Evidence of parallel evolution in the dental elements of Sweetognathus conodonts

The repeated emergence of similar morphologies in the dental elements of Permian Sweetognathus conodonts has been a hypothesized example of parallel evolution. To test if morphological parallelisms occur between isolated Sweetognathus lineages, this study uses two-dimensional-based geometric morphometrics combined with a revised and expanded phylogeny of Permian Sweetognathus conodonts to quantify dental element trait distributions and compare the phenotypic trajectories between lineages. A hierarchical clustering method was used to identify recurrent species pairs based on principal component scores describing their morphological variation, with the further incorporation of widely used ecological metrics such as limiting similarity and morphological overlap. Our research implies that a major contributor to conodont diversity in Palaeozoic marine trophic networks is the emergence of recurrent parallel morphologies via disruptive and directional selection. This study illustrates the mechanisms through which conodonts achieved their status as hyper-diverse predators and scavengers, contributing substantially to the complexity of Palaeozoic marine communities.

Inferred genetic architecture underlying evolution in a fossil stickleback lineage

Inferring the genetic architecture of evolution in the fossil record is difficult because genetic crosses are impossible, the acquisition of DNA is usually impossible and phenotype-genotype maps are rarely obvious. However, such inference is valuable because it reveals the genetic basis of microevolutionary change across many more generations than is possible in studies of extant taxa, thereby integrating microevolutionary process and macroevolutionary pattern. Here, we infer the genetic basis of pelvic skeleton reduction in Gasterosteus doryssus, a Miocene stickleback fish from a finely resolved stratigraphic sequence that spans nearly 17,000 years. Reduction in pelvic score, a categorical measure of pelvic structure, resulted primarily from reciprocal frequency changes of two discrete phenotypic classes. Pelvic vestiges also showed left-side larger asymmetry. These patterns implicate Pitx1, a large-effect gene whose deletion generates left-side larger asymmetry of pelvic vestiges in extant, closely related Gasterosteus aculeatus. In contrast, reductions in the length of the pelvic girdle and pelvic spines resulted from directional shifts of unimodal, continuous trait distributions, suggesting an additional suite of genes with minor, additive pelvic effects, again like G. aculeatus. Similar genetic architectures explain shared but phyletically independent patterns across 10 million years of stickleback evolution.

Morphological and physiological traits of Mediterranean sticklebacks living in the Camargue wetland (Rhone river delta)

Three-spined sticklebacks (Gasterosteus aculeatus L.) living at the southern limit of the species distribution range could possess specific morphological and physiological traits that enable these fish to live at the threshold of their physiological capacities. Morphological analysis was carried out on samples of sticklebacks living in different saline habitats of the Camargue area (Rhone delta, northern Mediterranean coast) obtained from 1993 to 2017. Salinity acclimation capacities were also investigated using individuals from freshwater-low salinity drainage canals and from mesohaline-euryhaline lagoons. Fish were maintained in laboratory conditions at salinity values close to those of their respective habitats: low salinity (LS, 5‰) or seawater (SW, 30‰). Fish obtained from a mesohaline brackish water lagoon (BW, 15‰) were acclimated to SW or LS. Oxygen consumption rates and branchial Na⁺ /K⁺ -ATPase (NKA) activity (indicator of fish osmoregulatory capacity) were measured in these LS or SW control fish and in individuals subjected to abrupt SW or LS transfers. At all the studied locations, only the low-plated "leiurus" morphotype showed no spatial or temporal variations in their body morphology. Gill rakers were only longer and denser in fish sampled from the LS-freshwater (FW) drainage canals. All fish presented similar physiological capacities. Oxygen consumption rates were not influenced by salinity challenge except in SW fish transferred to LS immediately and 1 h after transfer. However, and as expected, gill NKA activity was salinity dependent. Sticklebacks of the Camargue area sampled from habitats with contrasted saline conditions are homogenously euryhaline, have low oxygen consumption rates and do not appear to experience significantly greater metabolic costs when challenged with salinity. However, an observed difference in gill raker length and density is most probably related to the nutritional condition of their habitat, indicating that individuals can rapidly acclimatize to different diets.

Genetic divergence outpaces phenotypic evolution among threespine stickleback populations in old freshwater habitats

Species such as threespine stickleback (Gasterosteus aculeatus) that inhabit divergent selective environments and that have diversified on different time scales can be of value for understanding evolutionary processes. Here we synthesize high-resolution genotypic and phenotypic data to explore a largely unstudied distribution of threespine stickleback populations living in oceanic and freshwater habitats along coastal and inland regions of Oregon. Many inland aquatic habitats of Oregon remained unglaciated during the last ice age, meaning that some extant Oregon lake and river stickleback may have descended from freshwater populations established long before more well-studied, post-glacial freshwater populations. To address the degree of congruence between genetic and phenotypic divergence, we directly compared Oregon stickleback to much younger (post-glacial) Alaskan populations. We found phenotypic variation in Oregon stickleback to be primarily partitioned between oceanic and freshwater habitats, as has been documented in other stickleback systems. However, the main axis of genetic divergence was between coastal and inland regions regardless of habitat type. Furthermore, when comparing patterns between Oregon and Alaska we found similar levels of phenotypic divergence, but much greater genetic divergence among Oregon's populations. The Oregon stickleback system therefore appears well suited for future studies linking genotypic and phenotypic change, further extending the utility of this small fish to provide general insights into evolutionary processes.

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Larvae of the cosmopolitan family Limacodidae, commonly known as "slug" caterpillars, are well known because of the widespread occurrence of spines with urticating properties, a morpho-chemical adaptive trait that has been demonstrated to protect the larvae from natural enemies. However, while most species are armed with rows of spines ("nettle" caterpillars), slug caterpillars are morphologically diverse with some species lacking spines and thus are nonstinging. It has been demonstrated that the evolution of spines in slug caterpillars may have a single origin and that this trait is possibly derived from nonstinging slug caterpillars, but these conclusions were based on limited sampling of mainly New World taxa; thus, the evolution of spines and other traits within the family remains unresolved. Here, we analyze morphological variation in slug caterpillars within an evolutionary framework to determine character evolution of spines with samples from Asia, Australia, North America, and South America. The phylogeny of the Limacodidae was reconstructed based on a multigene dataset comprising five molecular markers (5.6 Kbp: COI, 28S, 18S, EF-1α, and wingless) representing 45 species from 40 genera and eight outgroups. Based on this phylogeny, we infer that limacodids evolved from a common ancestor in which the larval type possessed spines, and then slug caterpillars without spines evolved independently multiple times in different continents. While larvae with spines are well adapted to avoiding generalist predators, our results imply that larvae without spines may be suited to different ecological niches. Systematic relationships of our dataset indicate six major lineages, several of which have not previously been identified.

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

Evolution generates a remarkable breadth of living forms, but many traits evolve repeatedly, by mechanisms that are still poorly understood. A classic example of repeated evolution is the loss of pelvic hindfins in stickleback fish (Gasterosteus aculeatus). Repeated pelvic loss maps to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Here, we identify molecular features contributing to these recurrent deletions. Pitx1 enhancer sequences form alternative DNA structures in vitro and increase double-strand breaks and deletions in vivo. Enhancer mutability depends on DNA replication direction and is caused by TG-dinucleotide repeats. Modeling shows that elevated mutation rates can influence evolution under demographic conditions relevant for sticklebacks and humans. DNA fragility may thus help explain why the same loci are often used repeatedly during parallel adaptive evolution.

Developmental timing differences underlie armor loss across threespine stickleback populations

Comparing ontogenetic patterns within a well-described evolutionary context aids in inferring mechanisms of change, including heterochronies or deletion of developmental pathways. Because selection acts on phenotypes throughout ontogeny, any within-taxon developmental variation has implications for evolvability. We compare ontogenetic order and timing of locomotion and defensive traits in three populations of threespine stickleback that have evolutionarily divergent adult forms. This analysis adds to the growing understanding of developmental genetic mechanisms of adaptive change in this evolutionary model species by delineating when chondrogenesis and osteogenesis in two derived populations begin to deviate from the developmental pattern in their immediate ancestors. We found that differences in adult defensive morphologies arise through abolished or delayed initiation of these traits rather than via an overall heterochronic shift, that intra-population ontogenetic variation is increased for some derived traits, and that altered armor developmental timing differentiates the derived populations from each other despite parallels in adult lateral plate armor phenotypes. We found that changes in ossified elements of the pelvic armor are linked to delayed and incomplete development of an early-forming pelvic cartilage, and that this disruption likely presages the variable pelvic vestiges documented in many derived populations.

EVOLUTION OF PELVIC REDUCTION IN THREESPINE STICKLEBACK FISH: A TEST OF COMPETING HYPOTHESES

Reimchen hypothesized that pelvic reduction in threespine stickleback is favored by an absence of piscivorous fishes and the resulting increase in predation by insects, but Giles hypothesized that the predation regime is unimportant and that a low dissolved calcium concentration favors evolution of pelvic reduction. Substantial pelvic reduction in threespine stickleback sampled from 179 lakes around Cook Inlet, Alaska is strongly associated both with an absence of predatory fishes and a low calcium concentration. However, the association of pelvic reduction with low calcium concentration appears to be contingent on the absence of predatory fishes. These results emphasize the importance of interactions between seemingly unrelated environmental variables for selection of a single trait. However, these results also conflict with some observations elsewhere and do not rule out the possibility that other environmental factors are important for selection for pelvic reduction in threespine stickleback.

PARALLEL EVOLUTION OF LAKE-STREAM PAIRS OF THREESPINE STICKLEBACKS (GASTEROSTEUS) INFERRED FROM MITOCHONDRIAL DNA VARIATION

Three drainage systems in British Columbia, Canada, contain divergent parapatric lake-stream pairs of threespine sticklebacks (Gasterosteus aculeatus): Drizzle and Mayer Lakes on Graham Island, Queen Charlotte Islands, and Misty Lake on northeastern Vancouver Island. Ecological and morphological differences between members of all three lake-stream pairs are strikingly similar; lake fish are melanistic and slim bodied with smaller mouths and more gill rakers than the mottled-brown and robust-bodied stream sticklebacks. We estimated the level of genetic divergence between lake and stream fish in Misty Lake and tested hypotheses of single versus multiple origins of the pairs by assaying mitochondrial DNA (mtDNA) restriction site variation in samples from the three lake systems. MtDNA analysis revealed the existence of two highly divergent lineages differing by 2.7% in sequence. One lineage predominated in Misty stream fish (73%), whereas the other lineage predominated in Misty Lake samples (96%). Comparable forms (lake or stream) in the different lakes did not cluster together in terms of mtDNA nucleotide divergence, suggesting that the pairs have had independent origins. We concluded that: (1) divergent mtDNA lineages in North Pacific sticklebacks stem from historical isolation in the two major glacial refugia proposed for the North Pacific (Beringia and Cascadia); (2) the stream and lake pair in Misty Lake are distinct gene pools; (3) the divergence between parapatric lake and stream Gasterosteus represents parallel evolution having occurred at least twice in the North Pacific; and (4) different scales of evolutionary divergence exist in North Pacific Gasterosteus, that is, a relatively ancient divergence of mtDNA clades as well as recent (i.e., postglacial) divergence of ecotypes within major clades.

The Baculum was Gained and Lost Multiple Times during Mammalian Evolution

The rapid evolution of male genitalia is a nearly ubiquitous pattern across sexually reproducing organisms, likely driven by the evolutionary pressures of male-male competition, male-female interactions, and perhaps pleiotropic effects of selection. The penis of many mammalian species contains a baculum, a bone that displays astonishing morphological diversity. The evolution of baculum size and shape does not consistently correlate with any aspects of mating system, hindering our understanding of the evolutionary processes affecting it. One potential explanation for the lack of consistent comparative results is that the baculum is not actually a homologous structure. If the baculum of different groups evolved independently, then the assumption of homology inherent in comparative studies is violated. Here, we specifically test this hypothesis by modeling the presence/absence of bacula of 954 mammalian species across a well-established phylogeny and show that the baculum evolved a minimum of nine times, and was lost a minimum of ten times. Three different forms of bootstrapping show our results are robust to species sampling. Furthermore, groups with a baculum show evidence of higher rates of diversification. Our study offers an explanation for the inconsistent results in the literature, and provides insight into the evolution of this remarkable structure.

Postembryonic staging of wild-type goldfish, with brief reference to skeletal systems

Background: Artificial selection of postembryonic features is known to have established morphological variation in goldfish (Carassius auratus). Although previous studies have suggested that goldfish and zebrafish are almost directly comparable at the embryonic level, little is known at the postembryonic level. Results: Here, we categorized the postembryonic developmental process in the wild‐type goldfish into 11 different stages. We also report certain differences between the postembryonic developmental processes of goldfish and zebrafish, especially in the skeletal systems (scales and median fin skeletons), suggesting that postembryonic development underwent evolutionary divergence in these two teleost species. Conclusions: Our postembryonic staging system of wild‐type goldfish paves the way for careful and appropriate comparison with other teleost species. The staging system will also facilitate comparative ontogenic analyses between wild‐type and mutant goldfish strains, allowing us to closely study the relationship between artificial selection and molecular developmental mechanisms in vertebrates. Developmental Dynamics 244:1485–1518, 2015. © 2015 Wiley Periodicals, Inc.

This study provides the first reliable descriptions of normal post‐embryonic stages of wild type goldfish.

Several post‐embryonic features of goldfish and zebrafish are diverged in these two teleost lineages.

Goldfish larvae and juvenile provide a novel model for the investigation of the evolutionary relationship between domestication and ontogeny.

Molecular evolution of HoxA13 and the multiple origins of limbless morphologies in amphibians and reptiles

Developmental processes and their results, morphological characters, are inherited through transmission of genes regulating development. While there is ample evidence that cis-regulatory elements tend to be modular, with sequence segments dedicated to different roles, the situation for proteins is less clear, being particularly complex for transcription factors with multiple functions. Some motifs mediating protein-protein interactions may be exclusive to particular developmental roles, but it is also possible that motifs are mostly shared among different processes. Here we focus on HoxA13, a protein essential for limb development. We asked whether the HoxA13 amino acid sequence evolved similarly in three limbless clades: Gymnophiona, Amphisbaenia and Serpentes. We explored variation in ω (dN/dS) using a maximum-likelihood framework and HoxA13sequences from 47 species. Comparisons of evolutionary models provided low ω global values and no evidence that HoxA13 experienced relaxed selection in limbless clades. Branch-site models failed to detect evidence for positive selection acting on any site along branches of Amphisbaena and Gymnophiona, while three sites were identified in Serpentes. Examination of alignments did not reveal consistent sequence differences between limbed and limbless species. We conclude that HoxA13 has no modules exclusive to limb development, which may be explained by its involvement in multiple developmental processes.

Predation of Threespine Stickleback by Dragonfly Naiads

Threespine stickleback (Gasterosteus aculeatus) populations that have evolved pelvic girdle reduction are most commonly found in lakes with low dissolved ion concentration, a lack of piscivorous fishes, and abundant macroinvertebrate predators. Researchers have speculated that macroinvertebrates have a propensity to consume prey with pelvic spines. If this is true, perhaps macroinvertebrates use the stickleback's spines to facilitate capture and manipulation. This study tested whether dragonfly naiads differentially prey upon stickleback possessing either a complete or reduced pelvis and documented naiad hunting and capturing behavior. Results from an arena experiment suggest that naiads do not prey more heavily upon individuals with one pelvic phenotype over the other. However, results from trials where the naiads were presented with one stickleback with pelvic spines and another without suggest that naiads prey more heavily upon small stickleback with pelvic spines and large stickleback without pelvic spines and that they adjust their predatory behavior based upon the pelvic phenotype of the prey.

Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.

Predation-imposed selection on threespine stickleback (Gasterosteus aculeatus) morphology: a test of the refuge use hypothesis

The transition from marine to freshwater life in the threespine stickleback (Gasterosteus aculeatus) is accompanied by complex morphological changes-including reduction in bony armor and change in body shape-but experimental evidence for the selective agents behind these evolutionary transitions is sparse. We investigated whether selection by predatory fish affects threespine stickleback morphology differentially when refuge is absent (pelagic lifestyle-ancestral condition) or present (benthic lifestyle-derived condition). Our results show that selection favors low numbers of lateral plates in habitats with refuge, whereas fully plated individuals have a selective advantage in habitats without refuge. We also found that a decrease in the length of the caudal peduncle increased survival probability, irrespective of habitat. The effect of spine lengths on survival was evident only in a multivariate analysis of selection, implying that it is essential to account for phenotypic and genetic correlations between traits before drawing conclusions about the effects of selection on single traits. Apart from uncovering targets and patterns of predator-induced selection on threespine stickleback morphology, our results provide direct evidence to support the hypothesis that differences in antipredator strategies in pelagic versus benthic sticklebacks could play a role in the repeated, independent cases of plate number reduction following freshwater colonization in this species.

The role of gene expression in ecological speciation

Ecological speciation is the process by which barriers to gene flow between populations evolve due to adaptive divergence via natural selection. A relatively unexplored area in ecological speciation is the role of gene expression. Gene expression may be associated with ecologically important phenotypes not evident from morphology and play a role during colonization of new environments. Here we review two potential roles of gene expression in ecological speciation: (1) its indirect role in facilitating population persistence and (2) its direct role in contributing to genetically based reproductive isolation. We find indirect evidence that gene expression facilitates population persistence, but direct tests are lacking. We also find clear examples of gene expression having effects on phenotypic traits and adaptive genetic divergence, but links to the evolution of reproductive isolation itself remain indirect. Gene expression during adaptive divergence seems to often involve complex genetic architectures controlled by gene networks, regulatory regions, and “eQTL hotspots.” Nonetheless, we review how approaches for isolating the functional mutations contributing to adaptive divergence are proving to be successful. The study of gene expression has promise for increasing our understanding ecological speciation, particularly when integrative approaches are applied.

Pelvic fins in teleosts: structure, function and evolution

The pelvic fins of teleosts are paired appendages that are considered to be homologous to the hind limbs of tetrapods. Because they are less important for swimming, their morphology and function can be flexibly modified, and such modifications have probably facilitated the adaptations of teleosts to various environments. Recently, among these modifications, pelvic-fin loss has gained attention in evolutionary developmental biology. Pelvic-fin loss, however, has only been investigated in a few model species, and various biological aspects of pelvic fins in teleosts in general remain poorly understood. This review summarizes the current state of knowledge regarding pelvic fins, such as their structure, function and evolution, to elucidate their contribution to the considerable diversity of teleosts. This information could be invaluable for future investigations into various aspects of pelvic fins, which will provide clues to understanding the evolution, diversity and adaptations of teleosts.

Adaptive evolution of lateral plates in three-spined stickleback Gasterosteus aculeatus: a case study in functional analysis of natural variation

The three-spined stickleback Gasterosteus aculeatus is a model species for studying questions in ecology and evolution. The rapid diversification of G. aculeatus in post-glacial freshwater environments, combined with recently developed molecular tools, provides a unique opportunity to study the functional basis of fitness variation in natural populations. In derived freshwater populations, a number of morphological traits have diverged in parallel from the marine ancestral state, including the number of lateral armour plates. Evolution of reduced armour in freshwater populations is due to positive selection from both abiotic and biotic mechanisms. The major effect gene (ectodysplasin-A or Eda), along with several minor effect genetic regions, has recently been shown to control lateral plate variation. Field experiments have further determined the fitness consequences of allelic variation at the major effect locus. This work helps elucidate the mechanisms connecting genetic variation with phenotypic variation and fitness in the wild, a synthesis that should be applicable to many other phenotypic traits and species of fishes.

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer

The molecular mechanisms underlying major phenotypic changes that have evolved repeatedly in nature are generally unknown. Pelvic loss in different natural populations of threespine stickleback fish has occurred through regulatory mutations deleting a tissue-specific enhancer of the Pituitary homeobox transcription factor 1 (Pitx1) gene. The high prevalence of deletion mutations at Pitx1 may be influenced by inherent structural features of the locus. Although Pitx1 null mutations are lethal in laboratory animals, Pitx1 regulatory mutations show molecular signatures of positive selection in pelvic-reduced populations. These studies illustrate how major expression and morphological changes can arise from single mutational leaps in natural populations, producing new adaptive alleles via recurrent regulatory alterations in a key developmental control gene.

Implications of a fossil stickleback assemblage for Darwinian gradualism

Darwin postulated that a complete fossil record would contain numerous gradual transitions between ancestral and descendant species, but 150 years after publication of The Origin of Species, few such transitions have materialized. The fossil stickleback Gasterosteus doryssus and the deposit in which it occurs provide excellent conditions to detect such transitions. Abundant, well-preserved fossils occur in a stratigraphic setting with fine temporal resolution. The paleoecology of G. doryssus resembles the ecology of modern lakes that harbour the phenotypically similar three-spined stickleback Gasterosteus aculeatus. Gasterosteus aculeatus are primitively highly armoured, but G. doryssus comprised two contemporaneous biological species with relatively weak armour, including a near-shore, benthic feeder (benthic) and an offshore planktivore (limnetic). The benthic species expanded its range into the limnetic zone of the lake, where it apparently switched to planktivory and evolved reduced armour within c. 5000 years in response to directional selection. Although gradual evolution of mean phenotypes occurred, a single major gene caused much of evolutionary change of the pelvic skeleton. Thus, Darwin's expectation that transitions between species in the fossil record would be gradual was met at a fine time scale, but for pelvic structure, a well-studied trait, his expectation that gradual change would depend entirely on numerous, small, heritable differences among individuals was incorrect.

Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage

Natural selection has almost certainly shaped many evolutionary trajectories documented in fossil lineages, but it has proven difficult to demonstrate this claim by analyzing sequences of evolutionary changes. In a recently published and particularly promising test case, an evolutionary time series of populations displaying armor reduction in a fossil stickleback lineage could not be consistently distinguished from a null model of neutral drift, despite excellent temporal resolution and an abundance of indirect evidence implicating natural selection. Here, we revisit this case study, applying analyses that differ from standard approaches in that: (1) we do not treat genetic drift as a null model, and instead assess neutral and adaptive explanations on equal footing using the Akaike Information Criterion; and (2) rather than constant directional selection, the adaptive scenario we consider is that of a population ascending a peak on the adaptive landscape, modeled as an Orstein-Uhlenbeck process. For all three skeletal features measured in the stickleback lineage, the adaptive model decisively outperforms neutral evolution, supporting a role for natural selection in the evolution of these traits. These results demonstrate that, at least under favorable circumstances, it is possible to infer in fossil lineages the relationship between evolutionary change and features of the adaptive landscape.

Directional asymmetry of pelvic vestiges in threespine stickleback

Extensive reduction of the size and complexity of the pelvic skeleton (i.e., pelvic reduction) has evolved repeatedly in Gasterosteus aculeatus. Asymmetrical pelvic vestiges tend to be larger on the left side (i.e., left biased) in populations studied previously. Loss of Pitx1 expression is associated with pelvic reduction in G. aculeatus, and pelvic reduction maps to the Pitx1 locus. Pitx1 knockouts in mice have reduced hind limbs, but the left limb is larger. Thus left-biased directional asymmetry of stickleback pelvic vestiges may indicate the involvement of Pitx1 in pelvic reduction. We examined 6,356 specimens from 27 Cook Inlet populations of G. aculeatus with extensive pelvic reduction. Samples from 20 populations exhibit the left bias in asymmetrical pelvic vestiges expected if Pitx1 is involved, and three have a slight, non-significant left bias. However, samples from three populations have a significant right bias, and one large sample from another population has equal frequencies of specimens with larger vestiges on the left or right side. A sample of fossil threespine stickleback also has significantly left-biased pelvic vestiges. These results suggest that silencing of Pitx1 or the developmental pathway in which it functions in the pelvis is the usual cause of pelvic reduction in most Cook Inlet populations of G. aculeatu, and that it caused pelvic reduction at least 10 million years ago in a stickleback population. A different developmental genetic mechanism is implicated for three populations with right-biased pelvic vestiges and for the population without directional asymmetry.

Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes

Paired appendages were a key developmental innovation among vertebrates and they eventually evolved into limbs. Ancient developmental control systems for paired fins and limbs are broadly conserved among gnathostome vertebrates. Some lineages including whales, some salamanders, snakes, and many ray-fin fish, independently lost the pectoral, pelvic, or both appendages over evolutionary time. When different taxa independently evolve similar developmental morphologies, do they use the same molecular genetic mechanisms? To determine the developmental genetic basis for the evolution of pelvis loss in the pufferfish Takifugu rubripes (fugu), we isolated fugu orthologs of genes thought to be essential for limb development in tetrapods, including limb positioning (Hoxc6, Hoxd9), limb bud initiation (Pitx1, Tbx4, Tbx5), and limb bud outgrowth (Shh, Fgf10), and studied their expression patterns during fugu development. Results showed that bud outgrowth and initiation fail to occur in fugu, and that pelvis loss is associated with altered expression of Hoxd9a, which we show to be a marker for pelvic fin position in three-spine stickleback Gasterosteus aculeatus. These results rule out changes in appendage outgrowth and initiation genes as the earliest developmental defect in pufferfish pelvic fin loss and suggest that altered Hoxd9a expression in the lateral mesoderm may account for pelvis loss in fugu. This mechanism appears to be different from the mechanism for pelvic loss in stickleback, showing that different taxa can evolve similar phenotypes by different mechanisms.

Studies of threespine stickleback developmental evolution: progress and promise

A promising route for understanding the origin and diversification of organismal form is through studies at the intersection of evolution and development (evo-devo). While much has been learned over the last two decades concerning macroevolutionary patterns of developmental change, a fundamental gap in the evo-devo synthesis is the integration of mathematical population and quantitative genetics with studies of how genetic variation in natural populations affects developmental processes. This micro-evo-devo synthesis requires model organisms with which to ask empirical questions. Threespine stickleback fish (Gasterosteus aculeatus), long a model for studying behavior, ecology and evolution, is emerging as a prominent model micro-evo-devo system. Research on stickleback over the last decade has begun to address the genetic basis of morphological variation and sex determination, and much of this work has important implications for understanding the genetics of speciation. In this paper we review recent threespine stickleback micro-evo-devo results, and outline the resources that have been developed to make this synthesis possible. The prospects for stickleback research to speed the micro-(and macro-) evo-devo syntheses are great, and this workhorse model system is well situated to continue contributing to our understanding of the generation of diversity in organismal form for many more decades.

Fishing for the secrets of vertebrate evolution in threespine sticklebacks

The threespine stickleback (Gasterosteus aculeatus) is rapidly emerging as a new model genetic system to study questions at the interface of evolution and development. The relatively rapid and recent diversification of this small teleost fish, combined with the development of genetic and genomic tools for this fish, provides an unprecedented opportunity to identify the genetic and molecular basis of morphological variation in natural populations of vertebrates. Recently, the genes underlying two different adaptive morphological traits in stickleback have been identified. This work has provided answers to four longstanding questions in the field of evolution and development: (1) How many genes underlie morphological variation in natural populations? (2) What are the genes that underlie morphological variation in natural populations? (3) Do coding or regulatory mutations underlie morphological evolution? (4) What is the molecular and genetic basis of parallel morphological evolution? Because stickleback populations also display natural variation in morphology, life history, physiology, and behavior, extending the approaches used to identify the genetic basis of morphological variation in sticklebacks to other phenotypes is sure to yield further important insights into the genetic and developmental basis of diversity in natural populations.

Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland

In this study, we analyzed the cytochrome b gene in threespine stickleback (Gasterosteus aculeatus) populations from Scotland. We found evidence of a postglacial population expansion in Scotland and large differences in genetic diversity estimates among populations. Higher levels of genetic diversity are negatively correlated with distance from the ocean. In addition, distance from the ocean and predation risk both explain variation in plate count in Scottish populations. Overall, the mtDNA data support the racemic model of evolution in threespine stickleback.

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks

Hindlimb loss has evolved repeatedly in many different animals by means of molecular mechanisms that are still unknown. To determine the number and type of genetic changes underlying pelvic reduction in natural populations, we carried out genetic crosses between threespine stickleback fish with complete or missing pelvic structures. Genome-wide linkage mapping shows that pelvic reduction is controlled by one major and four minor chromosome regions. Pitx1 maps to the major chromosome region controlling most of the variation in pelvic size. Pelvic-reduced fish show the same left-right asymmetry seen in Pitx1 knockout mice, but do not show changes in Pitx1 protein sequence. Instead, pelvic-reduced sticklebacks show site-specific regulatory changes in Pitx1 expression, with reduced or absent expression in pelvic and caudal fin precursors. Regulatory mutations in major developmental control genes may provide a mechanism for generating rapid skeletal changes in natural populations, while preserving the essential roles of these genes in other processes.

Temporal variation in divergent selection on spine number in threespine stickleback

Short-term temporal cycles in ecological pressures, such as shifts in predation regime, are widespread in nature yet estimates of temporal variation in the direction and intensity of natural selection are few. Previous work on threespine stickleback (Gasterosteus aculeatus) has revealed that dorsal and pelvic spines are a defense against gape-limited predators but may be detrimental against grappling insect predators. In this study, we examined a 15-year database from an endemic population of threespine stickleback to look for evidence of temporal shifts in exposure to these divergent predation regimes and correlated shifts in selection on spine number. For juveniles, we detected selection for increased spine number during winter when gape-limited avian piscivores were most common but selection for decreased spine number during summer when odonate predation was more common. For subadults and adults, which are taken primarily by avian piscivores, we predicted selection should generally be for increased spine number in all seasons. Among 59 comparisons, four selection differentials were significant (Bonferroni corrected) and in the predicted direction. However, there was also substantial variability in remaining differentials, including two examples with strong selection for spine reduction. These reversals were associated with increased tendency of the fish to shift to a benthic niche, as determined from examination of stomach contents. These dietary data suggest that increased encounter rates with odonate predation select for spine reduction. Strong selection on spine number was followed by changes in mean spine number during subsequent years and a standard quantitative genetic formula revealed that spine number has a heritable component. Our results provide evidence of rapid morphological responses to selection from predators and suggest that temporal variation in selection may help maintain variation within populations. Furthermore, our findings indicate that variable selection can be predicted if the agents of selection are known.

Parasitism of asymmetrical pelvic phenotypes in stickleback

Subtle departures from bilateral symmetry in morphological traits result from environmental and genetic stresses and may signal an inferior genetic background. Because one correlate of an inferior genome is reduced resistance to infection, such asymmetry may provide a phenotypic signal of susceptibility to parasitism. I tested this hypothesis in a population of threespine stickleback (Gasterosteus aculeatus) with cestode and nematode infections and bilateral asymmetry of the pelvis. Seventeen percent of the fish had an asymmetrical pelvis and, of these, 78% had greater expression on the left side; this directionality suggests a genetic influence. Females had consistently greater left-side asymmetry than did males. The incidence of total infection (all parasite species) in the largest adult fish (> 60 mm body length) was greater in asymmetrical phenotypes, and this occurred in both sexes and for each parasite species (Schistocephalus solidus, Cyathocephalus truncatus, Eustrongylides spp.), even when multiple-species infections were excluded. Contrary to prediction, however, in juvenile fish (< 20 mm) and yearlings (20–40 mm) but not subadults and adults (40–60 mm), asymmetrical phenotypes had significantly lower infection rates than symmetrical fish. This pattern occurred in both sexes, but the extent of the association varied over the 14 years of sampling. Consequently, if the directional asymmetry of the pelvis is under genetic control, asymmetry would be favoured during early ontogeny but selected against during the adult stages. The data support the hypothesis that asymmetry is a phenotypic signal of parasitism, but the unexpected bidirectionality of the association within a single population suggests increased complexity of the processes coupling asymmetry and genetic background.

Origins of endemic stickleback from the Queen Charlotte Islands: mitochondrial and morphological evidence

Recently, two divergent mitochondrial lineages were described in a survey of 12 scattered populations of the threespine stickleback (Gasterosteus aculeatus) on the Queen Charlotte Islands (QCI), western Canada, one of which, possibly a relict lineage, was subsequently shown to characterize stickleback from the western Pacific near Japan. In the present study, we assayed 985 fish from 85 QCI populations for mitochondrial lineage using a restriction enzyme test. Our data indicate that the relict lineage was largely limited (18 of 20 populations) to adjacent watersheds in the northeast corner of the QCI close to a suspected glacial refugium, but we also found the lineage in two remote lakes on the west coast of the QCI, distant from any known refugia. We obtained a sample of 33 stickleback from the mid-Pacific and found both mitochondrial DNA (mtDNA) lineages, strongly suggesting ongoing dispersal of these fish across the Pacific, and inconsistent with previous suggestions of relict status for one of the lineages. Morphologically derived traits, such as loss of armour and loss of spines, occurred in both lineages, but these were more prevalent in the Japanese lineage. Surprisingly, 19 localities had both lineages, and within each of these there were no significant univariate or multivariate associations between lineages and morphology, suggesting few if any reproductive barriers between the divergent mtDNA lineages.