and refute this prediction. However, this evidence comes from a variety of different methodologies, some of which have been found to be unreliable when the phylogenetic model is misspecified, and different data types and it is therefore difficult to weigh together. Here, we synthesize phylogenetic comparative datasets and analyze the data in a consistent manner using both sister-clade comparisons and hidden-trait state-dependent speciation and extinction models. The results are mixed-for the majority of the datasets we find no evidence for an effect on diversification rates in either direction, with several showing significant positive associations and a few showing significant negative associations. In contrast to the generally mixed findings between datasets, we find that qualitative results to be consistent when analyzing taxonomically overlapping datasets using different methods, suggesting that the detected variation in diversification is due to the nature of the mutualism and not due to differences in methodology.
The Major Features of Macroevolution Henao-Diaz, L Francisco; Pennell, Matt
Systematic biology,
11/2023, Letnik:
72, Številka:
5
Journal Article
Recenzirano
Abstract
Evolutionary dynamics operating across deep time leave footprints in the shapes of phylogenetic trees. For the last several decades, researchers have used increasingly large and robust ...phylogenies to study the evolutionary history of individual clades and to investigate the causes of the glaring disparities in diversity among groups. Whereas typically not the focal point of individual clade-level studies, many researchers have remarked on recurrent patterns that have been observed across many different groups and at many different time scales. Whereas previous studies have documented various such regularities in topology and branch length distributions, they have typically focused on a single pattern and used a disparate collection (oftentimes, of quite variable reliability) of trees to assess it. Here we take advantage of modern megaphylogenies and unify previous disparate observations about the shapes embedded in the Tree of Life to create a catalog of the “major features of macroevolution.” By characterizing such a large swath of subtrees in a consistent way, we hope to provide a set of phenomena that process-based macroevolutionary models of diversification ought to seek to explain.
Recent research has revealed substantial interindividual variation in immunoglobulin (IG) loci as well as associations between germline IG genotypes and the humoral response.It is unknown how ...population- and species-level germline variation at IG loci is maintained or which are the mechanisms by which such variation leads to functional differences in the evolved B cell repertoire.Characterizing these mechanisms may be important for the design of vaccines and other therapeutics.Resolving this mystery includes studying the interplay of evolutionary processes at two different levels of biological organization: within individuals and within populations.
Substantial human inter-individual genetic variation at germline immunoglobulin (antibody) loci has been recently reported, in addition to associations between such variation and adaptive humoral responses. Certain hypotheses suggest that evolution may play a role in shaping germline IG loci and antibody repertoires, for which emerging evidence supports (or not) these hypotheses. There is a need to establish better evolutionary models that might better inform and could contribute to the development of candidate vaccines/therapeutics.
The recombination between immunoglobulin (IG) gene segments determines an individual’s naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity – from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
The recombination between immunoglobulin (IG) gene segments determines an individual’s naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that ...mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity – from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
Abstract
Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene ...expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here, we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level; this observation held true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and the translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic data.
Abstract
Phylogenetic comparative methods are increasingly used to test hypotheses about the evolutionary processes that drive divergence in gene expression among species. However, it is unknown ...whether the distributional assumptions of phylogenetic models designed for quantitative phenotypic traits are realistic for expression data and importantly, the reliability of conclusions of phylogenetic comparative studies of gene expression may depend on whether the data is well described by the chosen model. To evaluate this, we first fit several phylogenetic models of trait evolution to 8 previously published comparative expression datasets, comprising a total of 54,774 genes with 145,927 unique gene–tissue combinations. Using a previously developed approach, we then assessed how well the best model of the set described the data in an absolute (not just relative) sense. First, we find that Ornstein–Uhlenbeck models, in which expression values are constrained around an optimum, were the preferred models for 66% of gene–tissue combinations. Second, we find that for 61% of gene–tissue combinations, the best-fit model of the set was found to perform well; the rest were found to be performing poorly by at least one of the test statistics we examined. Third, we find that when simple models do not perform well, this appears to be typically a consequence of failing to fully account for heterogeneity in the rate of the evolution. We advocate that assessment of model performance should become a routine component of phylogenetic comparative expression studies; doing so can improve the reliability of inferences and inspire the development of novel models.
