Search

Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei , but also with Poecilia picta , which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation., Competing Interests: The authors declare no conflict of interest., (Copyright © 2019 the Author(s). Published by PNAS.)

The molecular basis of convergent phenotypes is often unknown. However, convergence at a genomic level is predicted when there are large population sizes, gene flow among diverging lineages or strong genetic constraints. We used whole-genome resequencing to investigate genomic convergence in fishes ( Poecilia spp.) that have repeatedly colonized hydrogen sulfide (H 2 S)-rich environments in Mexico. We identified genomic similarities in both single nucleotide polymorphisms (SNPs) and structural variants (SVs) among independently derived sulfide spring populations, with approximately 1.2% of the genome being shared among sulfidic ecotypes. We compared these convergent genomic regions to candidate genes for H 2 S adaptation identified from transcriptomic analyses and found that a significant proportion of these candidate genes (8%) were also in regions where sulfidic individuals had similar SNPs, while only 1.7% were in regions where sulfidic individuals had similar SVs. Those candidate genes included genes involved in sulfide detoxification, the electron transport chain (the main toxicity target of H 2 S) and other processes putatively important for adaptation to sulfidic environments. Regional genomic similarity across independent populations exposed to the same source of selection is consistent with selection on standing variation or introgression of adaptive alleles across divergent lineages. However, combined with previous analyses, our data also support that adaptive changes in mitochondrially encoded subunits arose independently via selection on de novo mutations. Pressing questions remain on what conditions ultimately facilitate the independent rise of adaptive alleles at the same loci in separate populations, and thus, the degree to which evolution is repeatable or predictable. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Identifying mechanisms of reproductive isolation is key to understanding speciation. Among the putative mechanisms underlying reproductive isolation, sperm-female interactions (post-mating-prezygotic barriers) are arguably the hardest to identify, not least because these are likely to operate at the cellular or molecular level. Yet sperm-female interactions offer great potential to prevent the transfer of genetic information between different populations at the initial stages of speciation. Here, we provide a preliminary test for the presence of a putative post-mating-prezygotic barrier operating between three populations of Trinidadian guppies (Poecilia reticulata), an internally fertilizing fish that inhabits streams with different levels of connectivity across Trinidad. We experimentally evaluate the effect of female ovarian fluid on sperm velocity (a predictor of competitive fertilization success) according to whether males and females were from the same (native) or different (foreign) populations. Our results reveal the potential for ovarian fluid to act as a post-mating-prezygotic barrier between two populations from different drainages, but also that the strength of this barrier is different among populations. This result may explain the previous finding that, in some populations, sperm from native males have precedence over foreign sperm, which could eventually lead to reproductive isolation between these populations., (© 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.)

megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs., (© 2016 John Wiley & Sons Ltd.)

The subgenus Mollienesia is a diverse group of freshwater fishes, including species that have served as important models across multiple biological disciplines. Nonetheless, the taxonomic history of this group has been conflictive and convoluted, in part because the evolutionary relationships have not been rigorously resolved. We conducted a comprehensive molecular phylogenetic analysis of the subgenus Mollienesia to identify taxonomic discrepancies and potentially identify undescribed species, estimate ancestral areas of origin and estimate dates of divergence, as well as explore biogeographical patterns. Our findings confirm the presence of three main clades composed of the P. latipinna, P. sphenops, and P. mexicana species complexes. Unlike previously hypothesized morphology-based analyses, species found on the Caribbean Islands are not part of Mollienesia, but are more closely related to species of the subgenus Limia. Our study also revealed several taxonomic inconsistencies and distinct lineages in the P. mexicana species complex that may represent undescribed species. The diversity in the subgenus Mollienesia is a result of dynamic geologic activity leading to vicariant events, dispersal across geologic blocks, and ecological speciation., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes. A divergence-dating analysis supported the hypothesis of the genus Poecilia dispersing into Central America in the early Pliocene (ancestors of Psychropoecilia+Allopoecilia+Mollienesia: 7.3-2.0Mya) from predominantly South America. Subsequently, one lineage (subgenus Allopoecilia: 5.1-1.3Mya) expanded deeper into South America from Lower-Central America, and one lineage expanded from Nuclear-Central America into South America (subgenus Mollienesia: 0.71-0.14Mya). The subgenus Mollienesia diverged into three monophyletic groups that can be identified by nuptial male dorsal fin morphology and inner jaw dentition. A subclade of the unicuspid short-fins (subgenus Mollienesia) was the lineage that expanded into South America during the middle Pleistocene. Species in this subclade are now distributed across northern South America, where they are partially sympatric with Allopoecilia. However the P. (A.) caucana complex was not monophyletic, with P. (A.) wandae clustering in the Mollienesia subclade that expanded into South America. It is apparent that characters (body size, scale count, pigmentation, and gonopodium morphology) used to define the P. (A.) caucana complex are homoplastic and suggestive of rapid convergence in northern South America. Our improved taxon sampling and divergence-time calibration allowed for insights into the timing and direction of dispersals, and provides an improved understanding of the biogeographic history of an enigmatic group of fishes. Furthermore, we provided strong evidence for the monophyly of the subgenus Mollienesia and further substantiated its species complexes; therefore, we advise a taxonomic re-evaluation for the P. (A.) caucana complex to maintain monophyly of both Mollienesia and Allopoecilia., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Background: Sensory Bias models for the evolution of mate preference place a great emphasis on the role of sensory system variation in mate preferences. However, the extent to which sensory systems vary across- versus within-species remains largely unknown. Here we assessed whether color vision varies in natural locations where guppies (Poecilia reticulata) and their two closest relatives, Poecilia parae and Poecilia picta, occur in extreme sympatry and school together. All three species base mate preferences on male coloration but differ in the colors preferred., Results: Measuring opsin gene expression, we found that within sympatric locations these species have similar color vision and that color vision differed more across populations of conspecifics. In addition, all three species differ across populations in the frequency of the same opsin coding polymorphism that influences visual tuning., Conclusions: Together, this shows sensory systems vary considerably across populations and supports the possibility that sensory system variation is involved in population divergence of mate preference.

Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci) from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively) 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the importance of testing for hybridization versus incomplete lineage sorting, which aids inference of not only species limits but also evolutionary processes influencing genetic diversity.

Cryptic species complexes are common among parasites, which tend to have large populations and are subject to rapid evolution. Such complexes may arise through host-parasite co-evolution and/or host switching. For parasites that reproduce directly on their host, there might be increased opportunities for sympatric speciation, either by exploiting different hosts or different micro-habitats within the same host. The genus Gyrodactylus is a specious group of viviparous monogeneans. These ectoparasites transfer between teleosts during social contact and cause significant host mortality. Their impact on the guppy (Poecilia reticulata), an iconic evolutionary and ecological model species, is well established and yet the population genetics and phylogenetics of these parasites remains understudied. Using mtDNA sequencing of the host and its parasites, we provide evidence of cryptic speciation in Gyrodactylus bullatarudis, G. poeciliae and G. turnbulli. For the COII gene, genetic divergence of lineages within each parasite species ranged between 5.7 and 17.2%, which is typical of the divergence observed between described species in this genus. Different lineages of G. turnbulli and G. poeciliae appear geographically isolated, which could imply allopatric speciation. In addition, for G. poeciliae, co-evolution with a different host species cannot be discarded due to its host range. This parasite was originally described on P. caucana, but for the first time here it is also recorded on the guppy. The two cryptic lineages of G. bullatarudis showed considerable geographic overlap. G. bullatarudis has a known wide host range and it can also utilize a killifish (Anablepsoides hartii) as a temporary host. This killifish is capable of migrating overland and it could act as a transmission vector between otherwise isolated populations. Additional genetic markers are needed to confirm the presence of these cryptic Gyrodactylus species complexes, potentially leading to more in-depth genetic, ecological and evolutionary analyses on this multi-host-parasite system.

Background: Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild., Results: To gain insight into molecular mechanisms underlying the guppy's sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions., Conclusions: Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues.

The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution)., (© 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.)

Background: The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique., Results: 83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly., Conclusions: We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.

Background: Geographic barriers to gene flow and divergence among populations in sexual traits are two important causes of genetic isolation which may lead to speciation. Genetic isolation may be facilitated if these two mechanisms act synergistically. The guppy from the Cumaná region (within the Cariaco drainage) of eastern Venezuela has been previously described as a case of incipient speciation driven by sexual selection, significantly differentiated in sexual colouration and body shape from the common guppy, Poecilia reticulata. The latter occurs widely in northern Venezuela, including the south-eastern side of Cordillera de la Costa, where it inhabits streams belonging to the San Juan drainage. Here, we present molecular and morphological analyses of differentiation among guppy populations in the Cariaco and San Juan drainages. Our analyses are based on a 953 bp long mtDNA fragment, a set of 15 microsatellites (519 fish from 20 populations), and four phenotypic traits., Results: Both microsatellite and mtDNA data showed that guppies inhabiting the two drainages are characterised by a significant genetic differentiation, but a higher proportion of the genetic variance was distributed among populations within regions. Most guppies in the Cariaco drainage had mtDNA from a distinct lineage, but we also found evidence for widespread introgression of mtDNA from the San Juan drainage into the Cariaco drainage. Phenotypically, populations in the two regions differed significantly only in the number of black crescents. Phenotypic clustering did not support existence of two distinct groupings, but indicated a degree of distinctiveness of Central Cumaná (CC) population. However, CC population showed little differentiation at the neutral markers from the proximate populations within the Cariaco drainage., Conclusions: Our findings are consistent with only partial genetic isolation between the two geographic regions and indicate that the geographic barrier of Cordillera de la Costa has not played an important role in strengthening the incomplete pre-zygotic reproductive barrier between Cumaná and common guppy. Significant phenotypic differentiation between genetically similar (in terms of neutral variation) populations suggests that mate choice can maintain divergence at sexually selected traits despite gene flow. However, neither genetic nor phenotypic clustering supported delineation of two species within the region.

The fitness of male guppies (Poecilia reticulata) highly depends on the size and number of their black, blue, and orange ornaments. Recently, progress has been made regarding the genetic mechanisms underlying male guppy pigment pattern formation, but we still know little about the pigment cell organization within these ornaments. Here, we investigate the pigment cell distribution within the black, blue, and orange trunk spots and selected fin color patterns of guppy males from three genetically divergent strains using transmission electron microscopy. We identified three types of pigment cells and found that at least two of these contribute to each color trait. Further, two pigment cell layers, one in the dermis and the other in the hypodermis, contribute to each trunk spot. The pigment cell organization within the black and orange trunk spots was similar between strains. The presence of iridophores in each of the investigated color traits is consistent with a key role for this pigment cell type in guppy color pattern formation.

Exotic fish species has caused several impacts on aquatic biodiversity. The Lago de Pátzcuaro has some well-studied exotic species, except the Lerma livebearer Poeciliopsis infans. This fish species was introduced into the Lago de Pátzcuaro before 1997 and the aspects of its biology are still unknown. In this study we assessed aspects of the trophic ecology of this exotic fish, P infans, using gut content and stable isotope analysis to understand its capacity to tolerate anthropogenic environmental degradation in the Lago de Pátzcuaro. We also determined its trophic guild position (TP) using the TrophLab Program and stable isotope. Niche breadth was calculated by standardized Levins' Index (Bi). Fish was captured with a seine during wet and dry seasons at six environmentally different sites and gut contents were obtained. We analyzed a total of 239 gut contents of P. infans. The contribution of each food item in the diet was quantified using frequency of occurrence and area percentage. The importance of each prey item was determined according to the index of relative importance (IRI), and the omnivory index (OI) was used to assess the feeding behavior. Fish were categorized by size and the diet was compared between fish sizes and sites. Dorsal muscle tissue and water hyacinth tissue was obtained for nitrogen isotope signature he fish can behave as a specialist (Bi = 0.39) or generalist (Bi = 0.68) and as a primary consumer (TROPH = 2.2; TP = 2.3) with a feeding strategy that was the same at dif- f erent sizes, seasons and sites. None of the evaluated sites showed good environmental quality. We argue that P infans can tolerate changes in water quality and feeding items availability, because it can exploit resources in multiple trophic webs. However, this species could be dependent on habitat complexity, especially in the aquatic vegetation cover.

The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations residing in adjacent sulfidic and non-sulfidic environments.

We inferred the phylogenetic relationships among members of the Poecilia sphenops species complex to resolve the colonization process and radiation of this group in Central America. We analyzed 2550 base pairs (bp) of mitochondrial DNA (mtDNA), including ATP synthase 6 and 8, cytochrome oxidase subunit I and NADH dehydrogenase subunit 2 genes, and 906bp of the nuclear S7 ribosomal protein of 86 ingroup individuals from 61 localities spanning most of its distribution from Mexico to Panama. Our mitochondrial data rendered a well-supported phylogeny for the P. sphenops complex that differed with the nuclear data set topology, which did not recover the monophyly of the P. mexicana mitochondrial lineage. Coalescent-based simulations tests indicated that, although hybridization cannot be completely ruled out, this incongruence is most likely due to incomplete lineage sorting in this group, which also showed the widest geographic distribution. A single colonization event of Central America from South America was estimated to have occurred between the early Paleocene and Oligocene (53-22millionyears ago). Subsequently, two largely differentiated evolutionary lineages diverged around the Early Oligocene-Miocene (38-13million years ago), which are considered two separate species complexes: P. sphenops and P. mexicana, which can also be distinguished by their tricuspid and unicuspid inner jaw teeth, respectively. Ultimately, within lineage diversification occurred mainly during the Miocene (22-5million years ago). All major cladogenetic events predated the final closure of the Isthmus of Panama. The allopatric distribution of lineages together with the long basal internodes suggest that vicariance and long term isolations could be the main evolutionary forces promoting radiation in this group, although dispersal through water barriers might also have occurred. Lastly, our results suggest the need to review the current species distribution and taxonomy of the P. sphenops complex sensu lato., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Understanding disease transmission is important to species management and human health. Host body condition, nutrition and disease susceptibility interact in a complex manner, and while the individual effects of these variables are well known, our understanding of how they interact and translate to population dynamics is limited. Our objective was to determine whether host relative body condition influences epidemic dynamics, and how this relationship is affected by food availability. Poecilia reticulata (guppies) of roughly similar size were selected and assembled randomly into populations of 10 guppies assigned to 3 different food availability treatments, and the relative condition index (Kn) of each fish was calculated. We infected 1 individual per group ('source' fish) with Gyrodactyus turnbulli and counted parasites on each fish every other day for 10 days. Epidemic parameters for each population were analysed using generalized linear models. High host Kn-particularly that of the 'source' fish-exerted a positive effect on incidence, peak parasite burden, and the degree of parasite aggregation. Low food availability increased the strength of the associations with peak burden and aggregation. Our findings suggest that host Kn and food availability interact to influence epidemic dynamics, and that the condition of the individual that brings the parasite into the host population has a profound impact on the spread of infection.

We investigated replicated ecological speciation in the livebearing fish Poecilia mexicana and P. sulphuraria (Poeciliidae), which inhabit freshwater habitats and have also colonized multiple sulfidic springs in southern Mexico. These springs exhibit extreme hypoxia and high concentrations of hydrogen sulfide, which is lethal to most metazoans. We used phylogenetic analyses to test whether springs were independently colonized, performed phenotypic assessments of body and gill morphology variation to identify convergent patterns of trait differentiation, and conducted an eco-toxicological experiment to detect differences in sulfide tolerances among ecotypes. Our results indicate that sulfidic springs were colonized by three different lineages, two within P. mexicana and one representing P. sulphuraria. Colonization occurred earlier in P. sulphuraria, whereas invasion of sulfidic springs in P. mexicana was more recent, such that each population is more closely related to neighboring populations from adjacent nonsulfidic habitats. Sulfide spring fish also show divergence from nonsulfidic phenotypes and a phenotypic convergence toward larger heads, larger gills, and increased tolerance to H(2) S. Together with previous studies that indicated significant reproductive isolation between fish from sulfidic and nonsulfidic habitats, this study provides evidence for repeated ecological speciation in the independent sulfide spring populations of P. mexicana and P. sulphuraria., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

Members of Poeciliidae are used as model organisms for experimental studies on natural and sexual selection, and comparative studies of life-history evolution. The latter have demonstrated multiple origins of both superfetation and placentotrophy within Poeciliidae. Most recently, placentotrophy has been described in five species of Poecilia (Pamphorichthys), but only one of these (P.hasemani) shows evidence of superfetation. Here, we use a molecular phylogeny based on concatenated nuclear and mitochondrial gene sequences to test hypotheses of correlated evolution between superfetation and placentotrophy in Poecilia. Taxon sampling included all species in the subgenera Micropoecilia and Pamphorichthys for which the presence or absence of placentotrophy and superfetation have been determined, as well as representatives of all other Poecilia subgenera (Acanthophacelus, Limia, Mollienesia, Poecilia, Pseudolimia). Phylogenetic analyses were performed with maximum parsimony, maximum likelihood, and Bayesian methods; ancestral states for life-history characters were reconstructed with parsimony and SIMMAP; correlation analyses were performed with SIMMAP; and divergence times were estimated using a relaxed molecular clock. All subgenera in Poecilia were recovered as monophyletic. The basal split in Poecilia is between P. (Acanthophacelus)+P. (Micropoecilia) and the other five subgenera. In the latter clade, P. (Poecilia) is the sister-group to the remaining four subgenera. Within P. (Pamphorichthys), all analyses with the combined data set recovered P. (Pamphorichthys) araguaiensis as the sister taxon to P. (Pamphorichthys) hollandi, and P. (Pamphorichthys) scalpridens as the sister taxon to P. (Pamphorichthys) minor. P. (Pamphorichthys) hasemani was either the sister taxon to P. (Pamphorichthys) hollandi+P. (Pamphorichthys) minor (maximum likelihood, Bayesian) or the sister taxon to all other Pamphorichthys species (maximum parsimony). Ancestral state reconstructions suggest that placentotrophy and superfetation evolved on the same branch in P. (Micropoecilia), whereas placentotrophy evolved before superfetation in P. (Pamphorichthys). SIMMAP analyses indicate a statistically significant association between placentotrophy and superfetation. Within P. (Micropoecilia) both placentotrophy and superfetation evolved in ≤4 million years. Within P. (Pamphorichthys), superfetation evolved in ≤9 million years on the P. (Pamphorichthys) hasemani branch, and placentotrophy evolved in ≤10 million years in the common ancestor of this subgenus., (Copyright © 2011. Published by Elsevier Inc.)

Diversification of freshwater fishes on islands is considered unlikely because the traits that enable successful colonization-specifically, broad salinity tolerances and the potential for oceanic dispersal-may also constrain post-colonization genetic differentiation. Some secondary freshwater fish, however, exhibit pronounced genetic differentiation and geographic structure on islands, whereas others do not. It is unclear what conditions give rise to contrasting patterns of differentiation because few comparative reconstructions of population history have been carried out for insular freshwater fishes. In this study, we examined the phylogeography of Hart's killifish (Rivulus hartii) across Trinidad, with reference to neighboring islands and northern South America, to test hypotheses of colonization and differentiation derived from comparable work on co-occurring guppies (Poecilia reticulata). Geographic patterns of mitochondrial DNA haplotype variation and microsatellite genotype variation provide evidence of genetic differentiation of R. hartii among islands and across Trinidad. Our findings are largely consistent with patterns of geographically structured ancestry and admixture found in Trinidadian guppies, which suggests that both species share a history of colonization and differentiation and that post-colonization diversification may be more common among members of insular freshwater fish assemblages than has been previously thought., (© 2010 Blackwell Publishing Ltd.)

Cave fish have rarely been investigated with regard to their inner ear morphology, hearing abilities, and acoustic communication. Based on a previous study that revealed morphological differences in the saccular otolith between a cave and two surface populations of Poecilia mexicana, we checked for additional differences in utricular and lagenar otoliths and tested whether different populations have similar hearing sensitivities. We found pronounced differences in the shape of all three otoliths. Otoliths of the saccule and lagena from cave fish differed from those of surface fish in the features of the face oriented towards the sensory epithelium. In addition, otoliths of the utricle and lagena were significantly heavier in cave fish. Auditory sensitivities were measured between 100 and 1500Hz, utilizing the auditory evoked potential recording technique. We found similar hearing abilities in cave and surface fish, with greatest sensitivity between 200 and 300Hz. An acoustic survey revealed that neither ecotype produced species-specific sounds. Our data indicate that cave dwelling altered the otolith morphology in Atlantic mollies, probably due to metabolic differences. Different otolith morphology, however, did not affect general auditory sensitivity or acoustic behavior., (Copyright 2010 Elsevier B.V. All rights reserved.)

Poeciliids are one of the most intensively studied groups within Cyprinodontiformes owing to their use as model organisms for experimental studies on natural and sexual selection, and comparative studies of life-history evolution. Life-history studies have demonstrated multiple origins of placentotrophy and superfetation in poeciliids, including the recent description of placentotrophy in three species of Poecilia (Micropoecilia): P. bifurca, P. branneri, and P. parae. Here, we use a concatenation of seven nuclear gene segments and two mitochondrial segments to examine relationships within Micropoecilia and between this subgenus and other subgenera in Poecilia (Mollienesia, Limia, Pamphorichthys, Acanthophacelus). The combined molecular data set (8668 bp) was analyzed with maximum parsimony, maximum likelihood, and Bayesian methods. We also employed a relaxed molecular clock method to estimate divergence times within Poecilia. All phylogenetic analyses with the combined DNA data set supported the monophyly of Poecilia and recovered a basal split between Poecilia (Acanthophacelus)+Poecilia (Micropoecilia) and the other three subgenera. Within Micropoecilia, P. bifurca grouped with P. branneri, and these joined P. parae to the exclusion of P. picta. Ancestral reconstructions based on parsimony and Bayesian methods suggest that placentotrophy evolved once in Micropoecilia in the common ancestor of P. bifurca, P. branneri, and P. parae. Divergence time estimates suggest that placentotrophy in Micropoecilia evolved in 4 million years., (Copyright 2009 Elsevier Inc. All rights reserved.)

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F(ST) values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F(ST) outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations.

The majority of studies on ecological speciation in animals have investigated the divergence caused by biotic factors like divergent food sources or predatory regimes. Here, we examined a system where ecological speciation can clearly be ascribed to abiotic environmental gradients of naturally occurring toxic hydrogen sulfide (H(2)S). In southern Mexico, two genera of livebearing fishes (Poeciliidae: Poecilia and Gambusia) thrive in various watercourses with different concentrations of H(2)S. Previous studies have revealed pronounced genetic differentiation between different locally adapted populations in one species (Poecilia mexicana), pointing towards incipient speciation. In the present study, we examined female reproductive life-history traits in two species pairs: Gambusia sexradiata (from a nonsulfidic and a sulfidic habitat) and Gambusia eurystoma (sulfide-endemic), as well as P. mexicana (nonsulfidic and sulfidic) and Poecilia sulphuraria (sulfide endemic). We found convergent divergence of life-history traits in response to sulfide; most prominently, extremophile poeciliids exhibit drastically increased offspring size coupled with reduced fecundity. Furthermore, within each genus, this trend increased with increasing sulfide concentrations and was most pronounced in the two endemic sulfur-adapted species. We discuss the adaptive significance of large offspring size in toxic environments and propose that divergent life-history evolution may promote further ecological divergence through isolation by adaptation.

The highly diverse genes of the major histocompatibility complex (MHC) are important in the adaptive immune system and are expected to be under selection from pathogens. Thus, the MHC genes provide an exceptional opportunity to investigate patterns of selection within and across populations. In this study, we analyzed genetic variation at the MHC class IIB gene and six microsatellite loci across 10 populations of guppies (Poecilia reticulata) in the northern range of Trinidad. We found a high level of diversity at the MHC, with a total of 43 alleles in 142 individuals. At the population level, we found that neutral evolution could not fully account for the variability found at the MHC. Instead, we found that MHC F(ST) statistics were lower than F(ST) derived from the microsatellite loci; 33 of 45 population pairwise estimates for the MHC were significantly lower than those for the microsatellite loci, and MHC F(ST) estimates were consistently lower than those predicted by a coalescent model of neutral evolution. These results suggest a similar selection acting across populations, and we discuss the potential roles of directional and balancing selection. At the sequence level, we found evidence for both positive and purifying selection. Furthermore, positive selection was detected within and adjacent to the putative peptide-binding region (PBR) of the MHC. Surprisingly, we also found a purifying selection at two sites within the putative PBR. Overall, our data provide evidence for selection for functional diversity at the MHC class IIB gene at both the population and nucleotide levels of guppy populations.

Insight into the processes of evolutionary change can be obtained by studying the distribution of genetic diversity among populations. Such diversity can be shaped by historical colonization events, population connectivity and adaptation to local selection pressures. Here we examine genetic differentiation of Trinidadian guppies, Poecilia reticulata, by genotyping 373 individuals from 15 populations located in three drainages (northern coast, Caroni and Oropouche) with 7 microsatellite loci. Our data provide little evidence to support previous claims of two major genetic lineages of guppies in northern Trinidad but instead suggest a more complex pattern of gene flow among populations from different drainages. First, some of the populations in the Caroni drainage show genetic signatures similar to those in the Oropouche drainage. Second, the populations in the northern coast are all highly differentiated from those in either the Caroni or Oropouche drainages. Despite differing selection regimes owing to predation pressure, populations from upstream and downstream locales typically cluster together, albeit upstream populations consistently have less genetic variability than the corresponding downstream population. There is, however, no overall pattern of isolation by distance. We also find evidence that an artificially transplanted population from the Caroni drainage is successfully invading into other populations within the Oropouche system. Our analysis details the genetic and phylogeographic structure of Trinidadian guppies in the northern range and provides insight into evolutionary processes at different timescales that have shaped genetic heterogeneity in this fish.

The life history of the trematode Pygidiopsis macrostomum Travassos, 1928 is described for the first time. Rediae and cercariae were obtained from naturally infected snails Heleobia australis (d Orbigny), a new first intermediate host. Metacercariae were found encysted in the mesenteries of three naturally infected guppies, Phalloptychus januarius (Hensel), Jenynsia multidentata (Jenyns) (new host records) and Poecilia vivipara Bloch and Schneider. Experimental infections were successfully completed in the intermediate hosts H. australis and Poe. vivipara reared in the laboratory and hamsters Mesocricetus auratus Waterhouse were utilised as a definitive host.

A reproductive analysis of 1225 specimens of Poeciliopsis gracilis obtained through monthly samples from Coatetelco, a tropical shallow lake in Central Mexico, was made. There was an evident sexual dimorphism, including a difference in body size at the onset of reproduction. Sex ratio deviated significantly from unity. Monthly variations in gonadosomatic (GSI), hepatosomatic (HSI) indexes and ovarian development stages showed that the spawning season was from July to October, coinciding with the rainy season and phytoplankton biomass increase. The largest sizes were 50 mm for females and 43 mm for males.

Background: Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation. In cichlids, for example, long wavelength-sensitive (LWS) opsins appear to play a role in mate choice and male color variation within and among species. To test the hypothesis that the evolution of elaborate coloration in male guppies (Poecilia reticulata) is also associated with opsin gene diversity, we sequenced long wavelength-sensitive (LWS) opsin genes in six species of the family Poeciliidae., Results: Sequences of four LWS opsin genes were amplified from the guppy genome and from mRNA isolated from adult guppy eyes. Variation in expression was quantified using qPCR. Three of the four genes encode opsins predicted to be most sensitive to different wavelengths of light because they vary at key amino acid positions. This family of LWS opsin genes was produced by a diversity of duplication events. One, an intronless gene, was produced prior to the divergence of families Fundulidae and Poeciliidae. Between-gene PCR and DNA sequencing show that two of the guppy LWS opsins are linked in an inverted orientation. This inverted tandem duplication event occurred near the base of the poeciliid tree in the common ancestor of Poecilia and Xiphophorus. The fourth sequence has been uncovered only in the genus Poecilia. In the guppies surveyed here, this sequence is a hybrid, with the 5' end most similar to one of the tandem duplicates and the 3' end identical to the other., Conclusion: Enhanced wavelength discrimination, a possible consequence of opsin gene duplication and divergence, might have been an evolutionary prerequisite for color-based sexual selection and have led to the extraordinary coloration now observed in male guppies and in many other poeciliids.

We use microsatellite loci to detail the multiple paternity patterns in broods from 10 wild populations of the guppy (Poecilia reticulata) found in Northern Trinidad. The populations span two major drainages comprising the Caroni and the Oropouche, and include sites that are characterized by either high or low predation. Across the populations the frequency of multiple paternity is high with 95% (range: 70%-100%) of broods having multiple sires. Broods have an average of 3.5 sires (range: 1-9) and a mixed-model analysis suggests that broods from high predation sites have marginally more sires than do those from low predation sites, but this is true only in the Oropouche drainage. There is no difference in sire number between predation sites in the Caroni drainage. Brood size, but not female body length, is correlated with the number of sires and the correlation cannot be attributed solely to the stochastic process associated with sperm competition and a 'fair raffle'. Within broods there is significant skew in reproductive success among males, which may reflect variation in sperm competitiveness or female choice. There is, however, no difference in the skew among populations from different predation regimes or drainages. Finally, high predation populations were characterized by increased genetic variability at the microsatellite loci, suggesting a larger effective population size. We discuss explanations for the high degree of multiple paternity but the general lack of any major differences among broods from ecologically different populations.

Background: The guppy, Poecilia reticulata, is a well-known model organism for studying inheritance and variation of male ornamental traits as well as adaptation to different river habitats. However, genomic resources for studying this important model were not previously widely available., Results: With the aim of generating molecular markers for genetic mapping of the guppy, cDNA libraries were constructed from embryos and different adult organs to generate expressed sequence tags (ESTs). About 18,000 ESTs were annotated according to BLASTN and BLASTX results and the sequence information from the 3' UTRs was exploited to generate PCR primers for re-sequencing of genomic DNA from different wild type strains. By comparison of EST-linked genomic sequences from at least four different ecotypes, about 1,700 polymorphisms were identified, representing about 400 distinct genes. Two interconnected MySQL databases were built to organize the ESTs and markers, respectively. A robust phylogeny of the guppy was reconstructed, based on 10 different nuclear genes., Conclusion: Our EST and marker databases provide useful tools for genetic mapping and phylogenetic studies of the guppy.

Since 1997, Poeciliopsis infans Woolman 1894 has been recognized as a new inhabitant of Lake Patzcuaro, Michoacan in Central Mexico. Between February 1997 and October 1998, nine fish samples were collected at Lake Patzcuaro. Morphometric and meristic counts were conducted on a random selection of 40 organisms of both sexes of Poeciliopsis infans. Males of these viviparous fish posses a modified anal fin called gonopodium. The characteristic hemal spine on the 18th caudal vertebra for this species is described herein and the bony components of the gonopodial structure and suspensoria that together comprise the gonopodial system, which is important for taxonomic studies at various levels of classification were reviewed. Poeciliopsis infans displays a high degree of sexual dimorphism in body shape and anal fin anatomy with the most conspicuous difference observed in anal fin height, which averages 40% of SI in males and 17% in females. Comparisons between male and female anal fins are described herein as well as the possible impacts of this species on Lake Patzcuaro fish fauna.

To assess the historical biogeography of freshwater topminnows in the genus Poeciliopsis, we examined sequence variation in two mitochondrial genes, cytochrome b (1140 bp) and NADH subunit 2 (1047 bp). This widespread fish genus is distributed from Arizona to western Colombia, and nearly half of its 21 named species have distributions that border on the geologically active Trans-Mexican Volcanic Belt (TMVB), a region that defines the uplifted plateau (Mesa Central) of Mexico. We used the parametric bootstrap method to test the hypothesis that a single vicariant event associated with the TMVB was responsible for divergence of taxa found to the north and south of this boundary. Because the single-event hypothesis was rejected as highly unlikely, we hypothesize that at least two geological events were responsible for divergence of these species. The first (8-16 million years ago) separated ancestral populations that were distributed across the present TMVB region. A second event (2.8-6.4 million years ago) was associated with northward dispersal and subsequent vicariance of two independent southern lineages across the TMVB. The geological history of this tectonically and volcanically active region is discussed and systematic implications for the genus are outlined.

Crossing experiments revealed that a diploid hybridogenetic fish (genus Poeciliopsis) from the Río Mocorito (Sinaloa, Mexico) is trihybrid. Its haploid maternal genome is inherited clonally (i.e., hemiclonally), and it expresses a mixture of morphological traits found in the closely related species P. monacha and P. viriosa. Its haploid paternal genome is replaced in each generation by mating with males of a more distantly related sexual species, P. lucida. However, expression of mixed (monacha X viriosa) traits by this hemiclone is also consistent with retention of shared ancestral polymorphisms. If true, this hemiclonal lineage would be one of the few examples of an ancient asexual taxon. We used mitochondrial DNA and allozymes to test whether the maternal progenitor of the Mocorito hybridogen was a recent P. monacha X P. viriosa hybrid or a remnant of their most recent common ancestor. Our results clearly link the hemiclonal genome to contemporary P. monacha and therefore support the hypothesis of a recent origin. Additionally, our findings suggest that this unisexual fish may serve as a vehicle for introgression between two allopatric sexual species.

Members of the genus Poecilia exhibit extensive morphological, behavioral, and life history variation within and between species. This natural variation, coupled with short generation times and the ease with which members of this genus can be cultured in the lab, have made several species model systems for studying the effects of sexual and natural selection on the evolution of natural populations. Given that there is no clear understanding of the phylogenetic relationships within the genus, these studies have not been put into a historical context, and between-species comparisons have been limited. We sequenced the complete NADH Dehydrogenase Subunit 2 (ND2) mitochondrial gene (1047 bp) in representatives of the major divisions of the genus in order to examine these relationships. The subgeneric groups of Rosen and Bailey (1963) are, for the most part, supported, with some adjustment within the subgenera Poecilia and Pamphorichthys. The morphological distinctness of the groups within Poecilia suggest that the original generic designations be reinstated, but this awaits a more thorough analysis. Two implications from the phylogeny are particularly relevant to sexual selection studies: within the North and Central American mollies, the three species of sailfin mollies form a monophyletic group, and within the subgenus Lebistes, the sister taxon to the guppy, P. reticulata, is most likely the group of species previously designated as Micropoecilia., (Copyright 1999 Academic Press.)

Experimental study of efficiency of Gambusia affinis holbrooki (GIRARD, 1859) (Fish-Poecilidae). Gambusia affinis is a culiciphage fish which was introduced in Tunisia in 1929 to control mosquito larvae. In the present study, we confirm, under laboratory conditions, the good efficacy of Gambusia affinis against mosquito larvae. The consumption of larvae decreases with the evolution of larvae instars and increases, for the same instar, in relation with the fish size. In fact, the size of the prey is related to the predator's size: fish belonging to the length class [20-24 mm] prefer IIIrd instar, fish from class length [25-29 mm] prefer pupae and IVth instar. The trophic test shows that G. affinis has a clear preference for Culicidae larvae, except fish belonging to the 2 length classes [35-39 mm] and [40-44 mm] for which Culicidae and Ephemeroptera have similar preference. In addition, at high temperature (30 degrees C), Gambusia affinis has a higher efficiency.