Browsing by Subject "evolution"

Now showing 1 - 12 of 12

Open Access
Faith, Fact, and Behaviorism
(BEHAVIOR ANALYST, 2013) Staddon, JER
Open Access
From divots to swales: Hillslope sediment transport across divers length scales
(2010) Furbish, David Jon; Haff, Peter K
In soil-mantled steeplands, soil motions associated with creep, ravel, rain splash, soil slips, tree throw, and rodent activity are patchy and intermittent and involve widely varying travel distances. To describe the collective effect of these motions, we formulate a nonlocal expression for the soil flux. This probabilistic formulation involves upslope and downslope convolutions of land surface geometry to characterize motions in both directions, notably accommodating the bidirectional dispersal of material on gentle slopes as well as mostly downslope dispersal on steeper slopes, and it distinguishes between the mobilization of soil material and the effect of surface slope in giving a downslope bias to the dispersal of mobilized material. The formulation separates dispersal associated with intermittent surface motions from the slower bulk behavior associated with small-scale bioturbation and similar dilational processes operating mostly within the soil column. With a uniform rate of mobilization of soil material, the nearly parabolic form of a hillslope profile at steady state resembles a diffusive behavior. With a slope-dependent rate of mobilization, the steady state hillslope profile takes on a nonparabolic form where land surface elevation varies with downslope distance x as x(a) with a similar to 3/2, consistent with field observations and where the flux increases nonlinearly with increasing slope. The convolution description of the soil flux, when substituted into a suitable expression of conservation, yields a nonlinear Fokker-Planck equation and can be mapped to discrete particle models of hillslope behavior and descriptions of soil-grain transport by rain splash as a stochastic advection-dispersion process.
Open Access
Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication
(2010) Rapp, Ryan A; Haigler, Candace H; Flagel, Lex; Hovav, Ran H; Udall, Joshua A; Wendel, Jonathan F
Background: Understanding the evolutionary genetics of modern crop phenotypes has a dual relevance to evolutionary biology and crop improvement. Modern upland cotton (Gossypium hirsutum L.) was developed following thousands of years of artificial selection from a wild form, G. hirsutum var. yucatanense, which bears a shorter, sparser, layer of single-celled, ovular trichomes ('fibre'). In order to gain an insight into the nature of the developmental genetic transformations that accompanied domestication and crop improvement, we studied the transcriptomes of cotton fibres from wild and domesticated accessions over a developmental time course. Results: Fibre cells were harvested between 2 and 25 days post-anthesis and encompassed the primary and secondary wall synthesis stages. Using amplified messenger RNA and a custom microarray platform designed to interrogate expression for 40,430 genes, we determined global patterns of expression during fibre development. The fibre transcriptome of domesticated cotton is far more dynamic than that of wild cotton, with over twice as many genes being differentially expressed during development (12,626 versus 5273). Remarkably, a total of 9465 genes were diagnosed as differentially expressed between wild and domesticated fibres when summed across five key developmental time points. Human selection during the initial domestication and subsequent crop improvement has resulted in a biased upregulation of components of the transcriptional network that are important for agronomically advanced fibre, especially in the early stages of development. About 15% of the differentially expressed genes in wild versus domesticated cotton fibre have no homology to the genes in databases. Conclusions: We show that artificial selection during crop domestication can radically alter the transcriptional developmental network of even a single-celled structure, affecting nearly a quarter of the genes in the genome. Gene expression during fibre development within accessions and expression alteration arising from evolutionary change appears to be 'modular' - complex genic networks have been simultaneously and similarly transformed, in a coordinated fashion, as a consequence of human-mediated selection. These results highlight the complex alteration of the global gene expression machinery that resulted from human selection for a longer, stronger and finer fibre, as well as other aspects of fibre physiology that were not consciously selected. We illustrate how the data can be mined for genes that were unwittingly targeted by aboriginal and/or modern domesticators during crop improvement and/or which potentially control the improved qualities of domesticated cotton fibre. See Commentary: http://www.biomedcentral.com/1741-7007/8/137
Open Access
Guyanagaster, a New Wood-Decaying Sequestrate Fungal Genus Related to Armillaria (Physalacriaceae, Agaricales, Basidiomycota)
(2010) Henkel, TW; Smith, ME; Aime, MC
Premise of the study : Sequestrate basidiomycete fungi (e. g. "gasteromycetes") have foregone ballistospory and evolved alternative, often elaborate mechanisms of basidiospore dispersal with highly altered basidioma morphology. Sequestrate fungi have independently evolved in numerous Agaricomycete lineages, confounding taxonomic arrangements of these fungi for decades. Understanding the multiple origins and taxonomic affinities of sequestrate fungi provides insight into the evolutionary forces that can drastically alter basidioma morphology. In the neotropical rainforests of the Guiana Shield, we encountered a remarkable sequestrate fungus fruiting directly on decaying hardwood roots. The fungus 'singular combination of traits include a wood-decaying habit; black, verrucose peridium; reduced stipe; and gelatinized basidiospore mass. Methods : Guyanagaster necrorhiza gen. et sp. nov. is described. Macro-and micromorphological characters were assessed and compared to most similar taxa. To determine the phylogenetic affinities of the fungus, DNA sequence data were obtained for the 18S, ITS, and 28S rDNA, RBP2, and EF1 alpha regions and subjected to single-and multi-gene analyses. DNA sequences from fungal vegetative organs growing on decaying woody roots confirmed the wood-inhabiting lifestyle of Guyanagaster. Key results : Guyanagaster is morphologically unique among sequestrate fungi worldwide. Phylogenetic evidence places Guyanagaster in close relation to the wood-decaying mushroom genus Armillaria in the Physalacriaceae (Agaricales, Agaricomycetes, Basidiomycota). Conclusions : Guyanagaster represents an independently evolved sequestrate form within the Physalacriaceae. Although molecular data confirm that Guyanagaster is closely related to Armillaria, the unusual features of this fungus suggest a case of radically divergent morphological evolution.
Open Access
Logic, passion and the problem of convergence.
(Interface focus, 2017-06) McShea, Daniel W
Our estimate of the likelihood of convergence on human-style intelligence depends on how we understand our various mental capacities. Here I revive David Hume's theory of motivation and action to argue that the most common understanding of the two conventionally recognized components of intelligence-reason and emotion-is confused. We say things like, 'Reason can overcome emotion', but to make this statement meaningful, we are forced to treat reason as a compound notion, as a forced and unhappy mixture of concepts that are incommensurate. An alternative is to parse intelligence in a different way, into two sets of capacities: (i) non-affective capacities, including logic, calculation and problem-solving; (ii) affective capacities, including wants, preferences and cares, along with the emotions. Thus, the question of convergence becomes two questions, one having to do with affective and one with non-affective capacities. What is the likelihood of convergence of these in non-human lineages, in other ecologies, on other worlds? Given certain assumptions, convergence of the non-affective capacities in thinking species seems likely, I argue, while convergence of the affective capacities seems much less likely.
Open Access
Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes
(2010) Hazkani-Covo, Einat; Zeller, Raymond M; Martin, William
The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time.
Open Access
Ordered structure of the transcription network inherited from the yeast whole-genome duplication
(2010) Fusco, Diana; Grassi, Luigi; Bassetti, Bruno; Caselle, Michele; Cosentino Lagomarsino, Marco
Background: Gene duplication, a major evolutionary path to genomic innovation, can occur at the scale of an entire genome. One such "whole-genome duplication" (WGD) event among the Ascomycota fungi gave rise to genes with distinct biological properties compared to small-scale duplications. Results: We studied the evolution of transcriptional interactions of whole-genome duplicates, to understand how they are wired into the yeast regulatory system. Our work combines network analysis and modeling of the large-scale structure of the interactions stemming from the WGD. Conclusions: The results uncover the WGD as a major source for the evolution of a complex interconnected block of transcriptional pathways. The inheritance of interactions among WGD duplicates follows elementary "duplication subgraphs", relating ancestral interactions with newly formed ones. Duplication subgraphs are correlated with their neighbours and give rise to higher order circuits with two elementary properties: newly formed transcriptional pathways remain connected (paths are not broken), and are preferentially cross-connected with ancestral ones. The result is a coherent and connected "WGD-network", where duplication subgraphs are arranged in an astonishingly ordered configuration.
Open Access
Phylogenetic relationships of the enigmatic fern families Hymenophyllopsidaceae and Lophosoriaceae: Evidence from rbcL nucleotide sequences
(Plant Systematics and Evolution, 1999-01-01) Wolf, PG; Sipes, SD; White, MR; Martines, ML; Pryer, KM; Smith, AR; Ueda, K
Nucleotide sequences from rbcL were used to infer relationships of Lophosoriaceae and Hymenophyllopsidaceae. The phylogenetic positions of these two monotypic fern families have been debated, and neither group had been included in recent molecular systematic studies of ferns. Maximum parsimony analysis of our data supported a sister relationship between Lophosoria and Dicksonia, and also between Hymenophyllopsis and Cyathea. Thus, both newly-examined families appear to be part of a previously characterized and well-supported clade of tree ferns. The inferred relationships of Lophosoria are consistent with most (but not all) recent treatments. However, Hymenophyllopsis includes only small delicate plants superficially similar to filmy ferns (Hymenophyllaceae), very different from the large arborescent taxa. Nevertheless, some synapomorphic characteristics are shared with the tree fern clade. Further studies on gametophytes of Hymenophyllopsis are needed to test these hypotheses of relationship.
Open Access
Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.
(Elife, 2016-05-10) Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E
Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast.
Open Access
Purpose in Thermodynamics
(Energies, 2021-01) Bejan, A; Tsatsaronis, G
This is a review of the concepts of purpose, direction, and objective in the discipline of thermodynamics, which is a pillar of physics, natural sciences, life science, and engineering science. Reviewed is the relentless evolution of this discipline toward accounting for evolutionary design with direction, and for establishing the concept of purpose in methodologies of modeling, analysis, teaching, and design optimization. Evolution is change after change toward flow access, with direction in time, and purpose. Evolution does not have an ‘end’. In thermodynamics, purpose is already the defining feature of methods that have emerged to guide and facilitate the generation, distribution, and use of motive power, heating, and cooling: thermodynamic optimization, exergy-based methods (i.e., exergetic, exergoeconomic, and exergoenvironmental analysis), entropy generation minimization, extended exergy, environomics, thermoecology, finite time thermodynamics, pinch analysis, animal design, geophysical flow design, and constructal law. What distinguishes these approaches are the purpose and the performance evaluation used in each method.
Open Access
Social disappointment explains chimpanzees' behaviour in the inequity aversion task.
(Proc Biol Sci, 2017-08-30) Engelmann, Jan M; Clift, Jeremy B; Herrmann, Esther; Tomasello, Michael
Chimpanzees' refusal of less-preferred food when an experimenter has previously provided preferred food to a conspecific has been taken as evidence for a sense of fairness. Here, we present a novel hypothesis-the social disappointment hypothesis-according to which food refusals express chimpanzees' disappointment in the human experimenter for not rewarding them as well as they could have. We tested this hypothesis using a two-by-two design in which food was either distributed by an experimenter or a machine and with a partner present or absent. We found that chimpanzees were more likely to reject food when it was distributed by an experimenter rather than by a machine and that they were not more likely to do so when a partner was present. These results suggest that chimpanzees' refusal of less-preferred food stems from social disappointment in the experimenter and not from a sense of fairness.
Open Access
The gut microbiome of nonhuman primates: Lessons in ecology and evolution.
(American journal of primatology, 2018-06-04) Clayton, Jonathan B; Gomez, Andres; Amato, Katherine; Knights, Dan; Travis, Dominic A; Blekhman, Ran; Knight, Rob; Leigh, Steven; Stumpf, Rebecca; Wolf, Tiffany; Glander, Kenneth E; Cabana, Francis; Johnson, Timothy J
The mammalian gastrointestinal (GI) tract is home to trillions of bacteria that play a substantial role in host metabolism and immunity. While progress has been made in understanding the role that microbial communities play in human health and disease, much less attention has been given to host-associated microbiomes in nonhuman primates (NHPs). Here we review past and current research exploring the gut microbiome of NHPs. First, we summarize methods for characterization of the NHP gut microbiome. Then we discuss variation in gut microbiome composition and function across different NHP taxa. Finally, we highlight how studying the gut microbiome offers new insights into primate nutrition, physiology, and immune system function, as well as enhances our understanding of primate ecology and evolution. Microbiome approaches are useful tools for studying relevant issues in primate ecology. Further study of the gut microbiome of NHPs will offer new insight into primate ecology and evolution as well as human health.

Browsing by Subject "evolution"

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