scholarly journals Belowground Carbohydrate Reserves of Mature Southern Pines Reflect Seedling Strategy to Evolutionary History of Disturbance

Forests ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 653 ◽  
Author(s):  
Joshua Mims ◽  
Joseph O’Brien ◽  
Doug Aubrey
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Pinus Palustris ◽  
Life History Stage ◽  
Southern Pine ◽  
Mature Trees ◽  
Carbohydrate Reserves ◽  
Selective Pressures ◽  
Southern Pines ◽  
History Of

Carbohydrate reserves provide advantages for mature trees experiencing frequent disturbances; however, it is unclear if selective pressures operate on this characteristic at the seedling or mature life history stage. We hypothesized that natural selection has favored carbohydrate reserves in species that have an evolutionary history of frequent disturbance and tested this using three southern pine species that have evolved across a continuum of fire frequencies. Longleaf pine (Pinus palustris) roots exhibited higher maximum starch concentrations than slash (P. elliottii) and loblolly (P. taeda), which were similar. Longleaf also relied on starch reserves in roots more than slash or loblolly, depleting 64, 41, and 23 mg g−1 of starch, respectively, between seasonal maximum and minimum, which represented 52%, 45%, and 26% of reserves, respectively. Starch reserves in stems did not differ among species or exhibit temporal dynamics. Our results suggest that an evolutionary history of disturbance partly explains patterns of carbohydrate reserves observed in southern pines. However, similarities between slash and loblolly indicate that carbohydrate reserves do not strictly follow the continuum of disturbance frequencies among southern pine, but rather reflect the different seedling strategies exhibited by longleaf compared to those shared by slash and loblolly. We propose that the increased carbohydrate reserves in mature longleaf may simply be a relic of selective pressures imposed at the juvenile stage that are maintained through development, thus allowing mature trees to be more resilient and to recover from chronic disturbances such as frequent fire.

scholarly journals Tribalism Is Human Nature

2019 ◽  
Vol 28 (6) ◽  
pp. 587-592 ◽  
Author(s):  
Cory J. Clark ◽  
Brittany S. Liu ◽  
Bo M. Winegard ◽  
Peter H. Ditto
Keyword(s):  
Evolutionary History ◽  
Cognitive Biases ◽  
Meta Analysis ◽  
Human Cognition ◽  
Partisan Bias ◽  
Selective Pressures ◽  
Group Loyalty ◽  
History Of ◽  
The Common ◽  
Political Spectrum

Humans evolved in the context of intense intergroup competition, and groups comprised of loyal members more often succeeded than groups comprised of nonloyal members. Therefore, selective pressures have sculpted human minds to be tribal, and group loyalty and concomitant cognitive biases likely exist in all groups. Modern politics is one of the most salient forms of modern coalitional conflict and elicits substantial cognitive biases. The common evolutionary history of liberals and conservatives gives little reason to expect protribe biases to be higher on one side of the political spectrum than the other. This evolutionarily plausible null hypothesis has been supported by recent research. In a recent meta-analysis, liberals and conservatives showed similar levels of partisan bias, and several protribe cognitive tendencies often ascribed to conservatives (e.g., intolerance toward dissimilar other people) were found in similar degrees in liberals. We conclude that tribal bias is a natural and nearly ineradicable feature of human cognition and that no group—not even one’s own—is immune.

β-Defensin evolution: selection complexity and clues for residues of functional importance

2006 ◽  
Vol 34 (2) ◽  
pp. 257-262 ◽  
Author(s):  
C.A.M. Semple ◽  
K. Taylor ◽  
H. Eastwood ◽  
P.E. Barran ◽  
J.R. Dorin
Keyword(s):  
Positive Selection ◽  
Evolutionary History ◽  
Mammalian Genome ◽  
Functional Importance ◽  
Selective Pressures ◽  
History Of ◽  
Orthologous Loci ◽  
Window Approach ◽  
First Time ◽  
Evolutionary Lineages

We have examined the evolution of the genes at the major human β-defensin locus and the orthologous loci in a range of other primates and mammals. For the first time, these data allow us to examine selective episodes in the more recent evolutionary history of this locus as well as in the ancient past. We have used a combination of maximum-likelihood-based tests and a maximum-parsimony-based sliding window approach to give a detailed view of the varying modes of selection operating at this locus. We provide evidence for strong positive selection soon after the duplication of these genes within an ancestral mammalian genome. During the divergence of primates, however, variable selective pressures have acted on β-defensin genes in different evolutionary lineages, with episodes of both negative and, more rarely, positive selection. Positive selection appears to have been more common in the rodent lineage, accompanying the birth of novel rodent-specific β-defensin gene clades. Sites in the second exon have been subject to positive selection and, by implication, are important in functional diversity. A small number of sites in the mature human peptides were found to have undergone repeated episodes of selection in different primate lineages. Particular sites were consistently implicated by multiple methods at positions throughout the mature peptides. These sites are clustered at positions that are predicted to be important for the function of β-defensins.

scholarly journals Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

2017 ◽  
Vol 4 (4) ◽  
pp. 160997 ◽  
Author(s):  
T. Cucchi ◽  
A. Mohaseb ◽  
S. Peigné ◽  
K. Debue ◽  
L. Orlando ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Temporal Dynamics ◽  
Phylogenetic Signal ◽  
Evolutionary Process ◽  
Archaeological Record ◽  
Motion Model ◽  
Geometric Morphometric ◽  
Spatial And Temporal Dynamics ◽  
History Of ◽  
Brownian Motion Model

The Plio–Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys.

scholarly journals Impact of homologous recombination on core genome phylogenies

2020 ◽  
Author(s):  
Caroline Marie Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.Results. In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.Conclusions. Overall these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Independent accretion of TIM22 complex subunits in the animal and fungal lineages

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1060
Author(s):  
Sergio A. Muñoz-Gómez ◽  
Shannon N. Snyder ◽  
Samantha J. Montoya ◽  
Jeremy G. Wideman
Keyword(s):  
Evolutionary History ◽  
Protein Import ◽  
Protein Complexes ◽  
Mitochondrial Protein ◽  
Mitochondrial Protein Import ◽  
Mutation Pressure ◽  
Selective Pressures ◽  
Fungal Evolution ◽  
Structural Divergence ◽  
History Of

Background: The mitochondrial protein import complexes arose early in eukaryogenesis. Most of the components of the protein import pathways predate the last eukaryotic common ancestor. For example, the carrier-insertase TIM22 complex comprises the widely conserved Tim22 channel core. However, the auxiliary components of fungal and animal TIM22 complexes are exceptions to this ancient conservation. Methods: Using comparative genomics and phylogenetic approaches, we identified precisely when each TIM22 accretion occurred. Results: In animals, we demonstrate that Tim29 and Tim10b arose early in the holozoan lineage. Tim29 predates the metazoan lineage being present in the animal sister lineages, choanoflagellate and filastereans, whereas the erroneously named Tim10b arose from a duplication of Tim9 at the base of metazoans. In fungi, we show that Tim54 has representatives present in every holomycotan lineage including microsporidians and fonticulids, whereas Tim18 and Tim12 appeared much later in fungal evolution. Specifically, Tim18 and Tim12 arose from duplications of Sdh3 and Tim10, respectively, early in the Saccharomycotina. Surprisingly, we show that Tim54 is distantly related to AGK suggesting that AGK and Tim54 are extremely divergent orthologues and the origin of AGK/Tim54 interaction with Tim22 predates the divergence of animals and fungi. Conclusions: We argue that the evolutionary history of the TIM22 complex is best understood as the neutral structural divergence of an otherwise strongly functionally conserved protein complex. This view suggests that many of the differences in structure/subunit composition of multi-protein complexes are non-adaptive. Instead, most of the phylogenetic variation of functionally conserved molecular machines, which have been under stable selective pressures for vast phylogenetic spans, such as the TIM22 complex, is most likely the outcome of the interplay of random genetic drift and mutation pressure.

scholarly journals Impact of homologous recombination on core genome phylogenies

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Caroline M. Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate. Results In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. Conclusions Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Evolutionary History of the phl Gene Cluster in the Plant-Associated Bacterium Pseudomonas fluorescens

2009 ◽  
Vol 75 (7) ◽  
pp. 2122-2131 ◽  
Author(s):  
Jennifer A. Moynihan ◽  
John P. Morrissey ◽  
Eric R. Coppoolse ◽  
Willem J. Stiekema ◽  
Fergal O'Gara ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Evolutionary History ◽  
Biological Control Agent ◽  
Control Agent ◽  
Systemic Resistance ◽  
Plant Association ◽  
Selective Pressures ◽  
Functional Implications ◽  
History Of

ABSTRACT Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene phl cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of P. fluorescens strains. Determination of the evolution of the phl cluster and understanding the selective pressures promoting its retention or loss in lineages of P. fluorescens will help in the development of P. fluorescens as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of P. fluorescens and the phl cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species P. fluorescens but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the phl cluster within the P. fluorescens genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the phl cluster and 2,4-DAPG production in some lineages of P. fluorescens are discussed.

scholarly journals Impact of homologous recombination on core genome phylogenies

2020 ◽  
Author(s):  
Caroline Marie Stott ◽  
Louis-Marie Bobay
Keyword(s):  
Homologous Recombination ◽  
Empirical Data ◽  
Gold Standard ◽  
Evolutionary History ◽  
Core Genome ◽  
Bacterial Strains ◽  
Recombination Rates ◽  
Selective Pressures ◽  
Large Sets ◽  
History Of

Abstract Background. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.Results. In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. Conclusions. Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

scholarly journals Japanese Macaques’ (Macaca fuscata) sensitivity to human gaze and visual perspective in contexts of threat, cooperation, and competition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alba Castellano-Navarro ◽  
Emilio Macanás-Martínez ◽  
Zhihong Xu ◽  
Federico Guillén-Salazar ◽  
Andrew J. J. MacIntosh ◽  
...  
Keyword(s):  
Animal Behavior ◽  
Evolutionary History ◽  
Macaca Fuscata ◽  
Japanese Macaques ◽  
Visual Perspective ◽  
Direct Gaze ◽  
Selective Pressures ◽  
History Of ◽  
Gaze Sensitivity ◽  
Free Ranging

AbstractGaze sensitivity allows us to interpret the visual perspective of others, inferring their intentions and attentional states. In order to clarify the evolutionary history of this ability, we assessed the response of free-ranging Japanese macaques (Macaca fuscata) to human gaze in three contexts: threat (Experiment 1), cooperation (Experiment 2), and competition (Experiment 3). Subjects interpreted the direct gaze of an approaching human as a sign of threat, showing a greater flight initiation distance and more threats towards the human in this condition than when the human gazed in another direction. Subjects also adapted their behavior to the attentional cues of a human who gave them food, by for example moving into his visual field. However, the macaques did not seem to take the visual perspective of a human competing with them over food, as they failed to first retrieve the food that was not visible to the human (i.e., located behind an opaque barrier). Our results support the idea that Japanese macaques can respond to a human’s gaze flexibly depending on the context. Moreover, they highlight the importance of studying animal behavior across different species and contexts to better understand the selective pressures that might have led to its evolution.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

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