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69 results for “directed evolution”
Figure 3. A in The evolution of anteriorly directed molar occlusion in mammals
Figure 3. A, reconstructions of muscle orientation that highlight the posited shift to anteriorly directed resultant force vectors in cladotherians. Although early cladotherians did not possess anterior occlusal movement, they did have increased transverse movement that might have been generated by anteriorly oriented muscles (see main text; Grossnickle, 2017). For simplicity, the temporalis is not included in the reconstructions, but it is expected to remain posteriorly oriented in all synapsids (Turnbull, 1970; DeMar & Barghusen, 1972; Lautenschlager et al., 2017). B, the evolution of a posterior angular process and detached middle ear (DME) in cladotherians, but note that the DME evolved independently in multituberculates (not illustrated here) and that there is uncertainty about the evolutionary timing of the DME in the lineage leading to therians (Urban et al., 2017; Luo & Manley, 2020; Mao et al., 2020). For the jaw representing eutriconodontans and spalacotherioids, the middle ear elements are displaced medially from the jaw, but the ossified Meckel's cartilage (MC; yellow) maintains an ear–jaw connection. Skull and jaw reconstructions are based on images in papers by Allin (1975), Sues (1986), Kermack et al. (1981), Krause (1982), Fish (1983), Krebs (1991), Rougier et al. (2003), Kielan-Jaworowska et al. (2004), Hu et al. (2005), Paéz Arango (2008), Wible et al. (2009), Lautenschlager et al. (2017), Bhullar et al. (2019) and Panciroli et al. (2021).
Figure 1 in The evolution of anteriorly directed molar occlusion in mammals
Figure 1. Jaw movement during molar occlusion in a didelphid opossum. The straight red arrows represent movement during the two phases of occlusion (Schwermann, 2014), and the dashed line is the outline of the upper molar. In both the occlusal view (left box) and posterior view (right box), the arrows follow the path of homologous cusps (the protoconids). The 'compass rose' illustrates the occlusal movement in occlusal view, with the lengths of the arrows reflecting the inclination angles of the phase; the shorter arrow represents a steeper, dorsomedial movement, and the longer arrow represents a shallower medial movement (von Koenigswald et al., 2013). We categorize this taxon (Monodelphis) as having an 'anterior component' because at least one of the phases includes anterior movement. Inserting on the jaw are three muscles that contract simultaneously in many therians to create medial movement via yaw (curved red arrow): working-side superficial masseter (SM), working-side medial pterygoid (MP) and balancing-side temporalis (T). The silhouette is by Sarah Werning (license CC BY 3.0, unaltered image).
Figure 2 in The evolution of anteriorly directed molar occlusion in mammals
Figure 2. Jaw directional movement during postcanine occlusion in synapsids, highlighting the evolutionary origin of anteriorly directed occlusion at or near the therian node. Lineage colours correspond to the 'compass rose' directions (see main text; Supporting Information, Table S1), with 'transverse-shearing' represented by black-and-grey dashed lines. For the didelphid, docodontan and ungulate jaws, the left hemimandible is the working side. Ancestral reconstructions of occlusal direction are based, in part, on ancestral molar morphologies. For instance, early therian lineages possess a tribosphenic molar morphology, which generally includes some degree of anterior occlusal movement (Fig. 1; Crompton & Hiiemae, 1970; Kallen & Gans, 1972; Kay & Hiiemae, 1974a; Schwermann, 2014). Lineages along the phylogenetic backbone of the non-mammalian cynodont portion of the phylogeny are likely to have possessed triconodont dentitions, with occlusion that is primarily orthal or 'transverse-shearing' (Crompton, 1972; Bonaparte et al., 2005; Jäger et al., 2019). For additional information and sources, see the Supporting Information (Table S1). The phylogeny and fossil ages are from Rougier et al. (2012), Huttenlocker et al. (2018), Jones et al. (2019), Upham et al. (2019), King & Beck (2020) and the Paleobiology Database (paleobiodb.org). The multituberculate silhouette is based on artwork by Misaki Ouchida. Additional silhouettes are from phylopic.org and attributed to Sarah Werning (licence CC BY 3.0, unaltered image; didelphid), Rebecca Groom (CC BY-SA 3.0; rodent), Dfoidl (CC BY-SA 3.0; ungulate) and FunkMonk Michael B. H. (CC BY-SA 3.0; docodontan).
A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases_NGS data analysis
<p>These data files are associated with the NGS analysis done in the publication :"A translation-independent directed evolution strategy to engineer aminoacyl-tRNA synthetases". This compressed file contains the raw file as well as the processed files to arrive at the conclusions published. The python scripts used for processing the data are available on github (link provided in the manuscript).</p>
Associated data for "Optimisation strategies for directed evolution without sequencing"
<p>Associated publication available at https://www.biorxiv.org/content/10.1101/2024.03.18.585521v1. Code for visualisation available at https://github.com/nesou2/direvo_sim (PLOS_figures/PLOS_figures.ipynb).</p>
Data for: Larval habitats impose trait-dependent limits on the direction and rate of adult evolution in dragonflies
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Data from: Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection
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Data from: Directional selection for flowering time leads to adaptive evolution in Raphanus raphanistrum (Wild radish)
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Data from: Cope’s Rule in a modular organism: directional evolution without an overarching macroevolutionary trend
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Data from: Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: evolution across a continuum of indicator mechanisms
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Evolution of moult-migration is directly linked to aridity of the breeding grounds in North American passerines
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Data from: Phylogeny suggests non-directional and isometric evolution of sexual size dimorphism in argiopine spiders
Sexual dimorphism describes substantial differences between male and female phenotypes. In spiders, sexual dimorphism research almost exclusively focuses on size, and recent studies have recovered steady evolutionary size increases in females, and independent evolutionary size changes in males. Their discordance is due to negative allometric size patterns caused by different selection pressures on male and female size (converse Rensch's rule). Here, we investigated macroevolutionary patterns of sexual size dimorphism (SSD) in Argiopinae, a global lineage of orb weaving spiders with varying degrees of SSD. We devised a Bayesian and maximum likelihood molecular species level phylogeny, then used it to reconstruct sex specific size evolution, to examine general hypotheses and different models of size evolution, to test for sexual size coevolution, and to examine allometric patterns of SSD. Our results, revealing ancestral moderate sizes and SSD, failed to reject the Brownian motion model, which suggests a non-directional size evolution. Contrary to predictions, male and female sizes were phylogenetically correlated, and SSD evolution was isometric. We interpret these results to question the classical explanations of female-biased SSD via fecundity, gravity, and differential mortality. In argiopines, SSD evolution may be driven by these or additional selection mechanisms, but perhaps at different phylogenetic scales.
Data from: Pervasive genetic integration directs the evolution of human skull shape
It has long been unclear whether the different derived cranial traits of modern humans evolved independently in response to separate selection pressures or whether they resulted from the inherent morphological integration throughout the skull. In a novel approach to this issue, we combine evolutionary quantitative genetics and geometric morphometrics to analyze genetic and phenotypic integration in human skull shape. We measured human skulls in the ossuary of Hallstatt (Austria), which offer a unique opportunity because they are associated with genealogical data. Our results indicate pronounced covariation of traits throughout the skull. Separate simulations of selection for localized shape changes corresponding to some of the principal derived characters of modern human skulls produced outcomes that were similar to each other and involved a joint response in all of these traits. The data for both genetic and phenotypic shape variation were not consistent with the hypothesis that the face, cranial base and cranial vault are completely independent modules but relatively strongly integrated structures. These results indicate pervasive integration in the human skull and suggest a reinterpretation of the selective scenario for human evolution where the origin of any one of the derived characters may have facilitated the evolution of the others.
Data from: Directional selection in the evolution of elongated upper canines in clouded leopards and sabre-toothed cats
Extremely developed or specialised traits such as the elongated upper canines of extinct sabre-toothed cats are often not analogous to those of any extant species, which limits our understanding of their evolutionary cause. However, an extant species may have undergone directional selection for a similar extreme phenotype. Among living felids, the clouded leopard, Neofelis nebulosa, has exceptionally long upper canines for its body size. We hypothesised that directional selection generated the elongated upper canines of clouded leopards in a manner similar to the process in extinct sabre-toothed cats. To test this, we developed an approach that compared the effect of directional selection among lineages in a phylogeny using a simulation of trait evolution and approximate Bayesian computation. This approach was applied to analyse the evolution of upper canine length in the Felidae phylogeny. Our analyses consistently showed directional selection favouring longer upper canines in the clouded leopard lineage and a lineage leading to the sabre-toothed cat with the longest upper canines, Smilodon. Most of our analyses detected an effect of directional selection for longer upper canines in the lineage leading to another sabre-toothed cat, Homotherium, although this selection may have occurred exclusively in the primitive species. In all the analyses, the clouded leopard and Smilodon lineages showed comparable directional selection. This implies that clouded leopards share a selection advantage with sabre-toothed cats in having elongated upper canines.
The role of common ancestry and gene flow in the evolution of human-directed play behavior in dogs
<p><span>Among-population variance of phenotypic traits is of high relevance for understanding evolutionary mechanisms that operate in relatively short timescales, but various sources of non-independence, such as common ancestry and gene flow can hamper the interpretations. In this comparative analysis of 138 dog breeds, we demonstrate how such confounders can independently shape the evolution of a behavioral trait (human-directed play behavior from the Dog Mentality Assessment project). We combined information on genetic relatedness and haplotype sharing to reflect common ancestry and gene flow, respectively, and entered these into a phylogenetic mixed model to partition the among-breed variance of human-directed play behavior while also accounting for within-breed variance. We found that 75% of the among-breed variance was explained by overall genetic relatedness among breeds, while 15% could be attributed to haplotype sharing that arises from gene flow. Therefore, most of the differences in human-directed play behavior among breeds have likely been caused by constraints of common ancestry as a likely consequence of past selection regimes. On the other hand, gene flow caused by crosses among breeds has played a minor, but not negligible role. Our study serves as an example of an analytical approach that can be applied to comparative situations where the effects of shared origin and gene flow require quantification and appropriate statistical control in a within-species/among-population framework. Altogether, our results suggest that the evolutionary history of dog breeds have left remarkable signatures on the among-breed variation of a behavioral phenotype.</span></p>
Data from: Directional selection can drive the evolution of modularity in complex traits
Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.
Dataset for "Equatorial evolution of the fast magnetosonic mode in the source region: Observation-simulation comparison of the preferential propagation direction"
<p>Includes 2D PIC simulation results presented in the paper.</p>
[DATA] The co-evolution of direct, indirect and generalized reciprocity
<p>The data for the project <em>"The Co-evolution of Direct, Indirect, and Generalized Reciprocity"</em> were generated through simulation code that models evolutionary processes. These data can be used to create all the figures in the manuscript.</p> <p>The code for the evolutionary simulations as well as the analysis code are available on GitHub. The repository can be found here: https://github.com/Saptarshi07/Direct-Indirect-Generalized-Reciprocity/.</p> <div> </div>
The role of common ancestry and gene flow in the evolution of human-directed play behavior in dogs
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Data from: A nonstationary Markov model detects directional evolution in hymenopteran morphology
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