Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae)

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.

Population structure of guppies in north-eastern Venezuela, the area of putative incipient speciation

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.

Multiple pigment cell types contribute to the black, blue, and orange ornaments of male guppies (Poecilia reticulata)

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.

Trophic ecology of the exotic Lerma livebearer Poeciliopsis infans (Cyprinodontiformes: Poeciliidae) in the Lago de Pátzcuaro, Central Mexico

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 rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs

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.

Otolith morphology and hearing abilities in cave- and surface-dwelling ecotypes of the Atlantic molly, Poecilia mexicana (Teleostei: Poeciliidae)

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.

The molecular basis of color vision in colorful fish: four long wave-sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites

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.

ESTs and EST-linked polymorphisms for genetic mapping and phylogenetic reconstruction in the guppy, Poecilia reticulata

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.

Gonopodial system review and a new fish record of Poeciliopsis infans (Cyprinodontiformes: Poeciliidae) for Lake Patzcuaro, Michoacan, central Mexico

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.

Historical biogeography of the livebearing fish genus Poeciliopsis (Poeciliidae: Cyprinodontiformes)

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.

Ancient versus reticulate origin of a hemiclonal lineage

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.

Molecular phylogeny of the live-bearing fish genus Poecilia (Cyprinodontiformes: Poeciliidae)

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.

[Experimental study of larval efficiency of Gambusia affinis holbrooki (GIRARD, 1859) (fish-Poecilidae)]

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.