Genomics and the Evolution of Phenotypic Traits

Abstract

Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions. 8.1

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…Identifying the genetic basis of specific traits is a major challenge, even in model species (Vasemägi and Primmer, 2005;Barrett and Hoekstra, 2011;Wray, 2013), and promising approaches to achieve this ambitious goal combine information from the fields of population genomics and quantitative genetics (Stinchcombe and Hoekstra, 2008). While several attributes of marine fishes render these species suitable for population genomic studies in natural populations (as reviewed in previous sections), the large effective population sizes indicate that family-based quantitative genetic approaches in natural populations (Slate, 2005;Schielzeth and Husby, 2014) may not be successful.…”

Understanding the molecular basis of adaptation to freshwater environments by prawns in the genus Macrobrachium

“…In addition, decapod crustaceans also appear particularly suitable for investigating life history adaptation to freshwater because none of the freshwater adapted taxa have apparently ever reinvaded the environment of origin (Wray, 2013). This is because there has been insufficient time for evolution back to a marine lifestyle (Vogt, 2013), suggesting that i) they are relatively recent colonizers to freshwater and ii) many taxa are likely to still be in the process of adapting to freshwater.…”

“…Invasion of freshwater can involve a multiplicity of complex adaptive responses including physiological, biochemical, mechanical, molecular and diverse environmental (phenotypic) traits (Wray, 2013;Moshtaghi et al, 2016). It is presumed that adaptations are a response to specific environmental conditions and are propagated by evolutionary forces.…”

“…The connection between genetic and phenotypic change is the result of changes in molecular function that in turn alter cellular and physiological processes that in some instances influence phenotypic traits and fitness. Wray (2013) hypothesized that most of the common genetic variants that influence important traits including life span, fecundity, reproductive performance, behavior and morphology are generated in non-coding regions of the genome. But this is difficult to confirm in non-model species because genomic information is often limited or non-existent.…”

“…Availability of genome sequences and related genomics tools provide unprecedented opportunities for addressing many key questions in evolutionary ecology not previously addressed easily. Thus, computationally intensive relationships between genomics and the biological core disciplines of ecology, evolution and systematics are developing rapidly (Orr, 2005;Marids, 2008;Geralds et al, 2011;Wray, 2013;Bernatchez, 2016). A common interest of some evolutionary biologists is to identify the molecular basis of freshwater adaptation, and to resolve if this has occurred via single or many genes/mutations that have evolved in different lineages.…”