The history of biodiversity is characterized by a continual replacement of branches in the tree of life. The rise and demise of these branches (clades) are ultimately determined by changes in ...speciation and extinction rates, often interpreted as a response to varying abiotic and biotic factors. However, understanding the relative importance of these factors remains a major challenge in evolutionary biology. Here we analyze the rich North American fossil record of the dog family Canidae and of other carnivores to tease apart the roles of competition, body size evolution, and climate change on the sequential replacement of three canid subfamilies (two of which have gone extinct). We develop a novel Bayesian analytic framework to show that competition from multiple carnivore clades successively drove the demise and replacement of the two extinct canid subfamilies by increasing their extinction rates and suppressing their speciation. Competitive effects have likely come from ecologically similar species from both canid and felid clades. These results imply that competition among entire clades, generally considered a rare process, can play a more substantial role than climate change and body size evolution in determining the sequential rise and decline of clades.
Extinction is a ubiquitous feature of biodiversity history, and although many lineages increase in diversity through time, most of them eventually decline and get replaced. Dinosaurs and mammals represent an extreme and iconic example of such replacement. Here we investigate the causes of the sequential wax and wane of three subfamilies in the dog family Canidae. Contrary to current expectation, we find that competition from phylogenetically distant, but ecologically similar, clades played a more substantial role in canid diversification than climate change and body size evolution. Our results provide novel quantitative evidence indicating that competition from multiple clades can actively drive the displacement and extinction of entire lineages.
The effects of specific functional groups of pollinators in the diversification of angiosperms are still to be elucidated. We investigated whether the pollination shifts or the specific association ...with hummingbirds affected the diversification of a highly diverse angiosperm lineage in the Neotropics. We reconstructed a phylogeny of 583 species from the Gesneriaceae family and detected diversification shifts through time, inferred the timing and amount of transitions among pollinator functional groups, and tested the association between hummingbird pollination and speciation and extinction rates. We identified a high frequency of pollinator transitions, including reversals to insect pollination. Diversification rates of the group increased through time since 25 Ma, coinciding with the evolution of hummingbird-adapted flowers and the arrival of hummingbirds in South America. We showed that plants pollinated by hummingbirds have a twofold higher speciation rate compared with plants pollinated by insects, and that transitions among functional groups of pollinators had little impact on the diversification process. We demonstrated that floral specialization on hummingbirds for pollination has triggered rapid diversification in the Gesneriaceae family since the Early Miocene, and that it represents one of the oldest identified plant–hummingbird associations. Biotic drivers of plant diversification in the Neotropics could be more related to this specific type of pollinator (hummingbirds) than to shifts among different functional groups of pollinators.
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of ...taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth—death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth—death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its ...internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.
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•SNARE-like factors are present in metagenomes of Heimdallarchaeota•Prototypic SNARE proteins of archaea can interact with eukaryotic SNARE proteins•Some γ-proteobacteria of the order Legionellales possess bona fide SNARE proteins
Neveu et al. discover SNARE-like factors in metagenomes of Heimdall archaeons, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that these prototypic SNARE proteins can interact with eukaryotic SNARE proteins. This suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor.
Clownfishes evolution below and above the species level Rolland, Jonathan; Silvestro, Daniele; Litsios, Glenn ...
Proceedings of the Royal Society. B, Biological sciences,
02/2018, Letnik:
285, Številka:
1873
Journal Article
Recenzirano
Odprti dostop
The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact ...role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here,we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated belowthe species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.
Abstract
Scientific understanding of biodiversity dynamics, resulting from past climate oscillations and projections of future changes in biodiversity, has advanced over the past decade. Little is ...known about how these responses, past or future, are spatially connected. Analyzing the spatial variability in biodiversity provides insight into how climate change affects the accumulation of diversity across space. Here, we evaluate the spatial variation of phylogenetic diversity of European seed plants among neighboring sites and assess the effects of past rapid climate changes during the Quaternary on these patterns. Our work shows a marked homogenization in phylogenetic diversity across Central and Northern Europe linked to high climate change velocity and large distances to refugia. Our results suggest that the future projected loss in evolutionary heritage may be even more dramatic, as homogenization in response to rapid climate change has occurred among sites across large landscapes, leaving a legacy that has lasted for millennia.
Phylogenetic turnover quantifies the evolutionary distance among species assemblages and is central to understanding the main drivers shaping biodiversity. It is affected both by geographic and ...environmental distance between sites. Therefore, analyzing phylogenetic turnover in environmental space requires removing the effect of geographic distance. Here, we apply a novel approach by deciphering phylogenetic turnover of European tetrapods in environmental space after removing geographic land distance effects. We demonstrate that phylogenetic turnover is strongly structured in environmental space, particularly in ectothermic tetrapods, and is well explained by macroecological characteristics such as niche size, species richness and relative phylogenetic diversity. In ectotherms, rather recent evolutionary processes were important in structuring phylogenetic turnover along environmental gradients. In contrast, early evolutionary processes had already shaped the current structure of phylogenetic turnover in endotherms. Our approach enables the disentangling of the idiosyncrasies of evolutionary processes such as the degree of niche conservatism and diversification rates in structuring biodiversity.
Summary
Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction ...rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes.
Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees.
We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth–death model to correlate the variation of speciation/extinction rates with changes of a continuous trait.
Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open‐source command‐line Python program available at http://sourceforge.net/projects/pyrate/.
Pi acquisition of crops via arbuscular mycorrhizal (AM) symbiosis is becoming increasingly important due to limited high-grade rock Pi reserves and a demand for environmentally sustainable ...agriculture. Here, we show that 70% of the overall Pi acquired by rice (Oryza sativa) is delivered via the symbiotic route. To better understand this pathway, we combined genetic, molecular, and physiological approaches to determine the specific functions of two symbiosis-specific members of the PHOSPHATE TRANSPORTER1 (PHT1) gene family from rice, ORYsa;PHT1;11 (PT11) and ORYsa;PHT1;13 (PT13). The PT11 lineage of proteins from mono- and dicotyledons is most closely related to homologs from the ancient moss, indicating an early evolutionary origin. By contrast, PT13 arose in the Poaceae, suggesting that grasses acquired a particular strategy for the acquisition of symbiotic Pi. Surprisingly, mutations in either PT11 or PT13 affected the development of the symbiosis, demonstrating that both genes are important for AM symbiosis. For symbiotic Pi uptake, however, only PT11 is necessary and sufficient. Consequently, our results demonstrate that mycorrhizal rice depends on the AM symbiosis to satisfy its Pi demands, which is mediated by a single functional Pi transporter, PT11.
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