levels, loss of circadian rhythmicity and increased wakefulness. (italics added; Borowski, 2018). Furthermore, over the past ten years “about eight new species have been discovered per year”, and there may by hundreds of undiscovered cavefish species (Borowski, 2018). Worldwide, the most recent estimates suggest there are almost 230 known species of cavefish (Maldonado et al. 2020). In Mexico’s El Abra region, there is only one predominant Astyanax species. These fish have independently colonized multiple cave systems, leading to repeated phenotypic convergence of particular cavefish morphotypes. Interestingly, such pronounced convergences “have occurred in spite of gene flow from surface fish populations” (Bradic et al. 2012). These authors imply that “strong natural or sexual selection” for specific alleles are responsible for such convergences. Based upon analyses of 47 whole genomes, Herman et al. (2018) concluded that “troglomorphic traits are maintained despite gene flow with surface populations”. They further conclude that “a key troglomorphic phenotype QTL” for cave phenotypes could be passed between caves by gene flow (Herman et al. 2018). Jeffery covers all possibilities with this statement: “the existence of cavefish populations evolving in parallel or by convergence from surface fish ancestors offers an excellent opportunity to study gene use during repeated evolution. (Jeffery 2020). And, although Astyanax populations are interfertile, Protos et al. (2006) combines definitions when stating that, “we have identified specific genetic lesions responsible for the parallel evolution of albinism in different cave populations of Astyanax, and found that they represent convergent genetic events in separate populations”. From a synthesis of the conventional explanations above there is a discernable pattern of interpretation. Multiple independent cave colonization events by Astyanax surface fish have repeatedly led to the convergence of cave-adapted phenotypes under strong natural or sexual selection. Those adaptations are maintained despite gene flow from surface fish populations, and between cave populations. However most, if not all, definitions of ‘convergent evolution’ require starting with unrelated or distantly related species and lineages. All A. mexicanus morphotypes are interfertile, and hybridize, because they are the same species. Cavefish researchers take advantage of such a highly reliable hybridization process. According to fundamental evolutionary theory, ‘convergence’ directly implies the absence of common ancestry. In this Astyanax system we find similar cave-adapted traits in one of two morphotypes of the same species; these traits are not the result of inheritance from two or more distant lineages sharing a common ancestor, which is defined as homology – the cornerstone of the entirety of evolutionary theory. Yet because a broad, common and necessary set of adaptive traits in multiple Astyanax cavefish populations is thought to be derived from an ancestral population of Astyanax surface fish (i.e. common ancestry), homology would be a more appropriate inference. The conventional research community cannot have it both ways. As similar troglomorphic trait adaptations are observed in animals as diverse as, for example, arachnids, myriapods, turbellarians, annelids, gastropods and teleosts, this pattern would indicate evolutionary convergence. So why does the Astyanax cavefish community uniformly infer trait convergence within a single species? And why do they infer two distinct evolutionary processes – parallelism and convergence – in the same species? Perhaps it is increasingly clear to them that as time marches on, a finite ‘evolutionary language’ (Gould 2002) is becoming fundamentally inadequate. Collectively, we can see that evolutionary process conceptions are consistently invoked across a spectrum of cavefish studies. Interpretations for the production of Astyanax cavefish morphotypes include parallel, convergent and repeated evolution; gene flow or in spite of gene flow; natural selection and/or sexual selection; millions of years or less than twenty thousand years; multiple isolated cave invasions and/or introgression and transmission between populations; pleiotropy through hyperactive regulatory control and/or biosynthetic pathway cooption; constructive or regressive loss-of-function mutations through deletion and/or transposition; epigenetic activation and/or silencing, etc. Let us also not forget some of the evolutionary categorical conceptions of trait gains and losses, tradeoffs, antagonism, redeployments, and sensory trait linkages put forth as possible reasons for the development and integration of many ‘exclusive’ adaptations in A. mexicanus, and by extension, global cavefish populations. Again, when considering the broad list of cave-adapted traits observed within an impressive biodiversity of other troglomorphic animals across this planet, there is little doubt that – of all the conventional evolutionary concepts – convergent evolution is the most common explanatory mechanism applied to those traits. Obviously, there are many outstanding questions: If there have been at least five independent colonization events into different cave populations over the past 1–2 million years, why do all cavefish arrive at nearly identical phenotypes? Why are the fish of different caves still completely interfertile with the ancestral surface form if they are interpreted as having been separated by convergent and/or divergent events? Can all tetra species become cave morphs when placed in cave environments? How do almost all other cave-adapted troglobites converge on similar adaptions when they possess such a disparate range of body plans? Why do all the cavefish in our experimental test groups respond in similar ways to treatment with high-intensity light, regardless of starting point or which pigmentation pathways are functional? As previously noted, we hold a very different view on the origin, function and deployment of adaptations in the Astyanax cavefish model. Common adaptations are the result of common engineering. Within all Astyanax cavefish there is an internal system of preprogrammed adjustments that actively deploy in response to distinct sets of environmental stimuli. In essence, these fish continuously track a range of environmental parameters, assess those parameters on all levels (e.g. molecule, gene, cell, organ system, physiology, anatomy), and adjust rapidly, and appropriately. This process is similar to, but far more complex than human engineered systems that utilize a series of sensors, logic mechanisms, and responders. In all cases, the organism is the agent in control of each adaptive response. Each adaptation, correlated with all other adaptive responses, is repeatable and reversable. Thus, nature (the environment) has no agency, and therefore, there is no selective agent acting through random, mutational error-prone mechanisms over long durations of time. Hence, a proposed mutation-selection mechanism of regressive or constructive trade-offs in trait production, refinement and establishment is purely hypothetical. And as for advocating an evolutionary concept of convergence to explain similar adaptations across Astyanax cavefish populations – what appears to be convergent evolution, we model as similar biological systems of engineered solutions activated by organisms when confronted with similar environmental challenges. Our view presents an original organism-focused Theory of Biological Design (TOBD) that is predictive and testable. Respectively, we have outlined a condensed engineering-based framework of assumptions, tenets, expectations, interpretations, and major inferences for a biological research program that is guided by an organism-focused TOBD (Table 2). BOYLE, ARLEDGE, THOMAS, TOMKINS, AND GULIUZZA Testing the cavefish model 2023 ICC 136
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