scholarly journals Are our phylomorphospace plots so terribly tangled? An investigation of disorder in data simulated under adaptive and nonadaptive models

2020 ◽  
Vol 66 (5) ◽  
pp. 565-574
Author(s):  
C Tristan Stayton
Keyword(s):  
Brownian Motion ◽  
Character Displacement ◽  
Tree Of Life ◽  
Tree Size ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Developmental Constraint ◽  
Simulated Evolution ◽  
Varying Parameters ◽  
Deterministic Processes

Abstract Contemporary methods for visualizing phenotypic evolution, such as phylomorphospaces, often reveal patterns which depart strongly from a naïve expectation of consistently divergent branching and expansion. Instead, branches regularly crisscross as convergence, reversals, or other forms of homoplasy occur, forming patterns described as “birds’ nests”, “flies in vials”, or less elegantly, “a mess”. In other words, the phenotypic tree of life often appears highly tangled. Various explanations are given for this, such as differential degrees of developmental constraint, adaptation, or lack of adaptation. However, null expectations for the magnitude of disorder or “tangling” have never been established, so it is unclear which or even whether various evolutionary factors are required to explain messy patterns of evolution. I simulated evolution along phylogenies under a number of varying parameters (number of taxa and number of traits) and models (Brownian motion, Ornstein–Uhlenbeck (OU)-based, early burst, and character displacement (CD)] and quantified disorder using 2 measures. All models produce substantial amounts of disorder. Disorder increases with tree size and the number of phenotypic traits. OU models produced the largest amounts of disorder—adaptive peaks influence lineages to evolve within restricted areas, with concomitant increases in crossing of branches and density of evolution. Large early changes in trait values can be important in minimizing disorder. CD consistently produced trees with low (but not absent) disorder. Overall, neither constraints nor a lack of adaptation is required to explain messy phylomorphospaces—both stochastic and deterministic processes can act to produce the tantalizingly tangled phenotypic tree of life.

scholarly journals Impact of transition to a subterranean lifestyle on morphological disparity and integration in talpid moles (Mammalia, Talpidae)

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Gabriele Sansalone ◽  
Paolo Colangelo ◽  
Anna Loy ◽  
Pasquale Raia ◽  
Stephen Wroe ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Morphological Variability ◽  
Phenotypic Integration ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Morphological Disparity ◽  
Morphological Diversification ◽  
Phylogenetic Conservatism ◽  
Selective Forces ◽  
Subterranean Species

Abstract Background Understanding the mechanisms promoting or constraining morphological diversification within clades is a central topic in evolutionary biology. Ecological transitions are of particular interest because of their influence upon the selective forces and factors involved in phenotypic evolution. Here we focused on the humerus and mandibles of talpid moles to test whether the transition to the subterranean lifestyle impacted morphological disparity and phenotypic traits covariation between these two structures. Results Our results indicate non-subterranean species occupy a significantly larger portion of the talpid moles morphospace. However, there is no difference between subterranean and non-subterranean moles in terms of the strength and direction of phenotypic integration. Conclusions Our study shows that the transition to a subterranean lifestyle significantly reduced morphological variability in talpid moles. However, this reduced disparity was not accompanied by changes in the pattern of traits covariation between the humerus and the mandible, suggesting the presence of strong phylogenetic conservatism within this pattern.

scholarly journals Phenotypic evolution is more constrained in simpler food webs

2019 ◽  
Author(s):  
Matthew A. Barbour ◽  
Christopher J. Greyson-Gaito ◽  
Arezoo Sootodeh ◽  
Brendan Locke ◽  
Jordi Bascompte
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Ecological Networks ◽  
Community Context ◽  
Relative Fitness ◽  
Adaptive Landscape ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Adaptive Landscapes ◽  
Food Web Complexity

AbstractGlobal change is simplifying the structure of ecological networks; however, we are currently in a poor position to predict how these simplified communities will affect the evolutionary potential of remaining populations. Theory on adaptive landscapes provides a framework for predicting how selection constrains phenotypic evolution, but often treats the community context of evolving populations as a “black box”. Here, we integrate ecological networks and adaptive landscapes to examine how changes in food-web complexity shape evolutionary constraints. We conducted a field experiment that manipulated the diversity of insect parasitoids (food-web complexity) that were able to impose selection on an insect herbivore. We then measured herbivore survival as a function of three key phenotypic traits. We found that more traits were under selection in simpler vs. more complex food webs. The adaptive landscape was more neutral in complex food webs because different parasitoid species impose different selection pressures, minimizing relative fitness differences among phenotypes. Our results suggest that phenotypic evolution becomes more constrained in simplified food webs. This indicates that the simplification of ecological communities may constrain the adaptive potential of remaining populations to future environmental change. “What escapes the eye, however, is a much more insidious kind of extinction: the extinction of ecological interactions.” Janzen (1974)

scholarly journals Phenotype-limited distributions: short-billed birds move away during times that prey bury deeply

2015 ◽  
Vol 2 (6) ◽  
pp. 150073 ◽  
Author(s):  
Sjoerd Duijns ◽  
Jan A. van Gils ◽  
Jennifer Smart ◽  
Theunis Piersma
Keyword(s):  
Breeding Season ◽  
Resource Use ◽  
Environmental Conditions ◽  
Wadden Sea ◽  
Phenotypic Traits ◽  
Sexually Dimorphic ◽  
Phenotypic Evolution ◽  
Main Prey ◽  
Limited Distribution ◽  
Widespread Phenomenon

In our seasonal world, animals face a variety of environmental conditions in the course of the year. To cope with such seasonality, animals may be phenotypically flexible, but some phenotypic traits are fixed. If fixed phenotypic traits are functionally linked to resource use, then animals should redistribute in response to seasonally changing resources, leading to a ‘phenotype-limited’ distribution. Here, we examine this possibility for a shorebird, the bar-tailed godwit ( Limosa lapponica ; a long-billed and sexually dimorphic shorebird), that has to reach buried prey with a probing bill of fixed length. The main prey of female bar-tailed godwits is buried deeper in winter than in summer. Using sightings of individually marked females, we found that in winter only longer-billed individuals remained in the Dutch Wadden Sea, while the shorter-billed individuals moved away to an estuary with a more benign climate such as the Wash. Although longer-billed individuals have the widest range of options in winter and could therefore be selected for, counterselection may occur during the breeding season on the tundra, where surface-living prey may be captured more easily with shorter bills. Phenotype-limited distributions could be a widespread phenomenon and, when associated with assortative migration and mating, it may act as a precursor of phenotypic evolution.

scholarly journals The probability of genetic parallelism and convergence in natural populations

2012 ◽  
Vol 279 (1749) ◽  
pp. 5039-5047 ◽  
Author(s):  
Gina L. Conte ◽  
Matthew E. Arnegard ◽  
Catherine L. Peichel ◽  
Dolph Schluter
Keyword(s):  
Adaptive Evolution ◽  
Natural Populations ◽  
Small Subset ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Genomic Studies ◽  
Genetic Level ◽  
Candidate Gene Studies ◽  
Different Populations ◽  
Using Data

Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.

scholarly journals Testing the neutral hypothesis of phenotypic evolution

2017 ◽  
Vol 114 (46) ◽  
pp. 12219-12224 ◽  
Author(s):  
Wei-Chin Ho ◽  
Yoshikazu Ohya ◽  
Jianzhi Zhang
Keyword(s):  
Morphological Traits ◽  
Genetic Model ◽  
Morphological Evolution ◽  
Model Organisms ◽  
Functional Genes ◽  
Phenotypic Traits ◽  
Phenotypic Evolution ◽  
Important Principle ◽  
Phenotypic Variations ◽  
Evolution By Natural Selection

Although evolution by natural selection is widely regarded as the most important principle of biology, it is unknown whether phenotypic variations within and between species are mostly adaptive or neutral due to the lack of relevant studies of large, unbiased samples of phenotypic traits. Here, we examine 210 yeast morphological traits chosen because of experimental feasibility irrespective of their potential adaptive values. Our analysis is based on the premise that, under neutrality, the rate of phenotypic evolution measured in the unit of mutational size declines as the trait becomes more important to fitness, analogous to the neutral paradigm that functional genes evolve more slowly than functionless pseudogenes. However, we find faster evolution of more important morphological traits within and between species, rejecting the neutral hypothesis. By contrast, an analysis of 3,466 gene expression traits fails to refute neutrality. Thus, at least in yeast, morphological evolution appears largely adaptive, but the same may not apply to other classes of phenotypes. Our neutrality test is applicable to other species, especially genetic model organisms, for which estimations of mutational size and trait importance are relatively straightforward.

scholarly journals Is the blunderbuss a misleading visual metaphor for stasis and punctuated evolution?

2018 ◽  
Author(s):  
John T. Waller
Keyword(s):  
Brownian Motion ◽  
Phenotypic Evolution ◽  
Visual Metaphor ◽  
Phenotypic Divergence ◽  
Original Analysis ◽  
Influential Paper ◽  
Punctuated Evolution

AbstractI discuss the usefulness of the so-called “blunderbuss pattern” of phenotypic evolution as a visual metaphor for stasis and punctuated evolution that was originally put forward in Uyeda et al. (2011) in their highly influential paper “The million-year wait for macroevolutionary bursts”. I argue the blunderbuss pattern is not surprising, and in some cases it is misleading. I review several publications that cite Uyeda et al. (2011) that seem to be confused about the meaning of the pattern and what it implies. I do not critique the original analysis within Uyeda et al (2011), but show the blunderbuss pattern itself would be produced even when assuming a Brownian motion (completely gradual) model of phenotypic divergence. Finally, I discuss how the interesting results of the paper have been overlooked in favor of the surprisingly powerful, but also misleading visual metaphor of the blunderbuss.

scholarly journals Morphology, Ecology, and Biogeography of Independent Origins of Cleaning Behavior Around the World

2019 ◽  
Vol 59 (3) ◽  
pp. 625-637 ◽  
Author(s):  
Vikram B Baliga ◽  
Rita S Mehta
Keyword(s):  
Body Shape ◽  
Morphological Evolution ◽  
Small Body ◽  
Character Displacement ◽  
Phenotypic Evolution ◽  
Ecological Specialization ◽  
Selective Pressures ◽  
Cleaning Behavior ◽  
Marine Habitats ◽  
The Caribbean

Abstract Members of an ecological guild may be anticipated to show morphological convergence, as similar functional demands exert similar selective pressures on phenotypes. Nature is rife with examples, however, where such taxa instead exhibit ‘incomplete’ convergence or even divergence. Incorporating factors such as character displacement by other guild members or variation in ecological specialization itself may therefore be necessary to gain a more complete understanding of what constrains or promotes diversity. Cleaning, a behavior in which species remove and consume ectoparasites from “clientele,” has been shown to exhibit variation in specialization and has evolved in a variety of marine habitats around the globe. To determine the extent to which specialization in this tropic strategy has affected phenotypic evolution, we examined the evolution of cleaning behavior in five marine fish families: Labridae, Gobiidae, Pomacanthidae, Pomacentridae, and Embiotocidae. We used a comparative framework to determine patterns of convergence and divergence in body shape and size across non-cleaning and cleaning members within these five clades. Highly specialized obligate cleaning, found in the Indo-Pacific and the Caribbean, evolved in the Labridae and Gobiidae at strikingly similar times. In these two regions, obligate cleaning evolves early, shows convergence on an elongate body shape, and is restricted to species of small body size. Facultative cleaning, shown either throughout ontogeny or predominately in the juvenile phase, exhibits a much more varied phenotype, especially in geographic regions where obligate cleaning occurs. Collectively, our results are consistent with varying extents of an ecological specialization constraining or spurring morphological evolution in recurrent ways across regions.

scholarly journals Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer

2019 ◽  
Vol 37 (2) ◽  
pp. 475-487 ◽  
Author(s):  
Dagmar Frisch ◽  
Dörthe Becker ◽  
Marcin W Wojewodzic
Keyword(s):  
Gene Networks ◽  
Fine Tuning ◽  
Transcriptional Networks ◽  
Phenotypic Traits ◽  
P Availability ◽  
Phenotypic Evolution ◽  
Before And After ◽  
Coexpression Networks ◽  
Phenotypic Responses ◽  
Genomic Model

Abstract Knowledge of the molecular basis of phenotypic responses to environmental cues is key to understanding the process of adaptation. Insights to adaptation at an evolutionary time scale can be gained by observing organismal responses before and after a shift in environmental conditions, but such observations can rarely be made. Using the ecological and genomic model Daphnia, we linked transcriptomic responses and phosphorus (P)-related phenotypic traits under high and low P availability. We mapped weighted gene coexpression networks to traits previously assessed in resurrected ancient (600 years old) and modern Daphnia pulicaria from a lake with a historic shift in P-enrichment. Subsequently, we assessed evolutionary conservation or divergence in transcriptional networks of the same isolates. We discovered highly preserved gene networks shared between ancient genotypes and their modern descendants, but also detected clear evidence of transcriptional divergence between these evolutionarily separated genotypes. Our study highlights that phenotypic evolution is a result of molecular fine-tuning on different layers ranging from basic cellular responses to higher order phenotypes. In a broader context, these findings advance our understanding how populations are able to persist throughout major environmental shifts.

scholarly journals Enriching for orthologs increases support for Xenacoelomorpha and Ambulacraria sister relationship

2021 ◽  
Author(s):  
Peter O Mulhair ◽  
Charley GP McCarthey ◽  
Karen Siu-Ting ◽  
Christopher J Creevey ◽  
Mary J O'Connell
Keyword(s):  
Tree Of Life ◽  
Quality Data ◽  
Phenotypic Traits ◽  
Gene Trees ◽  
Sister Relationship ◽  
Alternative Placement

Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum, or within Deuterostomia, sister to Ambulacraria. While their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral Bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. More recently, further studies have brought into question whether Deuterostomia should be considered monophyletic at all. Hidden paralogy presents a major challenge for reconstructing species phylogenies. Here we assess whether hidden paralogy has contributed to the conflict over the placement of Xenacoelomorpha. Our approach assesses previously published datasets, enriching for orthogroups whose gene trees support well resolved clans elsewhere in the animal tree of life. We find that the majority of constituent genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy is rife at this depth. We demonstrate that enrichment for genes with orthologous signal alters the final topology that is inferred, whilst simultaneously improving fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our orthology enriched set of genes. At a time when we are steadily progressing towards sequencing all of life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modelled adequately.

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