Evolution Commons^™

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

Size Estimates Of The Extinct Marine Snake Pterosphenus Schucherti From Eocene-Aged Sediments Of Central Georgia, Colin J. Calvert, Alfred J. Mead, Dennis Parmley

Georgia Journal of Science

Fossil snakes are most often identified from isolated vertebrae, complicating estimations of total body lengths of extinct taxa. Here we estimate the range of total body length of the late Eocene North American palaeophiid marine snake Pterosphenus schucherti based on 29 recently collected fossil vertebrae from Wilkinson County, Georgia, USA. Previous research suggests that the palaeophiids are most closely related to modern boids. Total body length estimates here are based on family-specific regressions of centrum length versus known total body length in extant members of Boidae, Pythonidae, and Colubridae. The high correlation coefficients for the family specific regressions supports previous …

Alfred Russel Wallace Notes 19: Social Evolution's Useful Idiots, Charles H. Smith

Faculty/Staff Personal Papers

In today’s world liberals look at conservatives as the villains, and vice versa. How did this come to pass? In this essay a model of the biological roots of liberalism and conservatism is advanced; this is followed by a discussion of why cognitive dissonance may represent the key process in our social evolution. Alfred Russel Wallace’s experience with cognitive dissonance is then detailed, including how he dealt with it.

Editorial: Ecology, Metabolism And Evolution Of Archaea-Perspectives From Proceedings Of The International Workshop On Geo-Omics Of Archaea, Brian P. Hedlund, Chuanlun Zhang, Fengping Wang, Christian Rinke, William F. Martin

Life Sciences Faculty Research

To facilitate global efforts in addressing fundamental questions related to the biology of archaea, an international consortium of experts organized the International Workshop on Geo-Omics of Archaea (IWGOA), with the overarching themes of Ecology/Biogeochemistry, Metabolism, and Evolution. The IWGOA was held in Shenzhen, China, from October 25th to 27th, 2019. The meeting was attended by more than 200 attendees from China, Japan, USA, Australia, Germany, and France. Some of the most exciting oral and poster presentations made at the IWGOA are celebrated in this Research Topic Figure 1. The 21 manuscripts herein span different aspects of archaeal biology in both …

Ethical, Legal, And Social Issues In The Earth Biogenome Project, Jacob S. Sherkow, Katharine B. Barker, Irus Braverman, Robert Cook-Deegan, Richard Durbin, Carla L. Easter, Melissa M. Goldstein, Maui Hudson, W. John Kress, Harris A. Lewin, Debra J. H. Mathews, Catherine Mccarthy, Ann M. Mccartney, Manuela Da Silva, Andrew W. Torrance, Henry T. Greely

Journal Articles

The Earth BioGenome Project (EBP) is an audacious endeavor to obtain whole-genome sequences of representatives from all eukaryotic species on Earth. In addition to the project’s technical and organizational challenges, it also faces complicated ethical, legal, and social issues. This paper, from members of the EBP’s Ethical, Legal, and Social Issues (ELSI) Committee, catalogs these ELSI concerns arising from EBP. These include legal issues, such as sample collection and permitting; the applicability of international treaties, such as the Convention on Biological Diversity and the Nagoya Protocol; intellectual property; sample accessioning; and biosecurity and ethical issues, such as sampling from the …

Observations On Regeneration Of The Pedipalp And Legs Of Scorpions, Martin Watz, Jason A. Dunlop

Euscorpius

An Opisthacanthus asper (Peters, 1861) (Hormuridae) shows a relatively rare example of pedipalp regeneration in which the lost tibia and tarsus was replaced by a smaller, curved element of uncertain homology to either the fixed or free finger. A comparable abnormal palp described in the literature hints that pedipalps can only regenerate a structure of this form, regardless of the site of amputation. An Olivierus caucasicus (Nordmann, 1840) (Buthidae) is described in which claws (pretarsus) of leg III regenerated directly at the distal end of the tibia, while in leg IV the claws regenerated at the end of a truncated …

Evolutionary Analyses Of Visual Opsin Genes In Frogs And Toads: Diversity, Duplication, And Positive Selection, Ryan K. Schott, Leah Perez, Matthew Kwiatkowski, Vance Imhoff, Jennifer M. Gumm

Faculty Publications

Among major vertebrate groups, anurans (frogs and toads) are understudied with regard to their visual systems, and little is known about variation among species that differ in ecology. We sampled North American anurans representing diverse evolutionary and life histories that likely possess visual systems adapted to meet different ecological needs. Using standard molecular techniques, visual opsin genes, which encode the protein component of visual pigments, were obtained from anuran retinas. Additionally, we extracted the visual opsins from publicly available genome and transcriptome assemblies, further increasing the phylogenetic and ecological diversity of our dataset to 33 species in total. We found …

Morphological Variation And Community Science In Orthoptera, Amy Byerly

Electronic Theses and Dissertations

Patterns of morphological divergence across species’ ranges provide insight into local adaptation and speciation. Here, we compare phenotypic divergence among 4,221 crickets from 337 populations of two related species of field cricket, Gryllus firmus and G. pennsylvanicus and their hybrids. We find that these species differ across their geographic range in key morphological traits, such as body size and ovipositor length, and we directly compare phenotype with genotype for a subset of crickets demonstrating nuclear genetic introgression, phenotypic intermediacy of hybrids, and essentially unidirectional mitochondrial introgression. We discuss how these morphological traits relate to life history differences between the species. …

Pain Sentience Criteria And Their Grading, Eva Jablonka, Simona Ginsburg

Animal Sentience

On the basis of the target article by Crump and colleagues, we suggest a more parsimonious scheme for evaluating the evidence for sentience. Since some of the criteria used by Crump et al. are not independent and some are uninformative we exclude some criteria and amalgamate others. We propose that evidence of flexible learning and prioritization, in conjunction with relevant data on brain organization, is sufficient for assigning pain-sentience to an animal and we suggest a scoring scheme based on four criteria.

Truly Minimal Criteria For Animal Sentience, Mark Solms

Animal Sentience

The criteria for determining animal sentience proposed in the target article are sensible but they lack an explicit functional justification for the focus on pain. This commentary provides an abbreviated account of the most basic functional principles that underpin animal sentience and articulates some minimal criteria for determining its presence.

Generalizing Frameworks For Sentience Beyond Natural Species, Michael Levin

Animal Sentience

Crump et al. (2022) offer a well-argued example of an essential development: a rigorous framework for assessing sentience from the perspective of moral concern over an agent’s welfare. Current and forthcoming developments in bioengineering, synthetic morphology, artificial intelligence, biorobotics, and exobiology necessitate an expansion and generalization of this effort. Verbal reports (the Turing Test) and homology to human brains are utterly inadequate criteria for assessing the status of novel, unconventional agents that offer no familiar touchstone of phylogeny or anatomy. We must develop principled approaches to evaluating the sentience of (and thus, our responsibility to) beings of unfamiliar provenance and …

Sentience In Decapods: An Open Question, Mark Briffa

Animal Sentience

Crump et al.’s framework is a powerful tool designed to assist decisions on the ethical treatment of decapod crustaceans. However, the question of whether decapods are sentient (i.e., whether they feel), remains open, perhaps indefinitely. More optimistically, we might design experiments that distinguish among different levels of awareness, sometimes viewed as components of sentience. We should strike a balance between assuming that all organisms are sentient and making unnecessary anatomical assumptions about sentience. Refining current experiments may provide concrete insights about awareness in Decapoda and other taxa.

Does The Sentience Framework Imply All Animals Are Sentient?, Kristin Andrews

Animal Sentience

The eight criteria proposed in Crump et al.’s framework for evaluating pain sentience in decapod crustaceans are just the tip of the iceberg when it comes to markers that could increase confidence in an animal’s sentience more generally. Some of the commentaries have already pointed out that pain is only one kind of sentience (Souza Valente). It has also already been pointed out that there are other criteria for pain that could be usefully added to the framework’s eight (Burrell). This expansive thinking about criteria that can be used to increase confidence in sentience raisess the question: in an expansive …

Distinguishing Epistemic And Moral Grounds For Legal Protection, Carlos Montemayor

Animal Sentience

The criteria proposed by Crump et al. are based on various cognitive roles associated with sentience. A subset of them may be sufficient for certain kinds of welfare, but the presence of all of them should be considered as clearly sufficient for substantial kinds of legal protection based on their relation to capacities that we consider essential for moral standing in human beings.

How Deep Do We Have To Go To Rehabilitate Evolutionary Psychology? Reply To Bjorklund, Ellis, & Geary (2022), David S. Moore, David C. Witherington, Darcia Narvaez, Timothy I. Vandiver, Robert Lickliter

Pitzer Faculty Publications and Research

Disciplines like evolutionary-developmental psychology admirably focus on trying to rehabilitate Narrow Evolutionary Psychology (NEP) from within, by adding a developmental focus to NEP’s tenets of adaptationism and computationalism. We argue, however, that these tenets are fundamentally incompatible with taking psychology and its development seriously, and that the kinds of modifications introduced by evolutionary-developmental psychologists do not go deep enough to qualitatively change the non-developmental outlook of NEP.

Evolving Evolutionary Psychology, Darcia Narvaez, David S. Moore, David C. Witherington, Timothy I. Vandiver, Robert Lickliter

Pitzer Faculty Publications and Research

Which evolutionary theory can best benefit psychological theory, research, and application? The most well-known school of evolutionary psychology has a narrow conceptual perspective (a.k.a., “Narrow Evolutionary Psychology” or NEP). Proponents of NEP have long argued that their brand of evolutionary psychology represents a full-fledged scientific revolution, with Buss (2020) recently likening NEP’s scientific impact to that of a Copernican or Darwinian paradigm shift. However, NEP stands on two traditions that are now the subjects of serious debate and revision: the neo-Darwinian adaptationist framework within evolutionary biology, and the computationalist “mind-as-computer” framework within cognitive science. Although NEP calls itself revolutionary, the …

Proteome Database, Mariana Rius, Jackie L. Collier, Joshua Rest

SoMAS Research Data

No abstract provided.

Seasonal Reproductive Allocation In Landlocked Alewife Alosa Pseudoharengus, In The Context Of Niche Construction And Eco-Evolutionary Feedbacks, Foivos Mouchlianitis, Eric T. Schultz, Kostas Ganias

EEB Articles

The bidirectional dynamics between species and their biotic and abiotic environments, known as eco-evolutionary feedbacks, may shift the direction of evolution and alter the ecological role of species. Alewife, Alosa pseudoharengus, is an exemplary species to study reciprocal feedbacks between ecology and evolution, owing to repeated independent derivations of a landlocked life history from an ancestral anadromous form. In this study we analysed the reproductive allocation during the spawning season in a landlocked Alewife population in the context of eco-evolutionary feedbacks. We also compared our findings with previous results from a neighbouring anadromous population of the species. Similarities were found …

Pain In Pleocyemata, But Not In Dendrobranchiata?, Gary Comstock

Animal Sentience

Crump et al.’s contribution to assessing whether decapods feel pain raises an important question: Is pain distributed unevenly across the order? The case for pain appears stronger in Pleocyemata than in Dendrobranchiata. Some studies report pain avoidance behaviors in Dendrobranchiata (Penaeidae) shrimp, but further studies are needed to determine whether the chemicals used are acting as analgesics to relieve pain, or as soporifics to reduce overall alertness. If the latter, the most farmed shrimp species may not require the same level of protection as crabs, crayfish, and lobsters.

Sentience As Part Of Emotional Lives, Frans B. M. De Waal

Animal Sentience

It is high time to explore the sentience of invertebrate animals, but this topic cannot be discussed without also exploring their emotional lives, including positive emotions. Sentience probably evolved to allow the regulation of emotions by endowing them with feelings.