Integrating Horizontal Gene Transfer and Common Descent to Depict Evolution and Contrast It with “Common Design”¹

Abstract

Horizontal gene transfer (HGT) and common descent interact in space and time. Because events of HGT co-occur with phylogenetic evolution, it is difficult to depict evolutionary patterns graphically. Tree-like representations of life’s diversification are useful, but they ignore the significance of HGT in evolutionary history, particularly of unicellular organisms, ancestors of multicellular life. Here we integrate the reticulated-tree model, ring of life, symbiogenesis whole-organism model, and eliminative pattern pluralism to represent evolution. Using Entamoeba histolytica alcohol dehydrogenase 2 (EhADH2), a bifunctional enzyme in the glycolytic pathway of amoeba, we illustrate how EhADH2 could be the product of both horizontally acquired features from ancestral prokaryotes (i.e. aldehyde dehydrogenase [ALDH] and alcohol dehydrogenase [ADH]), and subsequent functional integration of these enzymes into EhADH2, which is now inherited by amoeba via common descent. Natural selection has driven the evolution of EhADH2 active sites, which require specific amino acids (cysteine 252 in the ALDH domain; histidine 754 in the ADH domain), iron- and NAD+ as cofactors, and the substrates acetyl-CoA for ALDH and acetaldehyde for ADH. Alternative views invoking “common design” (i.e. the non-naturalistic emergence of major taxa independent from ancestry) to explain the interaction between horizontal and vertical evolution are unfounded.

Evidence of taxa-, clone-, and kin-discrimination in protists: ecological and evolutionary implications

“…In such a large, polyphyletic group of unicellular eukaryotes, convergence in trait acquisition for discrimination ability, combined with ubiquitous horizontal gene transfer (HGT), must be common (Paz-y-Miño-C and Espinosa 2010; Bruto et al 2013). …”

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

“…2), can be inferred from genomic analyses within (paralogous gene families) and between taxonomic lineages (orthologous gene families); (4) comparative DNA and amino-acid sequence analyses (e.g., Homo vs. Rattus vs. Mus vs. Drosophila vs. Caenorhabditis vs. Paramecium vs. Escherichia vs. Arabidopsis; Doyle et al 1998; Shealy et al 2003) reveal classical Darwinian patterns of ion-channel evolution via cumulative single-nucleotide mutations, gene duplications and fusions, and protein-domain junctions; and (5) neuronal networks, ganglia activity, and brain functions depend on ion-channels for sensitivity (i.e., touch/pressure/vibration, sound, light, chemosignals/odor, and electric fields) and electrical transmission of stimuli, motor (neuromuscular junction for voluntary or reflex movement) or excretory response (neuro-endocrine stimulation), behavior, and consciousness (Galliot et al 2009; Kress and Mennerick 2009; Miller 2009). Thus, the ubiquitous inclusion of ion channels in significant empirical and practical aspects of the biology and health-related careers' curricula makes them unique didactic tools for communicating evolutionary principles to all audiences, and promoting evolution literacy (innovation in science education has been prioritized by authors concerned with the misleading role of “design creationism” in public-outreach campaigns; Paz-y-Miño C. and Espinosa 2009a, b; Paz-y-Miño C. and Espinosa 2010a, b, c). …”

“…This logic has been dismissed by researchers (Schneider 2000; Pennock 2001; Long et al 2003; Young and Edis 2004; Lynch 2005; Forrest and Gross 2007; Petto and Godfrey 2007; Durrett and Schmidt 2008, 2009; Schneiderman and Allmon 2009; Paz-y-Miño C. and Espinosa 2010a) and journal editors (Hermodson 2005) based on fundamental evolutionary premises: (1) large variation in mutation rate between and within lineages, and/or protein sites, is susceptible to positive selection; (2) protein-site mutagenesis is associated with mutation and acceptance rates at multiple sites in a genome (= compensatory changes); (3) new protein functions after domain junction can experience faster evolution (e.g., fused genes); and (4) selection acts continuously and cumulatively (= “editing role”) on intermediate protein forms, increasing and maintaining molecular diversity, and expediting molecular evolution. Thus, single emergence of primordial genetic sequences or protein-adaptive change from “design creationism” is highly improbable.…”

Educators of Prospective Teachers Hesitate to Embrace Evolution Due to Deficient Understanding of Science/Evolution and High Religiosity

“…In conceptually mistaken, type-I-error-based arguments to discredit evolution, ID has attributed randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time or population size for molecular improvements to occur, and invoked “design intervention” to account for complexity in molecular structures and biological processes (Paz-y-Miño-C and Espinosa 2010; Paz-y-Miño-C et al 2011). In 2005, ID was exposed in court (Dover, Pennsylvania, Kitzmiller et al versus Dover School District et al 2005; Padian and Matzke 2009; Wexler 2010) for violating the rules of science by “invoking and permitting supernatural causation” in matters of evolution, and for “failing to gain acceptance in the scientific community.” Today, “design creationism” (as we refer to ID due to its designer/creator-based foundations; Pennock 2001; Paz-y-Miño-C and Espinosa 2010, 2011b; Paz-y-Miño-C et al 2011) although defeated by science and in the courts, grows influential in the U.S., Europe, Australia and South America (Cornish-Bowden and Cárdenas 2007; Padian 2009; Branch et al 2010; Forrest 2010; Matzke 2010; Wexler 2010). …”