Scientists Prefer them Blind: The History of Hypogean Fish Research

The history of hypogean fish research has been strongly influenced by neo-Lamarckism (including orthogenesis) and typological thinking. Only in the last few decades neo-Darwinism has made any inroads in the research approach to this subject. The majority of the most distinguished and productive hypogean fish researchers have used their research subjects to confirm their own views on evolution rather than to use those subjects as a spring of knowledge to enrich mainstream biological thought. Of these views, I found that the most perversive of all is the notion of evolutionary progress that has led many researchers to envision hypogean fishes as prime examples of regressive evolution. I propose that the utilization of hypogean fishes for the study of convergent evolution should catapult these subjects of research into prime objects of evolutionary ideas.     

Ecology of Subterranean Fishes: An Overview

A synthesis of ecological data available for subterranean fishes throughout the world is presented, and comparatively analyzed in an evolutionary context. Methods of ecological research are described, and their potential and limitations for the study of hypogean fishes are discussed. Ecology of troglobitic (exclusively subterranean) fishes is discussed with focus on distribution areas, population densities and sizes, use of habitat and movements, life cycle and feeding. When data are available, these species are compared with their epigean relatives. Putative ecological autapomorphies of troglobitic fishes, including habitat change, adaptations to cope with food scarcity, and precocial lifestyles, are interpreted in ecological and evolutionary contexts. Species interactions among subterranean species, including cases of syntopy and predation are briefly analyzed. Non-troglobitic hypogean fishes, with their ecological importance and evolutionary role, are also addressed. Problems of classification of subterranean fishes according to the Schiner-Racovitza system (troglobites, troglophiles and trogloxenes) are discussed, and a scenario of evolution of subterranean populations is presented.     

Plasticity paves the way in an adaptive radiation

Phenotypic plasticity has been hypothesized to play a central role in the evolution of phenotypic diversity across species (West‐Eberhard 2003 ). Through ‘genetic assimilation’, phenotypes that are initially environmentally induced within species become genetically fixed over evolutionary time. While genetic assimilation has been shown to occur in both the laboratory and the field (Waddington 1953 ; Aubret & Shine 2009 ), it remains to be shown whether it can account for broad patterns of phenotypic diversity across entire adaptive radiations. Furthermore, our ignorance of the underlying molecular mechanisms has hampered our ability to incorporate phenotypic plasticity into models of evolutionary processes. In this issue of Molecular Ecology, Parsons et al. ( 2016 ) take a significant step in filling these conceptual gaps making use of cichlid fishes as a powerful study system. Cichlid jaw and skull morphology show adaptive, plastic changes in response to early dietary experiences (Fig. 1). In this research, Parsons et al. ( 2016 ) first show that the direction of phenotypic plasticity aligns with the major axis of phenotypic divergence across species. They then dissect the underlying genetic architecture of this plasticity, showing that it is specific to the developmental environment and implicating the patched locus in genetic assimilation (i.e. a reduction in the environmental sensitivity of that locus in the derived species).     

HYPERMUTABILITY OF HOXA13A AND FUNCTIONAL DIVERGENCE FROM ITS PARALOG ARE ASSOCIATED WITH THE ORIGIN OF A NOVEL DEVELOPMENTAL FEATURE IN ZEBRAFISH AND RELATED TAXA (CYPRINIFORMES)

Gene duplication is widely regarded as the predominant mechanism by which genes with new functions and associated phenotypic novelties arise. A whole genome duplication occurred shortly before the most recent common ancestor of teleosts, the most diverse chordate group, resulting in duplication and retention of many Hox cluster genes. Because they play a key role in determination of body plan morphology, it has been widely assumed that Hox genes play a key role in the evolution of diverse metazoan body plans. However, it is not clear whether certain aspects of molecular evolution, such as asymmetric divergence and neofunctionalization, contribute to the initial retention of paralogs. We investigate the molecular evolution and functional divergence of the duplicated HoxA13 paralogs in zebrafish to determine when asymmetric divergence and functional divergence occurred after the duplication event. Our findings demonstrate the contribution of gene duplication to the evolution of novel features through evolutionary mechanisms other than those traditionally investigated, such as positive selection occurring immediately after gene duplication. Rather, we find a latent build up of molecular changes in a gene associated with the development of a novel feature in a very diverse group of fishes.     

The bitterling–mussel interaction as a test case for co‐evolution

The European bitterling Rhodeus sericeus (Cyprinidae) spawns in the gills of freshwater mussels (Unionidae) and shows some obvious adaptations to this type of spawning, such as the development of an ovipositor. Furthermore, recent studies have shown that the fish avoid species of mussels that have a high likelihood of ejecting their eggs prematurely. This leads to the question of whether the interaction between bitterling and mussels could represent a case of co‐evolution, involving evolutionary responses by both species to selection imposed by the other. The evidence for and against co‐evolution is reviewed, incorporating new results from two sets of experiments designed to test for adaptive choices by bitterling according to the mussels' sex and reproductive state, as well as a preliminary study of potential benefits for mussels from exposure to bitterling. Host preferences by bitterling, both among and within mussel species, may indeed have evolved in response to differences in benefits for offspring survival. There is no evidence yet for any benefits to mussels from receiving eggs, whereas there are costs due to reduced ventilation rates when the gills contain bitterling eggs. While there are differences among mussel species and individuals in their tendency to reject bitterling embryos, these differences do not provide strong evidence for co‐evolution. For example, they may reflect differences in host physiology such as ventilation rate and generalized responses to expelling objects from their gills. Therefore, while bitterling are well adapted for their obligate spawning relationship with mussels, it has been much more difficult to find evidence for adaptations by mussels for dealing with bitterling. This suggests that any co‐evolutionary dynamics between bitterling and mussels may be asymmetric, with stronger responses to selection by the fish than by mussels.     

洞穴鱼类:概念、多样性及研究进展

洞穴鱼类是淡水鱼类中一个特殊的生态类群,其生活史的自然完成离不开洞穴或地下水环境。洞穴鱼类可分为典型和非典型两种类型,前者具有易辨识的特殊适应性形态结构(如眼消失、身体透明等),后者此类特征不明显。目前世界典型洞穴鱼类共记录有107种,其中鲤形目和鲇形目的种类最多,分别占49.5%和24.3%;在科级水平上以鲤科和爬鳅科最为丰富。东南亚和中南美是洞穴鱼类多样性最高的地区,有着世界上75.0%的典型洞穴鱼类。中国的洞穴鱼类具有物种多样性高、但集中出现在个别类群(如金线鲃属(Sinocyclocheilus)和高原鳅属(Triplophysa))、物种分化强烈、分布范围狭窄、种群数量小等特点。洞穴鱼类学是一门交叉科学,研究涉及系统学、生态学、生理学、保护生物学等众多学科领域,但目前研究仍多围绕演化问题展开。中国洞穴鱼类研究还处于系统分类和区系研究水平,其他有关学科的研究有待开展。     

The fellowship of the hobbit: the fauna surrounding Homo floresiensis

The Late Pleistocene Flores fauna shows a pattern observed on many other islands. It is neither aberrant nor exclusive, but the result of non‐random selective forces acting upon an impoverished and disharmonic insular fauna. By comparing the Flores vertebrate fauna with other fossil insular biotas, it is apparent that the evolution of Homo floresiensis is part of a general pattern affecting all the inhabitants of Pleistocene Flores. Vertebrate evolution on Flores appears to have been characterized by phylogenetic continuity, low species richness and a disharmonic fauna. All three aspects stem from the isolated position of the island and have resulted in the distinct morphological characteristics of the Flores fauna. Evidence reviewed herein shows that features exhibited by H. floresiensis, such as small stature, a small brain, relatively long arms, robust lower limbs and long feet, are not unique, but are shared by other insular taxa. Therefore, the evolution of H. floresiensis can be explained by existing models of insular evolution and followed evolutionary pathways similar to those of the other terrestrial vertebrates inhabiting Pleistocene Flores.     

Predicting evolution with generalized models of divergent selection: a case study with poeciliid fish

Over the past century and half since the process of natural selection was first described, one enduring question has captivated many, "how predictable is evolution?" Because natural selection comprises deterministic components, the course of evolution may exhibit some level of predictability across organismal groups. Here, I provide an early appraisal of the utility of one particular approach to understanding the predictability of evolution: generalized models of divergent selection (GMDS). The GMDS approach is meant to provide a unifying framework for the science of evolutionary prediction, offering a means of better understanding the causes and consequences of phenotypic and genetic evolution. I describe and test a GMDS centered on the evolution of body shape, size of the gonopodium (sperm-transfer organ), steady-swimming abilities, fast-start swimming performance, and reproductive isolation between populations in Gambusia fishes (Family Poeciliidae). The GMDS produced some accurate evolutionary predictions in Gambusia, identifying variation in intensity of predation by piscivorous fish as a major factor driving repeatable and predictable phenotypic divergence, and apparently playing a key role in promoting ecological speciation. Moreover, the model's applicability seems quite general, as patterns of differentiation in body shape between predator regimes in many disparate fishes match the model's predictions. The fact that such a simple model could yield accurate evolutionary predictions in distantly related fishes inhabiting different geographic regions and types of habitat, and experiencing different predator species, suggests that the model pinpointed a causal factor underlying major, shared patterns of diversification. The GMDS approach appears to represent a promising method of addressing the predictability of evolution and identifying environmental factors responsible for driving major patterns of replicated evolution.     

Synthetic circuits reveal how mechanisms of gene regulatory networks constrain evolution

Phenotypic variation is the raw material of adaptive Darwinian evolution. The phenotypic variation found in organismal development is biased towards certain phenotypes, but the molecular mechanisms behind such biases are still poorly understood. Gene regulatory networks have been proposed as one cause of constrained phenotypic variation. However, most pertinent evidence is theoretical rather than experimental. Here, we study evolutionary biases in two synthetic gene regulatory circuits expressed in Escherichia coli that produce a gene expression stripe—a pivotal pattern in embryonic development. The two parental circuits produce the same phenotype, but create it through different regulatory mechanisms. We show that mutations cause distinct novel phenotypes in the two networks and use a combination of experimental measurements, mathematical modelling and DNA sequencing to understand why mutations bring forth only some but not other novel gene expression phenotypes. Our results reveal that the regulatory mechanisms of networks restrict the possible phenotypic variation upon mutation. Consequently, seemingly equivalent networks can indeed be distinct in how they constrain the outcome of further evolution.     

It's a Wonderful Hypogean Life: A Guide to the Troglomorphic Fishes of the World

There are at least 86 species of troglomorphic fishes belonging to 18 families. Some of those families are characterized by features that can be labeled as preadaptations to the hypogean life; others are not. The level of structural reduction in eye development and pigmentation is highly variable, even within some populations. Reduction in number and complexity of scales does occur but has yet to be fully documented. Reduction in the size and structure of the swim(gas)bladder may be another troglomorphic feature. There is considerable doubt on the taxonomic position of many species of troglomorphic fishes given that a number of them have been described solely on the basis of morphology while genetically they may be very closely correlated to genera different from those they have been assigned to. Geographically speaking there are no evident patterns since many of those species are not found in karstic areas but in phreatic waters. These fishes represent an excellent example of convergent evolution.     

Which evolutionary processes influence natural genetic variation for phenotypic traits?

Although many studies provide examples of evolutionary processes such as adaptive evolution, balancing selection, deleterious variation and genetic drift, the relative importance of these selective and stochastic processes for phenotypic variation within and among populations is unclear. Theoretical and empirical studies from humans as well as natural animal and plant populations have made progress in examining the role of these evolutionary forces within species. Tentative generalizations about evolutionary processes across species are beginning to emerge, as well as contrasting patterns that characterize different groups of organisms. Furthermore, recent technical advances now allow the combination of ecological measurements of selection in natural environments with population genetic analysis of cloned QTLs, promising advances in identifying the evolutionary processes that influence natural genetic variation.     

Turnover of sex chromosomes and speciation in fishes

Closely related species of fishes often have different sex chromosome systems. Such rapid turnover of sex chromosomes can occur by several mechanisms, including fusions between an existing sex chromosome and an autosome. These fusions can result in a multiple sex chromosome system, where a species has both an ancestral and a neo-sex chromosome. Although this type of multiple sex chromosome system has been found in many fishes, little is known about the mechanisms that select for the formation of neo-sex chromosomes, or the role of neo-sex chromosomes in phenotypic evolution and speciation. The identification of closely related, sympatric species pairs in which one species has a multiple sex chromosome system and the other has a simple sex chromosome system provides an opportunity to study sex chromosome turnover. Recently, we found that a population of threespine stickleback (Gasterosteus aculeatus) from Japan has an X₁X₂Y multiple sex chromosome system resulting from a fusion between the ancestral Y chromosome and an autosome, while a sympatric threespine stickleback population has a simple XY sex chromosome system. Furthermore, we demonstrated that the neo-X chromosome (X ₂) plays an important role in phenotypic divergence and reproductive isolation between these sympatric stickleback species pairs. Here, we review multiple sex chromosome systems in fishes, as well as recent advances in our understanding of the evolutionary role of sex chromosome turnover in stickleback speciation.     

Developmental Dynamics and G-Matrices: Can Morphometric Spaces be Used to Model Phenotypic Evolution?

Modern morphometrics, especially geometric morphometrics, is a powerful tool for modeling the evolution and development of the phenotype. Complicated morphological transformations can be simulated by using standard evolutionary genetic equations for processes such as selection and drift in the same morphospaces that are used for empirical morphometric studies. Such applications appear to be consistent with the theory of quantitative evolution of the phenotype. Nevertheless, concerns exist whether simulations of phenotypic changes directly in morphospaces is realistic because trajectories traced in such spaces describe continuous gradations in the phenotype and because the gain and loss of structures is often impossible because morphospaces are necessarily constructed from variables shared in common by all the phenotypes being considered. Competing models of phenotypic change emphasize morphological discontinuity and novelty. Recently developed models of phenotypic evolution that introduce a “phenotypic landscape” between evolutionary genetic constructs like the adaptive landscape and morphospace may correct this shortcoming.     

Evolution of adult male horn developmental phenotypes and character displacement in Xylotrupes beetles (Scarabaeidae)

Character displacement that leads to divergent phenotypes between sympatric species has been hypothesized to facilitate coexistence and promote the accumulation of biodiversity. However, there are alternative evolutionary mechanisms that may also lead to the evolution of phenotypic divergence between sympatric species; one of the mechanisms is evolutionary contingency. We studied the evolution of the presence and absence of a major male horn phenotype, which may have ecological implications for promoting coexistence between sympatric beetles, across geographic populations from different Xylotrupes beetles. By using a previously published phylogeny with 80 Xylotrupes taxa, we estimated the transition rates between the two phenotypic states (i.e., presence vs. absence of a major male phenotype). Based on the estimated transition rates, we then simulated possible phenotypic outcomes between sympatric species. We found that sympatric species were equally likely to evolve the same versus distinct phenotypic states based on the estimated transition rates given the phylogeny. The empirically observed number of sympatric species showing different phenotypic states can be explained by evolutionary contingency alone. We discussed the importance of applying phylogenetic comparative methods when studying phenotypic evolution and more generally to investigate the effect of stochastic processes before making deterministic inferences.     

Genetic and developmental basis for parallel evolution and its significance for hominoid evolution

Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.^1–4 However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan‐Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo‐devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.     

Revealing the mechanisms of the rostral shift of pelvic fins among teleost fishes

In teleost fishes, the position of the pelvic fins shift during evolution; this positional shift seems to have diversified their locomotion and feeding behavior, thereby expanding the habitats of these fishes. Thus, such a positional shift of the pelvic fins is one of the significant features of teleost fishes from evolutionary, embryological, and taxonomic viewpoints, but no studies to date have investigated the mechanism for the rostral shift of the pelvic fins from the anal region in teleosts. Examining the fate of the prospective pelvic fin cells of the zebrafish Danio rerio and the Nile tilapia Oreochromis niloticus embryos demonstrates that the prospective pelvic fin cells are originally located near the anus, as seen in tetrapods, but their position shifts with respect to the body trunk after its protrusion from the yolk surface. In this article, we highlight such recent findings and discuss the mechanisms of pelvic fin evolution among teleost fishes.     

The locus of sexual selection: moving sexual selection studies into the post‐genomics era

Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology.     

Evolvability of cell specification mechanisms

The architecture of gene action during development is relevant to phenotypic evolution as it links genotype to morphological phenotype. Analysis of development at the level of cell fate specification mechanisms illuminates some of the properties of developmental evolution. In this article, we first review examples of evolutionary change in mechanisms of cell fate specification, with an emphasis on evolution in the dependence on inductive signaling and on evolution of the mechanisms that result in spatial asymmetries. We then focus on properties of development that bias possible phenotypic change and present how the distribution of phenotypes that are available by mutational change of the starting genotype can be experimentally tested by systematic mutagenesis. We finally discuss ways in which selection pressures on phenotypes can be inferred from a comparison of the phenotypic spectrum found on mutation with that found in the wild.