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 Avian and serpentine endogenous foamy viruses, and new insights into the macroevolutionary history of foamy viruses

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Pakorn Aiewsakun
Keyword(s):  
Phylogenetic Analyses ◽  
Endogenous Retroviruses ◽  
Time Dependent ◽  
Sea Snake ◽  
Dependent Rate ◽  
Foamy Viruses ◽  
History Of ◽  
Paraphyletic Group ◽  
Vertebrate Hosts

Abstract This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork (Ciconia boyciana) and other was found in the genome of spine-bellied sea snake (Hydrophis hardwickii), designated ERV-Spuma.N-Cbo (where 'N' runs from one to thirteen) and ERV-Spuma.1-Hha, respectively. This discovery of avian and serpentine endogenous FVs adds snakes, and perhaps more crucially, birds to the list of currently known hosts of FVs, in addition to mammals, reptiles, amphibians, and fish. This indicates that FVs are, or at least were, capable of infecting all major lineages of vertebrates. Moreover, together with other FVs, phylogenetic analyses showed that both of them are most closely related to mammalian FVs. Further examination revealed that reptilian FVs form a deep paraphyletic group that is basal to mammalian and avian FVs, suggesting that there were multiple ancient FV cross-class transmissions among their hosts. Evolutionary timescales of various FV lineages were estimated in this study, in particular, the timescales of reptilian FVs and that of the clade of mammalian, avian, and serpentine FVs. This was accomplished by using the recently established time-dependent rate phenomenon models, inferred using mainly the knowledge of the co-speciation history between FVs and mammals. It was found that the estimated timescales matched very well with those of reptiles. Combined with the observed phylogenetic patterns, these results suggested that FVs likely co-speciated with ancient reptilian animals, but later jumped to a protomammal and/or a bird, which ultimately gave rise to mammalian and avian FVs. These results contribute to our understanding of FV emergence, specifically the emergence of mammalian and avian FVs, and provide new insights into how FVs co-evolved with their non-mammalian vertebrate hosts in the distant past.

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 Phylogenetic position of Neotropical Bursera-specialist mistletoes: the evolution of deciduousness and succulent leaves in Psittacanthus (Loranthaceae)

2018 ◽  
Vol 96 (3) ◽  
pp. 443 ◽  
Author(s):  
Andrés Ernesto Ortiz-Rodriguez ◽  
Eydi Yanina Guerrero ◽  
Juan Francisco Ornelas
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Morphological Evolution ◽  
Divergence Time ◽  
Molecular Dating ◽  
Phylogenetic Position ◽  
Long Time ◽  
History Of ◽  
Nuclear Its ◽  
Divergence Timing

<p><strong>Background:</strong> The phylogenetic relationships of the <em>Bursera</em>-host specialist <em>Psittacanthus nudus</em>, <em>P. palmeri </em>and <em>P. sonorae</em> (Loranthaceae) remain uncertain. These mistletoe species exhibit morphological and phenological innovations probably related to their dry habitats, so that determining their phylogenetic position is key to the understanding of factors associated with the morphological evolution within <em>Psittacanthus</em>.</p><p><strong>Questions:</strong> (1) Is the evolution of some morphological innovations in the <em>Bursera</em>-host specialists associated with the ecological conditions linked to host diversification? (2) Does time of diversification in both lineages coincide?<strong></strong></p><p><strong>Study species:</strong> Fourteen species of <em>Psittacanthus</em>.</p><p><strong>Methods: </strong>Sequences of nuclear (ITS) and plastid (<em>trnL-trnF</em>) markers are analyzed with Bayesian inference, maximum likelihood and maximum parsimony methods, and molecular dating under a Bayesian approach estimated to elucidate the phylogenetic position and divergence timing of the<em> Bursera</em>-host specialists.</p><p><strong>Results:</strong> The <em>Bursera</em>-host specialists form a strongly supported clade, named here the ‘<em>Bursera</em> group’. The divergence time for the <em>Bursera</em>-host specialists was estimated at 7.89 Ma. Interestingly, phylogenetic relationships between <em>P. nudus</em> and <em>P. palmeri</em>, as currently circumscribed, were not fully resolved, making <em>P. palmeri</em> paraphyletic.</p><p><strong>Conclusions</strong>: Based on these results, the plants collected by type locality of <em>P. nudus</em> in Honduras should be named <em>P. palmeri</em>. The seasonal deciduousness of <em>P. palmeri </em>(including <em>P. nudus</em>) and morphology of <em>P. sonorae</em> (small size, fleshy leaves) are clearly adaptations to dry ecosystems where these species have lived for a long time. In parallel, the evolutionary history of these mistletoes seems to be correlated with the evolutionary history and diversification patterns of <em>Bursera</em>.</p>

scholarly journals New insights into the earlier evolutionary history of epiphytic macrolichens

2021 ◽  
Author(s):  
Qiuxia Yang ◽  
Yanyan Wang ◽  
Robert Lucking ◽  
H. Thorsten Lumbsch ◽  
Xin Wang ◽  
...  
Keyword(s):  
Morphometric Analysis ◽  
Evolutionary History ◽  
Terrestrial Ecosystems ◽  
Molecular Dating ◽  
Geometric Morphometric ◽  
New Family ◽  
Family Level ◽  
History Of ◽  
New Material ◽  
Geometric Morphometric Analysis

Lichens are well known as pioneer organisms colonizing bare surfaces such as rocks and therefore have been hypothesized to play a role in the early formation of terrestrial ecosystems. Given the rarity of fossil evidence, our understanding of the evolutionary history of lichen-forming fungi is primarily based on molecular dating approaches. These studies suggest extant clades of macrolichens diversified after the K-Pg boundary. Here we corroborate the mid-Mesozoic fossil Daohugouthallus ciliiferus as an epiphytic macrolichen that predates the K-Pg boundary by 100 Mys. Based on new material and geometric morphometric analysis, we demonstrate that the Jurassic fossil is morphologically most similar to Parmeliaceae, but cannot be placed in Parmeliaceae or other similar family-level clades forming macrolichens as these evolved much later. Consequently, a new family, Daohugouthallaceae, is proposed here to accommodate this fossil, which reveals macrolichens may have been diverse long before the Cenozoic diversification of extant lineages.

Genomic regression of claw keratin, taste receptor and light-associated genes inform biology and evolutionary origins of snakes

2017 ◽  
Author(s):  
Christopher A. Emerling
Keyword(s):  
Evolutionary History ◽  
Light Adaptation ◽  
Gene Loss ◽  
Taste Receptor ◽  
Taste Buds ◽  
Molecular Dating ◽  
Evolutionary Origins ◽  
Associated Functions ◽  
History Of ◽  
Dim Light

AbstractRegressive evolution of anatomical traits corresponds with the regression of genomic loci underlying such characters. As such, studying patterns of gene loss can be instrumental in addressing questions of gene function, resolving conflicting results from anatomical studies, and understanding the evolutionary history of clades. The origin of snakes coincided with the regression of a number of anatomical traits, including limbs, taste buds and the visual system. By studying the genomes of snakes, I was able to test three hypotheses associated with the regression of these features. The first concerns two keratins that are putatively specific to claws. Both genes that encode these keratins were pseudogenized/deleted in snake genomes, providing additional evidence of claw- specificity. The second hypothesis is whether snakes lack taste buds, an issue complicated by unequivocal, conflicting results in the literature. I found evidence that different snakes have lost one or more taste receptors, but all snakes examined retained at least some capacity for taste. The final hypothesis I addressed is that the earliest snakes were adapted to a dim light niche. I found evidence of deleted and pseudogenized genes with light- associated functions in snakes, demonstrating a pattern of gene loss similar to other historically nocturnal clades. Together these data also provide some bearing on the ecological origins of snakes, including molecular dating estimates that suggest dim light adaptation preceded the loss of limbs.

The origins and evolutionary history of xerophytic vegetation in Australia

2020 ◽  
Vol 68 (3) ◽  
pp. 195 ◽  
Author(s):  
Margaret Byrne ◽  
Daniel J. Murphy
Keyword(s):  
Evolutionary History ◽  
Arid Zone ◽  
Major Change ◽  
Significant Component ◽  
Multiple Origins ◽  
Geographic Structure ◽  
Speciation Rates ◽  
History Of ◽  
Australian Flora ◽  
Plant Families

The xeromorphic vegetation is a significant component of the Australian flora and phylogenetic and phylogeographic analysis of xeromorphic plants provides a basis for understanding the origins and evolutionary history of the Australian vegetation. Here we expand on previous reviews of the origins and maintenance of the Australian flora with an emphasis on the xeromorphic component. Phylogenetic evidence supports fossil evidence for evolution of sclerophyll and xeromorphic vegetation from the Eocene with lineages becoming more common in the Oligocene and Miocene, a time of major change in climate and vegetation in Australia. Phylogenetic evidence supports the mesic biome as ancestral to the arid zone biome in Australia in phylogenies of key groups. The diversification and radiation of Australian species shows single origins of xeromorphic group mainly at deeper levels in phylogenies as well as multiple origins of arid occurring species at shallower levels. Divergence across the Nullarbor is also evident and speciation rates in south-western Australia were higher than in the south-east in several plant families. Estimates of timing of diversification generally show either constant rates of diversification or increased diversification from the mid to late Miocene. Phylogeographic studies consistently demonstrate high localised genetic diversity and geographic structure in xeromorphic species occupying both mesic and arid biomes.

scholarly journals Evolution of a key enzyme of aerobic metabolism reveals Proterozoic functional subunit duplication events and an ancient origin of animals

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bruno Santos Bezerra ◽  
Flavia Ariany Belato ◽  
Beatriz Mello ◽  
Federico Brown ◽  
Christopher J. Coates ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Krebs Cycle ◽  
Divergence Time ◽  
Life Forms ◽  
Molecular Dating ◽  
Regulatory Subunits ◽  
Key Enzyme ◽  
Duplication Events ◽  
History Of ◽  
Oxidative State

AbstractThe biological toolkits for aerobic respiration were critical for the rise and diversification of early animals. Aerobic life forms generate ATP through the oxidation of organic molecules in a process known as Krebs’ Cycle, where the enzyme isocitrate dehydrogenase (IDH) regulates the cycle's turnover rate. Evolutionary reconstructions and molecular dating of proteins related to oxidative metabolism, such as IDH, can therefore provide an estimate of when the diversification of major taxa occurred, and their coevolution with the oxidative state of oceans and atmosphere. To establish the evolutionary history and divergence time of NAD-dependent IDH, we examined transcriptomic data from 195 eukaryotes (mostly animals). We demonstrate that two duplication events occurred in the evolutionary history of NAD-IDH, one in the ancestor of eukaryotes approximately at 1967 Ma, and another at 1629 Ma, both in the Paleoproterozoic Era. Moreover, NAD-IDH regulatory subunits β and γ are exclusive to metazoans, arising in the Mesoproterozoic. Our results therefore support the concept of an ‘‘earlier-than-Tonian’’ diversification of eukaryotes and the pre-Cryogenian emergence of a metazoan IDH enzyme.

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 Early diversifications of angiosperms and their insect pollinators: Were they unlinked?

2021 ◽  
Author(s):  
Yasmin Asar ◽  
Simon Y. W. Ho ◽  
Hervé Sauquet
Keyword(s):  
Mass Extinction ◽  
Evolutionary History ◽  
Molecular Dating ◽  
Insect Pollination ◽  
Early Angiosperm ◽  
Insect Pollinators ◽  
Extinction Event ◽  
History Of ◽  
Mass Extinction Event

The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article we examine (i) the discrepancies between dates of emergence for major clades of angiosperm and insect lineages; (ii) the long history of gymnosperm–insect pollination modes, which likely shaped early angiosperm–insect pollination mutualisms; and (iii) how the K–Pg mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled, until the end of the Cretaceous.

Sign in / Sign up

Export Citation Format

Share Document