scholarly journals Slow and fast evolutionary rates in the history of lepidosaurs

Palaeontology ◽  
2021 ◽  
Author(s):  
Jorge A. Herrera‐Flores ◽  
Armin Elsler ◽  
Thomas L. Stubbs ◽  
Michael J. Benton
Keyword(s):  
Evolutionary Rates ◽  
History Of

A Phylogeographic Analysis of Allozyme Variation among Populations of Persoonia mollis (Proteaceae)

1998 ◽  
Vol 46 (6) ◽  
pp. 571 ◽  
Author(s):  
Siegfried L. Krauss
Keyword(s):  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Vegetation History ◽  
Allozyme Variation ◽  
Evolutionary Rates ◽  
Upgma Tree ◽  
History Of ◽  
Parsimony Trees ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The phylogeography of 18 populations representing all nine subspecies within Persoonia mollis R.Br. (Proteaceae) was estimated from allozyme frequency data. Trees were constructed using UPGMA, maximum likelihood (CONTML) and maximum parsimony (FREQPARS) procedures. Major differences in topology between the UPGMA tree and other trees indicated that evolutionary rates are probably heterogeneous in different lineages in P. mollis, and that the UPGMA tree is inaccurate as it assumes constant evolutionary rates in all lineages. The maximum likelihood and maximum parsimony trees produced near-identical topologies. The major patterns produced by these trees included the early differentiation of subspecies maxima, the well-supported clade of all other P. mollis populations and, within this clade, the split into two clades that, although distinct, was weakly differentiated at their base. Within these two clades, there is a strong correlation between geographical distance between populations and the position of populations on the tree. These trees are consistent with a scenario of range expansion along two distinct paths in a southerly direction from northern refugia since the last glacial maximum, which is supported by data on the vegetation history of the area. These southern paths currently terminate in populations that share a hybrid zone of apparently secondary origin west of the Budawang Range.

scholarly journals Phylogenetic non-independence in rates of trait evolution

2018 ◽  
Vol 14 (10) ◽  
pp. 20180502 ◽  
Author(s):  
Manabu Sakamoto ◽  
Chris Venditti
Keyword(s):  
Statistical Power ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Small Sample ◽  
Evolutionary Rates ◽  
Biological Traits ◽  
Beak Shape ◽  
Rates Of Evolution ◽  
Shared Ancestry ◽  
History Of

Statistical non-independence of species’ biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here, we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals, beak shape in birds and bite force in amniotes. Specifically, we test if evolutionary rates are phylogenetically interdependent. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g. owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time—including associations of rates with traits—need to account for the undesired effects of shared ancestry.

scholarly journals Emerging novel porcine parvoviruses in Europe: origin, evolution, phylodynamics and phylogeography

2013 ◽  
Vol 94 (10) ◽  
pp. 2330-2337 ◽  
Author(s):  
Dániel Cadar ◽  
Márta Lőrincz ◽  
Timea Kiss ◽  
Dinko Novosel ◽  
Katarzyna Podgorska ◽  
...  
Keyword(s):  
Gene Flow ◽  
Positive Selection ◽  
Host Adaptation ◽  
Genetic Exchange ◽  
Evolutionary Rates ◽  
European Countries ◽  
Capsid Gene ◽  
Porcine Parvovirus ◽  
History Of ◽  
Complete Capsid

To elucidate the spatiotemporal phylodynamics, dispersion and evolutionary processes underlying the emergence of novel porcine parvovirus 2 (PPV2), PPV3 and PPV4 species, we analysed all available complete capsid genes, together with ours, obtained in Europe. Bayesian phylogeography indicates that Romania (PPV2 and PPV4) and Croatia (PPV3) are the most likely ancestral areas from which PPVs have subsequently spread to other European countries and regions. The timescale of our reconstruction supported a relatively recent history of the currently circulating novel PPV species (1920s to 1980s) in the domestic or sylvatic host. While PPV2 strains exhibited a large genetic exchange characterized by significant recombination and gene flow between distinct regions and hosts, PPV3 and PPV4 showed a diversification reflected by the accumulation of geographically structured polymorphisms. The RNA-like evolutionary rates detected inter- and intrahost recombination and the positive selection sites provided evidence that the PPV2–4 capsid gene plays a prominent role in host adaptation.

scholarly journals Ecological opportunity as a driving force for radiation events and time-dependent evolutionary rates in papillomaviruses

2020 ◽  
Author(s):  
Anouk Willemsen ◽  
Ignacio G. Bravo
Keyword(s):  
Driving Force ◽  
Evolutionary History ◽  
Evolutionary Rates ◽  
Molecular Dating ◽  
Time Dependent ◽  
Ecological Opportunity ◽  
Dependent Rate ◽  
Evolutionary Scenario ◽  
Speciation Rates ◽  
History Of

AbstractPapillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, and snakes. The recent discovery of PVs in different fish species allows for a more complete reconstruction of the evolutionary history of the viral family. In this study we perform phylogenetic dating to analyse evolutionary events that occurred during PV evolution, as well as to estimate speciation and evolutionary rates.We have used four different data sets to explore and correct for potential biases that particular taxa combinations may introduce during molecular time inference. When considering the evolution of substitution rates we observed that short-term rate estimates are much higher than long-term rate estimates, also known as the time-dependent rate phenomenon. We discuss that for PVs the time-dependent evolutionary rates may reflect changes in the available host niches. When considering the evolution of viral branching events (as a proxy for speciation rates), we show that these are not constant through time, suggesting the occurrence of distinct evolutionary events such as adaptive radiations. In a joint analysis with host speciation rates, we identify at least four different evolutionary periods, demonstrating that the evolution of PVs is multiphasic, and refining the previously suggested biphasic evolutionary scenario.Thanks to the discovery of novel PVs in basal hosts and to the implementation of a time-dependent rate model for molecular dating, our results provide new insights into the evolutionary history of PVs. In this updated evolutionary scenario, ecological opportunity appears as one main driving force for the different radiation and key-innovation events we observe.

scholarly journals Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida

2021 ◽  
Author(s):  
Jesus A Ballesteros ◽  
Carlos Eduardo Santibanez-Lopez ◽  
Caitlin M Baker ◽  
Ligia R Benavides ◽  
Tauana J Cunha ◽  
...  
Keyword(s):  
Evolutionary Rates ◽  
Data Matrix ◽  
Morphological Data ◽  
Systematic Bias ◽  
Rapid Radiation ◽  
Tree Inference ◽  
Horseshoe Crabs ◽  
Terrestrial Habitats ◽  
History Of ◽  
Algorithmic Approaches

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. While conflicting hypotheses prevail in morphological and molecular datasets alike, the monophyly of Arachnida is nearly universally accepted. Though a small number of phylotranscriptomic analyses have recovered arachnid monophyly, these did not sample all living chelicerate orders. We generated a dataset of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternatives algorithmic approaches to species tree inference. Investigation of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the effect of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

Diversity and evolutionary rates of Cambro-Ordovician nautiloids

Paleobiology ◽  
1981 ◽  
Vol 7 (2) ◽  
pp. 216-229 ◽  
Author(s):  
Rex E. Crick
Keyword(s):  
North American ◽  
Fossil Record ◽  
Evolutionary Rates ◽  
Time Interval ◽  
Time Intervals ◽  
Frequency Distributions ◽  
Extinction Rates ◽  
History Of ◽  
Biological Aspects ◽  
Stratigraphic Ranges

The history of diversity, origination and extinction of Cambro-Ordovician nautiloid cephalopods is explored to determine if differences in evolutionary rates between nautiloid orders are sufficient to document significantly high or low rates of evolutionary turnover (taxotely of Raup and Marshall 1980). The stratigraphic ranges of 425 nautiloid genera are analyzed for this purpose.Evolutionary rates for five of the seven time intervals analyzed fall within frequency distributions of rates which are thought to be characteristic for a given time interval (horotelic distribution of Simpson 1944). Sufficient heterogeneity is present among extinction rates of Arenigian orders and origination rates of Caradocian orders to reject the null hypotheses of horotely in favor of taxotely. The orders Ellesmerocerida and Tarphycerida, each with a significantly high rate of extinction (P ≥ 0.99), and the Actinocerida, with a significantly low rate of extinction (P ≥ 0.99), were responsible for taxotely during the Arenigian. The Oncocerida and Discosorida, each with a significantly high rate of origination (P ≥ 0.99), were responsible for taxotely during the Caradocian. In each case, taxotely is attributable to the influence of North American endemics. This effect is believed to be more the result of real biological aspects of nautiloid evolution than an artifact of the fossil record.

scholarly journals Phylogenetic non-independence in rates of trait evolution

2018 ◽  
Author(s):  
Manabu Sakamoto ◽  
Chris Venditti
Keyword(s):  
Statistical Power ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Small Sample ◽  
Evolutionary Rates ◽  
Biological Traits ◽  
Beak Shape ◽  
Rates Of Evolution ◽  
Shared Ancestry ◽  
History Of

Statistical non-independence of species’ biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals; beak shape in birds; and bite force in amniotes. Specifically, we test whether rates are non-independent throughout the evolutionary history of each tree. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g., owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time – including associations of rates with traits – need account for the undesired effects of shared ancestry.

scholarly journals Graptoloid evolutionary rates track Ordovician–Silurian global climate change

2013 ◽  
Vol 151 (2) ◽  
pp. 349-364 ◽  
Author(s):  
ROGER A. COOPER ◽  
PETER M. SADLER ◽  
AXEL MUNNECKE ◽  
JAMES S. CRAMPTON
Keyword(s):  
Species Richness ◽  
Evolutionary Dynamics ◽  
Global Climate ◽  
Mean Value ◽  
Evolutionary Rates ◽  
Extinction Rate ◽  
Extinction Rates ◽  
History Of ◽  
Mass Depletion ◽  
Climatic Regime

AbstractGraptoloid evolutionary dynamics show a marked contrast from the Ordovician to the Silurian. Subdued extinction and origination rates during the Ordovician give way, during the late Katian, to rates that were highly volatile and of higher mean value through the Silurian, reflecting the significantly shorter lifespan of Silurian species. These patterns are revealed in high-resolution rate curves derived from the CONOP (constrained optimization) scaled and calibrated global composite sequence of 2094 graptoloid species. The end-Ordovician mass depletion was driven primarily by an elevated extinction rate which lasted forc. 1.2 Ma with two main spikes during the Hirnantian. The early Silurian recovery, although initiated by a peak in origination rate, was maintained by a complex interplay of origination and extinction rates, with both rates rising and falling sharply. The global δ13C curve echoes the graptoloid evolutionary rates pattern; the prominent and well-known positive isotope excursions during the Late Ordovician and Silurian lie on or close to times of sharp decline in graptoloid species richness, commonly associated with extinction rate spikes. The graptoloid and isotope data point to a relatively steady marine environment in the Ordovician with mainly background extinction rates, changing during the Katian to a more volatile climatic regime that prevailed through the Silurian, with several sharp extinction episodes triggered by environmental crises. The correlation of graptoloid species diversity with isotopic ratios was positive in the Ordovician and negative in the Silurian, suggesting different causal linkages. Throughout the history of the graptoloid clade all major depletions in species richness except for one were caused by elevated extinction rate rather than decreased origination rate.

scholarly journals Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Tiago R. Simões ◽  
Michael W. Caldwell ◽  
Stephanie E. Pierce
Keyword(s):  
Evolutionary History ◽  
Evolutionary Rates ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Trees ◽  
Model Choice ◽  
Rates Of Evolution ◽  
History Of ◽  
Living Species ◽  
The Impact

Abstract Background The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. Results Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. Conclusions We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

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