The complete mitochondrial genome of the Variable Platyfish Xiphophorus variatus

We present the complete mitochondrial genome sequence of the Variable Platyfish, Xiphophorus variatus (Meek 1904) (Cyprinodontiformes: Poeciliidae). The genome consists of 16,624 bp which encodes 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 1 control region. Genome-wide nucleotide composition is 27.79% adenine, 31.11% cytosine, 15.63% guanine, and 25.48% thymine. The X. variatus mitochondrial genome shares similar GC content and identical gene order and gene strand location with other members of Poeciliidae. The sequence presented herein will be of utility for future phylogenetic and biomedical research and for designing primers for species detection from environmental DNA samples.

Ichthyological Differentiation and Homogenization in the Pánuco Basin, Mexico

Species introductions and extirpations are key aspects of aquatic ecosystem change that need to be examined at large geographic and temporal scales. The Pánuco Basin (Eastern Mexico) has high ichthyological diversity and ecological heterogeneity. However, freshwater fish (FWF) introductions and extirpations since the mid-1900s have modified species range and distribution. We examine changes in FWF species composition in and among four sub-basins of the Pánuco by comparing fish collection records pre-1980 to 2018. Currently, the FWF of the Pánuco includes 95 species. Fishes in the Poeciliidae, Cyprinidae, and Cichlidae, respectively, comprised most records over time. Significant differences in species composition were found between the first (pre-1980) and last (2011–2018) study periods, but not for periods in-between. Eight independent species groups were key for explaining changes in Pánuco river ichthyofauna; one group was dominated by invasive species, and saw increases in the number of records across study periods (faunal homogenization). Another group was formed by species with conservation concern with a declining number of records over time. Thirteen (2 native and 11 non-native) species were responsible for temporal turnover. These results strongly suggest high rates of differentiation over time (via native species loss) following widespread non-native species introductions.

Technical and conceptual considerations for using animated stimuli in studies of animal behavior

Rapid technical advances in the field of computer animation (CA) and virtual reality (VR) have opened new avenues in animal behavior research. Animated stimuli are powerful tools as they offer standardization, repeatability, and complete control over the stimulus presented, thereby "reducing" and "replacing" the animals used, and "refining" the experimental design in line with the 3Rs. However, appropriate use of these technologies raises conceptual and technical questions. In this review, we offer guidelines for common technical and conceptual considerations related to the use of animated stimuli in animal behavior research. Following the steps required to create an animated stimulus, we discuss (I) the creation, (II) the presentation, and (III) the validation of CAs and VRs. Although our review is geared toward computer-graphically designed stimuli, considerations on presentation and validation also apply to video playbacks. CA and VR allow both new behavioral questions to be addressed and existing questions to be addressed in new ways, thus we expect a rich future for these methods in both ultimate and proximate studies of animal behavior.

The virtual lover: variable and easily guided 3D fish animations as an innovative tool in mate-choice experiments with sailfin mollies-I. Design and implementation

Animal behavior researchers often face problems regarding standardization and reproducibility of their experiments. This has led to the partial substitution of live animals with artificial virtual stimuli. In addition to standardization and reproducibility, virtual stimuli open new options for researchers since they are easily changeable in morphology and appearance, and their behavior can be defined. In this article, a novel toolchain to conduct behavior experiments with fish is presented by a case study in sailfin mollies Poecilia latipinna. As the toolchain holds many different and novel features, it offers new possibilities for studies in behavioral animal research and promotes the standardization of experiments. The presented method includes options to design, animate, and present virtual stimuli to live fish. The designing tool offers an easy and user-friendly way to define size, coloration, and morphology of stimuli and moreover it is able to configure virtual stimuli randomly without any user influence. Furthermore, the toolchain brings a novel method to animate stimuli in a semiautomatic way with the help of a game controller. These created swimming paths can be applied to different stimuli in real time. A presentation tool combines models and swimming paths regarding formerly defined playlists, and presents the stimuli onto 2 screens. Experiments with live sailfin mollies validated the usage of the created virtual 3D fish models in mate-choice experiments.

The virtual lover: variable and easily guided 3D fish animations as an innovative tool in mate-choice experiments with sailfin mollies-II. Validation

The use of computer animation in behavioral research is a state-of-the-art method for designing and presenting animated animals to live test animals. The major advantages of computer animations are: (1) the creation of animated animal stimuli with high variability of morphology and even behavior; (2) animated stimuli provide highly standardized, controlled and repeatable testing procedures; and (3) they allow a reduction in the number of live test animals regarding the 3Rs principle. But the use of animated animals should be attended by a thorough validation for each test species to verify that behavior measured with live animals toward virtual animals can also be expected with natural stimuli. Here we present results on the validation of a custom-made simulation for animated 3D sailfin mollies Poecilia latipinna and show that responses of live test females were as strong to an animated fish as to a video or a live male fish. Movement of an animated stimulus was important but female response was stronger toward a swimming 3D fish stimulus than to a "swimming" box. Moreover, male test fish were able to discriminate between animated male and female stimuli; hence, rendering the animated 3D fish a useful tool in mate-choice experiments with sailfin mollies.

Ecological divergence and conservatism: spatiotemporal patterns of niche evolution in a genus of livebearing fishes (Poeciliidae: Xiphophorus)

Background

Ecological factors often have a strong impact on spatiotemporal patterns of biodiversity. The integration of spatial ecology and phylogenetics allows for rigorous tests of whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence. We address this question in a genus of livebearing fishes for which the role of sexual selection in speciation has long been studied, but in which the potential role of ecological divergence during speciation has not been tested.

Results

By combining reconstruction of ancestral climate tolerances and disparity indices, we show that the earliest evolutionary split in Xiphophorus was associated with significant divergence for temperature variables. Niche evolution and present day niches were most closely associated with each species’ geographic distribution relative to a biogeographic barrier, the Trans-Mexican Volcanic Belt. Tests for similarity of the environmental backgrounds of closely related species suggested that the relative importance of niche conservatism and divergence during speciation varied among the primary clades of Xiphophorus. Closely related species in the two swordtail clades exhibited higher levels of niche overlap than expected given environmental background similarity indicative of niche conservatism. In contrast, almost all species of platyfish had significantly divergent niches compared to environmental backgrounds, which is indicative of niche divergence.

Conclusion

The results suggest that the relative importance of niche conservatism and divergence differed among the clades of Xiphophorus and that traits associated with niche evolution may be more evolutionarily labile in the platyfishes. Our results ultimately suggest that the taxonomic scale of tests for conservatism and divergence could greatly influence inferences of their relative importance in the speciation process.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0593-4) contains supplementary material, which is available to authorized users.

Spatiotemporal environmental heterogeneity and the maintenance of the tailspot polymorphism in the variable platyfish (Xiphophorus variatus)

Genetic variation is critical for adaptive evolution. Despite its importance, there is still limited evidence in support of some prominent theoretical models explaining the maintenance of genetic polymorphism within populations. We examined 84 populations of Xiphophorus variatus, a livebearing fish with a genetic polymorphism associated with physiological performance, to test: (1) whether niche differentiation explains broad-scale maintenance of polymorphism, (2) whether polymorphism is maintained among populations by local adaptation and migration, or (3) whether heterogeneity in explicit environmental variables could be linked to levels of polymorphism within populations. We found no evidence of climatic niche differentiation that could generate or maintain broad geographic variation in polymorphism. Subsequently, hierarchical partitioning of genetic richness and partial mantel tests revealed that 76% of the observed genetic richness was partitioned within populations with no effect of geographic distance on polymorphism. These results strongly suggest a lack of migration-selection balance in the maintenance of polymorphism, and model selection confirmed a significant relationship between environmental heterogeneity and genetic richness within populations. Few studies have demonstrated such effects at this scale, and additional studies in other taxa should examine the generality of gene-by-environment interactions across populations to better understand the dynamics and scale of balancing selection.

Condition-dependence, pleiotropy and the handicap principle of sexual selection in melanin-based colouration

The signalling function of melanin-based colouration is debated. Sexual selection theory states that ornaments should be costly to produce, maintain, wear or display to signal quality honestly to potential mates or competitors. An increasing number of studies supports the hypothesis that the degree of melanism covaries with aspects of body condition (e.g. body mass or immunity), which has contributed to change the initial perception that melanin-based colour ornaments entail no costs. Indeed, the expression of many (but not all) melanin-based colour traits is weakly sensitive to the environment but strongly heritable suggesting that these colour traits are relatively cheap to produce and maintain, thus raising the question of how such colour traits could signal quality honestly. Here I review the production, maintenance and wearing/displaying costs that can generate a correlation between melanin-based colouration and body condition, and consider other evolutionary mechanisms that can also lead to covariation between colour and body condition. Because genes controlling melanic traits can affect numerous phenotypic traits, pleiotropy could also explain a linkage between body condition and colouration. Pleiotropy may result in differently coloured individuals signalling different aspects of quality that are maintained by frequency-dependent selection or local adaptation. Colouration may therefore not signal absolute quality to potential mates or competitors (e.g. dark males may not achieve a higher fitness than pale males); otherwise genetic variation would be rapidly depleted by directional selection. As a consequence, selection on heritable melanin-based colouration may not always be directional, but mate choice may be conditional to environmental conditions (i.e. context-dependent sexual selection). Despite the interest of evolutionary biologists in the adaptive value of melanin-based colouration, its actual role in sexual selection is still poorly understood.

Environmental heterogeneity generates opposite gene-by-environment interactions for two fitness-related traits within a population

Theory predicts that environmental heterogeneity offers a potential solution to the maintenance of genetic variation within populations, but empirical evidence remains sparse. The live-bearing fish Xiphophorus variatus exhibits polymorphism at a single locus, with different alleles resulting in up to five distinct melanistic "tailspot" patterns within populations. We investigated the effects of heterogeneity in two ubiquitous environmental variables (temperature and food availability) on two fitness-related traits (upper thermal limits and body condition) in two different tailspot types (wild-type and upper cut crescent). We found gene-by-environment (G × E) interactions between tailspot type and food level affecting upper thermal limits (UTL), as well as between tailspot type and thermal environment affecting body condition. Exploring mechanistic bases underlying these G × E patterns, we found no differences between tailspot types in hsp70 gene expression despite significant overall increases in expression under both thermal and food stress. Similarly, there was no difference in routine metabolic rates between the tailspot types. The reversal of relative performance of the two tailspot types under different environmental conditions revealed a mechanism by which environmental heterogeneity can balance polymorphism within populations through selection on different fitness-related traits.

Does fin coloration signal social status in a dominance hierarchy of the livebearing fish Xiphophorus variatus?

In each population of the livebearing fish Xiphophorus variatus, only a small portion of the adult males develop bright yellow-red (YR) coloration on the dorsal and caudal fins. Here we characterized the dominance hierarchy in X. variatus and tested whether YR coloration is related to a male's position in the hierarchy and can therefore serve as a reliable cue to rival males. Populations varied considerably in the frequency of YR males. Across all populations, males with YR coloration were significantly larger than the rest of the males in the population. Observations of aggressive interactions among males in small groups in the laboratory revealed a sized-based dominance hierarchy with YR males at the top. Aggression was more common among males of a similar size and fighting increased as male body size differences decreased. However, despite the reliability of YR coloration as a signal of dominance status, males at lower social ranks did not avoid aggression with YR males and YR males did not experience fewer aggressive attacks compared to non-YR males. Our findings demonstrate that fin coloration is a reliable cue of a male's social status but rival males appear to not use this information to avoid potentially costly interactions with dominant males, suggesting that YR fin coloration has not evolved as a cue in agonistic interactions.

Pigmentation in Xiphophorus: an emerging system in ecological and evolutionary genetics

The genus Xiphophorus has great potential to contribute to the study of vertebrate pigmentation and elucidating the relative influence of ecology, physiology, and behavior on evolution at the molecular level. More importantly, the association between pigmentation and a functional oncogene offers the potential to understand the evolution and maintenance of cancer-causing genetic elements. Using criteria laid out recently in the literature, I demonstrate the power of the Xiphophorus system for studying pigment evolution through integrative organismal biology. Using the most recent phylogeny, the phylogenetic distribution of several important pigmentation loci are reevaluated. I then review support for existing hypotheses of the functional importance of pigmentation. Finally, new observations and hypotheses regarding some of the characteristics of pigment patterns in natural populations and open questions and future directions in the study of the evolution of these traits are discussed.