scholarly journals An early burst in brachiopod evolution corresponding with significant climatic shifts during the Great Ordovician Biodiversification Event

2021 ◽  
Vol 288 (1958) ◽  
pp. 20211450
Author(s):  
Curtis R. Congreve ◽  
Mark E. Patzkowsky ◽  
Peter J. Wagner
Keyword(s):  
Environmental Changes ◽  
Atmospheric Oxygen ◽  
Rapid Evolution ◽  
Divergence Times ◽  
Developmental Constraints ◽  
High Frequencies ◽  
Prior Probabilities ◽  
Anatomical Change ◽  
Dating Methods ◽  
Speciation Rates

We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million years and rapid divergences shortly before the clade first appears in the fossil record. These divergence times indicate much higher rates of cladogenesis than are typical of brachiopods during this interval. The correspondence of high speciation rates and high anatomical disparity suggests punctuated (speciational) change drove the high frequencies of early anatomical change, which in turn suggests increased ecological opportunities rather than shifting developmental constraints account for high rates of anatomical change. The pulse of rapid evolution began coincident with cooling temperatures, the start of major oscillations in sea level and increased levels of atmospheric oxygen. Our results suggest that these factors permitted major geographical and ecological expansion of strophomenoids with intervals of geographical isolation, resulting in elevated speciation rates and corresponding elevated frequencies of punctuated change.

scholarly journals How humans drive speciation as well as extinction

2016 ◽  
Vol 283 (1833) ◽  
pp. 20160600 ◽  
Author(s):  
J. W. Bull ◽  
M. Maron
Keyword(s):  
Species Diversity ◽  
Human Activities ◽  
Rapid Evolution ◽  
Novel Ecosystem ◽  
No Net Loss ◽  
Extinction Rates ◽  
Trade Offs ◽  
Speciation Rates ◽  
Nuanced Understanding ◽  
Comparable Magnitude

A central topic for conservation science is evaluating how human activities influence global species diversity. Humanity exacerbates extinction rates. But by what mechanisms does humanity drive the emergence of new species? We review human-mediated speciation, compare speciation and known extinctions, and discuss the challenges of using net species diversity as a conservation objective. Humans drive rapid evolution through relocation, domestication, hunting and novel ecosystem creation—and emerging technologies could eventually provide additional mechanisms. The number of species relocated, domesticated and hunted during the Holocene is of comparable magnitude to the number of observed extinctions. While instances of human-mediated speciation are known, the overall effect these mechanisms have upon speciation rates has not yet been quantified. We also explore the importance of anthropogenic influence upon divergence in microorganisms. Even if human activities resulted in no net loss of species diversity by balancing speciation and extinction rates, this would probably be deemed unacceptable. We discuss why, based upon ‘no net loss’ conservation literature—considering phylogenetic diversity and other metrics, risk aversion, taboo trade-offs and spatial heterogeneity. We conclude that evaluating speciation alongside extinction could result in more nuanced understanding of biosphere trends, clarifying what it is we actually value about biodiversity.

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

2021 ◽  
Author(s):  
Andrew M Ritchie ◽  
Xia Hua ◽  
Lindell Bromham
Keyword(s):  
Dna Sequences ◽  
Empirical Studies ◽  
Divergence Time ◽  
Molecular Dating ◽  
Rate Variation ◽  
Substitution Rates ◽  
Molecular Change ◽  
Dna Evidence ◽  
Dating Methods ◽  
Speciation Rates

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 models of molecular rate variation, such as the uncorrelated and autocorrelated lognormal clocks, rely on idealised models of rate variation 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 evidence indicates, 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 two 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, to up to 93% when punctuated simulations are reconstructed under an autocorrelated prior. 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.

scholarly journals Lack of signal for the impact of venom gene diversity on speciation rates in cone snails

2018 ◽  
Author(s):  
Mark A Phuong ◽  
Michael E Alfaro ◽  
Gusti N Mahardika ◽  
Ristiyanti M Marwoto ◽  
Romanus Edy Prabowo ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Rapid Evolution ◽  
Limiting Factor ◽  
Exon Capture ◽  
Speciation Rates ◽  
Intrinsic Capacity ◽  
Cone Snails ◽  
Species Specific ◽  
Capture Techniques ◽  
The Impact

AbstractUnderstanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or lineages’ intrinsic capacity for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, >900 spp.) provide a unique opportunity to test this prediction because their venom genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though whether or not we detected a signal depended on the dataset and the method. If our results remain true with increased sampling in future studies, they suggest that the rapid evolution of Conidae venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

scholarly journals Re-Envisioning Anti-Apicomplexan Parasite Drug Discovery Approaches

2021 ◽  
Vol 11 ◽  
Author(s):  
Gabriel W. Rangel ◽  
Manuel Llinás
Keyword(s):  
Drug Discovery ◽  
Drug Targets ◽  
Large Scale ◽  
Environmental Changes ◽  
Rapid Evolution ◽  
Antimalarial Drugs ◽  
Life Cycles ◽  
Drug Pressure ◽  
Apicomplexan Parasites ◽  
Resistance Evolution

Parasites of the phylum Apicomplexa impact humans in nearly all parts of the world, causing diseases including to toxoplasmosis, cryptosporidiosis, babesiosis, and malaria. Apicomplexan parasites have complex life cycles comprised of one or more stages characterized by rapid replication and biomass amplification, which enables accelerated evolutionary adaptation to environmental changes, including to drug pressure. The emergence of drug resistant pathogens is a major looming and/or active threat for current frontline chemotherapies, especially for widely used antimalarial drugs. In fact, resistant parasites have been reported against all modern antimalarial drugs within 15 years of clinical introduction, including the current frontline artemisinin-based combination therapies. Chemotherapeutics are a major tool in the public health arsenal for combatting the onset and spread of apicomplexan diseases. All currently approved antimalarial drugs have been discovered either through chemical modification of natural products or through large-scale screening of chemical libraries for parasite death phenotypes, and so far, none have been developed through a gene-to-drug pipeline. However, the limited duration of efficacy of these drugs in the field underscores the need for new and innovative approaches to discover drugs that can counter rapid resistance evolution. This review details both historical and current antimalarial drug discovery approaches. We also highlight new strategies that may be employed to discover resistance-resistant drug targets and chemotherapies in order to circumvent the rapid evolution of resistance in apicomplexan parasites.

scholarly journals AVALIAÇÃO QUÍMICA DE LENHOS CARBONIZADOS DE Araucaria columnaris SOB DIFERENTES CONCENTRAÇÕES DE OXIGÊNIO COMO COMPARATIVO DE ANÁLISE DE charcoal FÓSSIL

Química Nova ◽  
2020 ◽  
Author(s):  
Fernanda Marder ◽  
Daniela Lara ◽  
André Jasper ◽  
Eduardo Ethur ◽  
Dieter Uhl ◽  
...  
Keyword(s):  
Climate Change ◽  
Environmental Changes ◽  
Atmospheric Oxygen ◽  
Firing Process ◽  
Chemical Evaluation ◽  
Fossil Coal ◽  
The Face ◽  
Life Trajectory ◽  
Carbonized Wood ◽  
Oxygen Concentrations

CHEMICAL EVALUATION OF Araucaria columnaris CARBONIZED WOODS UNDER DIVERSE OXYGEN CONCENTRATIONS AS COMPARATIVE ANALYSIS OF FOSSIL charcoal. In the face of environmental changes concerns, the study of climate change becomes essential to understand the life trajectory of planet earth. For this purpose, this work seeks to understand climate change and fluctuations in the amount of atmospheric oxygen across geological ages, carbonizing the Araucaria columnaris wood in varying oxygen concentrations, and comparing them to the fossil coal from Quiteria Outcrop. In this study, pyrolysis of Araucaria columnaris wood occurred with the use of TGA, under an atmosphere of 21% and 30% O2, analyzed in FTIR, distinguishing the constituent compounds of the wood. Multivariate analysis of the mains components (PCA) was applied, for data crossing. There is a distinction between carbonized wood and fossil charcoal, the charcoal burning temperature as well as the atmospheric oxygen composition being inconclusive. However, FTIR results indicate that the amount of oxygen has an influence on the degradation of the wood, and samples at 450 °C have greater similarities with fresh wood. Thus, it was observed that the temperature and the burning time are the main factors of the fires, being that the amount of oxygen available in the atmosphere influences the firing process.

scholarly journals Fluvial architecture of Belgian river systems in contrasting environments: implications for reconstructing the sedimentation history

2011 ◽  
Vol 90 (1) ◽  
pp. 31-50 ◽  
Author(s):  
B. Notebaert ◽  
G. Houbrechts ◽  
G. Verstraeten ◽  
N. Broothaerts ◽  
J. Haeckx ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Land Use Changes ◽  
Temporal Variations ◽  
Sediment Dynamics ◽  
Metal Mining ◽  
Point Bar ◽  
Dating Methods ◽  
Dominant Process ◽  
Fluvial Architecture ◽  
Floodplain Sediments

AbstractAccurate dating is necessary to get insight in the temporal variations in sediment deposition in floodplains. The interpretation of such dates is however dependent on the fluvial architecture of the floodplain. In this study we discuss the fluvial architecture of three contrasting Belgian catchments (Dijle, Geul and Amblève catchment) and how this influences the dating possibilities of net floodplain sediment storage. Although vertical aggradation occurred in all three floodplains during the last part of the Holocene, they differ in the importance of lateral accretion and vertical aggradation during the entire Holocene. Holocene floodplain aggradation is the dominant process in the Dijle catchment. Lateral reworking of the floodplain sediments by river meandering was limited to a part of the floodplain, resulting in stacked point bar deposits. The fluvial architecture allows identifying vertical aggradation without erosional hiatuses. Results show that trends in vertical floodplain aggradation in the Dijle catchment are mainly related to land use changes. In the other two catchments, lateral reworking was the dominant process, and channel lag and point bar deposits occur over the entire floodplain width. Here, tracers were used to date the sediment dynamics: lead from metal mining in the Geul and iron slag from ironworks in the Amblève catchment. These methods allow the identification of two or three discrete periods, but their spatial extent and variations is identified in a continuous way. The fluvial architecture and the limitation in dating with tracers hampered the identification of dominant environmental changes for sediment dynamics in both catchments. Dating methods which provide only discrete point information, like radiocarbon or OSL dating, are best suited for fluvial systems which contain continuous aggradation profiles. Spatially more continuous dating methods, e.g. through the use of tracers, allow to reconstruct past surfaces and allow to reconstruct reworked parts of the floodplain. As such they allow a better reconstruction of past sedimentation rates in systems with important lateral reworking.

scholarly journals Selection analysis on the rapid evolution of a secondary sexual trait

2015 ◽  
Vol 282 (1813) ◽  
pp. 20151244 ◽  
Author(s):  
Swanne P. Gordon ◽  
David Reznick ◽  
Jeff D. Arendt ◽  
Allen Roughton ◽  
Michelle N. Ontiveros Hernandez ◽  
...  
Keyword(s):  
Reproductive Success ◽  
Environmental Changes ◽  
Rapid Evolution ◽  
Evolutionary Process ◽  
Common Garden ◽  
Evolutionary Change ◽  
Black Pigment ◽  
Sexually Selected Traits ◽  
Evolutionary Response ◽  
In The Wild

Evolutionary analyses of population translocations (experimental or accidental) have been important in demonstrating speed of evolution because they subject organisms to abrupt environmental changes that create an episode of selection. However, the strength of selection in such studies is rarely measured, limiting our understanding of the evolutionary process. This contrasts with long-term, mark–recapture studies of unmanipulated populations that measure selection directly, yet rarely reveal evolutionary change. Here, we present a study of experimental evolution of male colour in Trinidadian guppies where we tracked both evolutionary change and individual-based measures of selection. Guppies were translocated from a predator-rich to a low-predation environment within the same stream system. We used a combination of common garden experiments and monthly sampling of individuals to measure the phenotypic and genetic divergence of male coloration between ancestral and derived fish. Results show rapid evolutionary increases in orange coloration in both populations (1 year or three generations), replicating the results of previous studies. Unlike previous studies, we linked this evolution to an individual-based analysis of selection. By quantifying individual reproductive success and survival, we show, for the first time, that males with more orange and black pigment have higher reproductive success, but males with more black pigment also have higher risk of mortality. The net effect of selection is thus an advantage of orange but not black coloration, as reflected in the evolutionary response. This highlights the importance of considering all components of fitness when understanding the evolution of sexually selected traits in the wild.

scholarly journals Lack of Signal for the Impact of Conotoxin Gene Diversity on Speciation Rates in Cone Snails

2019 ◽  
Vol 68 (5) ◽  
pp. 781-796 ◽  
Author(s):  
Mark A Phuong ◽  
Michael E Alfaro ◽  
Gusti N Mahardika ◽  
Ristiyanti M Marwoto ◽  
Romanus Edy Prabowo ◽  
...  
Keyword(s):  
Gene Diversity ◽  
Rapid Evolution ◽  
Limiting Factor ◽  
Exon Capture ◽  
Speciation Rates ◽  
Intrinsic Capacity ◽  
Cone Snails ◽  
Species Specific ◽  
Capture Techniques ◽  
The Impact

Abstract Understanding why some groups of organisms are more diverse than others is a central goal in macroevolution. Evolvability, or the intrinsic capacity of lineages for evolutionary change, is thought to influence disparities in species diversity across taxa. Over macroevolutionary time scales, clades that exhibit high evolvability are expected to have higher speciation rates. Cone snails (family: Conidae, $>$900 spp.) provide a unique opportunity to test this prediction because their toxin genes can be used to characterize differences in evolvability between clades. Cone snails are carnivorous, use prey-specific venom (conotoxins) to capture prey, and the genes that encode venom are known and diversify through gene duplication. Theory predicts that higher gene diversity confers a greater potential to generate novel phenotypes for specialization and adaptation. Therefore, if conotoxin gene diversity gives rise to varying levels of evolvability, conotoxin gene diversity should be coupled with macroevolutionary speciation rates. We applied exon capture techniques to recover phylogenetic markers and conotoxin loci across 314 species, the largest venom discovery effort in a single study. We paired a reconstructed timetree using 12 fossil calibrations with species-specific estimates of conotoxin gene diversity and used trait-dependent diversification methods to test the impact of evolvability on diversification patterns. Surprisingly, we did not detect any signal for the relationship between conotoxin gene diversity and speciation rates, suggesting that venom evolution may not be the rate-limiting factor controlling diversification dynamics in Conidae. Comparative analyses showed some signal for the impact of diet and larval dispersal strategy on diversification patterns, though detection of a signal depended on the dataset and the method. If our results remain true with increased taxonomic sampling in future studies, they suggest that the rapid evolution of conid venom may cause other factors to become more critical to diversification, such as ecological opportunity or traits that promote isolation among lineages.

Probabilistic Phylogenetic Inference in the Fossil Record: Current and Future Applications

2010 ◽  
Vol 16 ◽  
pp. 189-211 ◽  
Author(s):  
Peter J. Wagner ◽  
Jonathan D. Marcot
Keyword(s):  
Morphological Change ◽  
Fossil Record ◽  
Phylogenetic Inference ◽  
Nuisance Parameters ◽  
Character State ◽  
Prior Probabilities ◽  
Sampling Intensity ◽  
Future Goals ◽  
Speciation Rates ◽  
Over Time

Quantitative phylogenetic inference estimates the probability of observed character distributions given trees and rates. Most available programs for doing this assume (tacitly or explicitly) that the sampled taxa are contemporaneous. However, paleontologists usually sample taxa over a clade's history. Thus, we must estimate the probability of observed character-state distributions over time given trees and rates. When we include information about sampling intensity, then we really are estimating the probability of the observed record given trees and rates. Some additional problems that should be issues for neontologists, but which are much more obvious concerns for paleontologists include: 1) ancestor-descendant relationships; 2) punctuated versus continuous morphological change; and, 3) the effects of extinction and speciation rates on prior probabilities of trees. Future goals of paleosystematists include incorporating these and other “nuisance” parameters so that, ultimately, our tests of phylogeny are really tests of evolutionary histories.

scholarly journals Incorporating uncertainty is essential to macroecological inferences: Grass, grit, and the evolution of kangaroos

2019 ◽  
Author(s):  
Ian G. Brennan
Keyword(s):  
Intraspecific Variation ◽  
Environmental Variables ◽  
Divergence Times ◽  
Sources Of Uncertainty ◽  
Multiple Factors ◽  
Australian Continent ◽  
Dating Methods ◽  
Evolutionary Studies ◽  
Testing Patterns ◽  
Organismal Ecology

AbstractStudying organismal ecology and evolution on deep timescales provides us opportunities to identify the processes driving patterns in diversity and forms. Macroecological and macroevolutionary studies of trait evolution however, often fail to account for sources of artifactual variation in the data—be it phylogenetic, temporal, or other. In some instances, this may not affect our evolutionary understanding, and accounting for sources of uncertainty may only subdue confidence in our inferences. In more dramatic cases, narrow views of trait uncertainty may result in conclusions that are misleading. Because macroevolutionary analyses are built atop a number of preconceived hypotheses regarding the relationships between taxa, origination and divergence times, intraspecific variation, and environmental variables, it is important to incorporate and present this uncertainty. Here I use a dataset for Australian kangaroos to demonstrate the importance of incorporating uncertainty when testing patterns of diversification. After accounting for fossil age uncertainty, I provide evidence that a proposed Pliocene origin of Macropus kangaroos is at odds with combined evidence molecular and morphological dating methods. Depending on the estimated crown age of kangaroos, the evolution of hypsodonty is as likely caused by the continental expansion of C4 grasses as it is by increasing windborne dust levels or paleotemperature fluctuations. These results suggest that previous interpretations of the radiation of modern kangaroos are not as bulletproof as we believe, and that multiple factors have likely influenced their remarkable diversification across the Australian continent. More broadly, this demonstrates the importance of incorporating uncertainty in comparative ecological and evolutionary studies, and the value in testing the assumptions inherent in our data and the methods we employ.

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