Microsatellite allele size homoplasy in the guppy (Poecilia reticulata)

Can female guppies learn to like male colours? A test of the role of associative learning in originating sexual preferences

How do female sexual preferences for male ornamental traits arise? The developmental origins of female preferences are still an understudied area, with most explanations pointing to genetic mechanisms. One intriguing, little-explored, alternative focuses on the role of associative learning in driving this process. According to this hypothesis, a preference learned in an ecological context can be transferred into a sexual context, resulting in changes in mating preferences as a by-product. I tested this hypothesis by first training female guppies to associate either orange or black colour with food delivery; I then presented videos of males with computer-manipulated coloured spots and measured female preference towards them. I also allowed females from both treatments to mate with males differing in their ratio of orange-to-black spots and measured the males' reproductive success. After training, female sexual preferences significantly diverged among treatments in the expected direction. In addition, orange males sired a greater proportion of offspring with females food-conditioned on orange compared to those conditioned on black. These results show that mating preferences can arise as a by-product of associative learning, which, via translation into variation in male fitness, can become associated with indirect genetic benefits, potentially leading to further evolution.

What do orange spots reveal about male (and female) guppies? A test using correlated responses to selection

Female preferences for male ornamental traits can arise from indirect benefits, such as increased attractiveness or better viability of progeny, but empirical evidence for such benefits is inconsistent. Artificial selection offers a powerful way to investigate indirect effects of male ornaments. Here, we selected for the area of orange spots on male guppies, a trait subject to female preferences in our population, in replicated up‐ and down‐selected lines. We found a significant direct response to selection, and a correlated response in female preferences, with females from down‐selected lines showing less interest in more orange males. Nevertheless, up‐selected males sired more offspring in direct competition with low‐selected males, irrespective of female origin. We did not find a significantly correlated response to selection among any other fitness correlates we measured. Our results imply that female preferences for orange spots can lead to increased reproductive success of their sons, with no effect on general viability of progeny. Furthermore, although we demonstrate that female preferences may evolve via linkage disequilibrium with the preferred trait, the potential for runaway selection by positive feedback may be constrained by the lack of corresponding linkage with male reproductive competitiveness.

Female sperm storage mediates post-copulatory costs and benefits of ejaculate anticipatory plasticity in the guppy

Males of many species evolved the capability of adjusting their ejaculate phenotype in response to social cues to match the expected mating conditions. When females store sperm for a prolonged time, the expected fitness return of plastic adjustments of ejaculate phenotype may depend on the interval between mating and fertilization. Although prolonged female sperm storage (FSS) increases the opportunity for sperm competition, as a consequence of the longer temporal overlap of ejaculates from several males, it may also create variable selective forces on ejaculate phenotype, for example by exposing trade-offs between sperm velocity and sperm survival. We evaluated the relationship between the plasticity of ejaculate quality and FSS in the guppy, Poecilia reticulata, a polyandrous live-bearing fish in which females store sperm for several months and where stored sperm contribute significantly to a male's lifelong reproductive success. In this species, males respond to the perception of future mating opportunities by increasing the quantity (number) and quality (swimming velocity) of ready-to-use sperm (an anticipatory response called 'sperm priming'). Here we investigated (a) the effect of sperm priming on in vitro sperm viability at stripping and its temporal decline (as an estimate of sperm survival), and (b) the in vivo competitive fertilization success in relation to female sperm storage using artificial insemination. As expected, sperm-primed males produced more numerous and faster sperm, but with a reduced in vitro sperm viability at stripping and after 4 hr, compared with their counterparts. Artificial insemination revealed that the small (nonsignificant) advantage of primed sperm when fertilization immediately follows insemination is reversed when eggs are fertilized by female-stored sperm, weeks after insemination. By suggesting a plastic trade-off between sperm velocity and viability, these results demonstrate that prolonged female sperm storage generates divergent selection pressures on ejaculate phenotype.

Directional postcopulatory sexual selection is associated with female sperm storage in Trinidadian guppies

Female sperm storage (FSS) is taxonomically widespread and often associated with intense sperm competition, yet its consequences on postcopulatory sexual selection (PCSS) are poorly known. Theory predicts that FSS will reduce the strength of PCSS, because sperm characteristics favored before and after FSS may be traded-off, and opportunities for nondirectional PCSS should increase. We explored these questions in the guppy (Poecilia reticulata), by allowing females to mate multiply and by comparing the paternity pattern in two successive broods. Contrary to predictions, the variance in male fertilization success increased after FSS, driven by a change in male paternity share across broods. This change was positively associated with sperm velocity (measured before FSS) but not with the duration of FSS, indirectly suggesting that faster sperm were better in entering female storage organs, rather than in persisting within them. Other male traits, such as male size and orange color, heterozygosity, and relatedness to the female, did not influence paternity after FSS. These results indicate that processes associated with FSS tend to reinforce the strength of PCSS in guppies, rather than weaken it. Further work is necessary to test whether this pattern changes in case of more prolonged FSS.

Multivariate selection drives concordant patterns of pre- and postcopulatory sexual selection in a livebearing fish

In many species, females mate with multiple partners, meaning that sexual selection on male traits operates across a spectrum that encompasses the competition for mates (that is, before mating) and fertilizations (after mating). Despite being inextricably linked, pre- and postcopulatory sexual selection are typically studied independently, and we know almost nothing about how sexual selection operates across this divide. Here we bridge this knowledge gap using the livebearing fish Poecilia reticulata. We show that both selective episodes, as well as their covariance, explain a significant component of variance in male reproductive fitness. Moreover, linear and nonlinear selection simultaneously act on pre- and postcopulatory traits, and interact to generate multiple phenotypes with similar fitness.

In species in which females mate with multiple partners, sexual selection acts on male traits involved in mating and fertilization. Here, the authors show that selection acting before and after mating explains a significant component of variance in male reproductive fitness in a livebearing fish.

Molecular detection of hybridization between sympatric kangaroo species in south-eastern Australia

Introgressive hybridization has traditionally been regarded as rare in many vertebrate groups, including mammals. Despite a propensity to hybridize in captivity, introgression has rarely been reported between wild sympatric macropodid marsupials. Here we investigate sympatric populations of western (Macropus fuliginosus) and eastern (Macropus giganteus) grey kangaroos through 12 autosomal microsatellite loci and 626 bp of the hypervariable mitochondrial DNA (mtDNA) control region. M. fuliginosus and M. giganteus within the region of sympatry corresponded, both genetically and morphologically, to their respective species elsewhere in their distributions. Of the 223 grey kangaroos examined, 7.6% displayed evidence of introgression, although no F1 hybrids were detected. In contrast to captive studies, there was no evidence for unidirectional hybridization in sympatric grey kangaroos. However, a higher portion of M. giganteus backcrosses existed within the sample compared with M. fuliginosus. Hybridization in grey kangaroos is reflective of occasional breakdowns in species boundaries, occurring throughout the region and potentially associated with variable conditions and dramatic reductions in densities. Such rare hybridization events allow populations to incorporate novel diversity while still retaining species integrity.

Landscape discontinuities influence gene flow and genetic structure in a large, vagile Australian mammal, Macropus fuliginosus

Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.

Development of a multilocus microsatellite typing approach for discriminating strains of Leishmania (Viannia) species

A multilocus microsatellite typing (MLMT) approach based on the analysis of 15 independent loci has been developed for the discrimination of strains belonging to different Viannia species. Thirteen microsatellite loci were isolated de novo from microsatellite-enriched libraries for both Leishmania braziliensis and L. guyanensis. Two previously identified markers, AC01 and AC16, were modified and added to our marker set. Markers were designed to contain simple dinucleotide repeats flanked by the minimal possible number of nucleotides in order to allow variations in repeat numbers to be scored as size variations of the PCR products. The 15 markers in total were amplified for almost all of the strains of Viannia tested; one marker did not amplify from the two L. peruviana strains included in the study. When 30 strains of L. braziliensis, 21 strains of L. guyanensis, and 2 strains of L. peruviana were tested for polymorphisms, all strains except two strains of L. guyanensis had individual MLMT types. Distance-based analysis identified three main clusters. All strains except one strain of L. guyanensis grouped together. Two clusters consisted of strains of L. braziliensis according to their geographical origins. The two strains of L. peruviana grouped together with strains of L. braziliensis from Peru and the adjacent Brazilian state of Acre. MLMT has proven capable of individualizing strains even from the same areas of endemicity and of detecting genetic structures at different levels. MLMT is thus applicable for epidemiological and population genetic studies of strains within the subgenus Viannia.

Complex mutational patterns and size homoplasy at maize microsatellite loci

Microsatellite markers have become one of the most popular tools for germplasm characterization, population genetics and evolutionary studies. To investigate the mutational mechanisms of maize microsatellites, nucleotide sequence information was obtained for ten loci. In addition, Single-Strand Conformation Polymorphism (SSCP) analysis was conducted to assess the occurrence of size homoplasy. Sequence analysis of 54 alleles revealed a complex pattern of mutation at 8/10 loci, with only 2 loci showing allele variation strictly consistent with stepwise mutations. The overall allelic diversity resulted from changes in the number of repeat units, base substitutions, and indels within repetitive and non-repetitive segments. Thirty-one electromorphs sampled from six maize landraces were considered for SSCP analysis. The number of conformers per electromorph ranged from 1 to 7, with 74.2% of the electromorphs showing more than one conformer. Size homoplasy was apparent within landraces and populations. Variation in the amount of size homoplasy was observed within and between loci, although no differences were detected among populations. The results of the present study provide useful information on the interpretation of genetic data derived from microsatellite markers. Further efforts are still needed to determine the impact of these findings on the estimation of population parameters and on the inference of phylogenetic relationships in maize investigations.

Mutational bias in penguin microsatellite DNA

Analysis of nucleotide sequence variation at a microsatellite DNA locus revealed extensive size homoplasy of alleles in Adélie penguins (Pygoscelis adeliae). Variation in the flanking regions at this locus allowed discrimination between mechanisms proposed for length changes in microsatellite DNA alleles. We further examined the structure of alleles for the same microsatellite DNA locus across 11 additional species of penguin (Spheniscidae) by mapping allele sequences onto an independent penguin phylogeny. Our analysis indicated that the repeat motifs appear to have evolved independently on several occasions. We observed sequence instability in the region bordering the repeat tract with a transversional bias predominating. We propose that this bias results from inaccurate DNA replication owing to the sequence context of this repeat tract. Because we show that regions flanking repeat sequences exhibit this mutational bias, this cautions against the use of such regions for phylogeny reconstruction.

The impact of microsatellite electromorph size homoplasy on multilocus population structure estimates in a tropical tree (Corythophora alta) and an anadromous fish (Morone saxatilis)

Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical tree Corythophora alta and 11 loci in the anadromous fish Morone saxatilis by sequencing 14-23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy for M. saxatilis loci. Seven C. alta loci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy in C. alta generally produced little or no change in single-locus estimates of RST, except for two loci in which some additional differentiation among populations was revealed. Twelve-locus estimates of RST (including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% for C. alta and M. saxatilis, respectively. Simulations showed that the increase in RST produced by homoplasy correction was only slightly larger than variation in RST estimates expected to be caused by methodological errors.

Patterns of population subdivision and gene flow in the ant Nothomyrmecia macrops reflected in microsatellite and mitochondrial DNA markers

The Australian endemic ant Nothomyrmecia macrops is renowned for having retained a large proportion of 'primitive' morphological and behavioural characters. Another less studied peculiarity of this species is the production of short-winged (brachypterous) female sexuals, which presumably are poor dispersers. The males, in contrast, bear a full set of normally developed wings and thus may disperse widely. We investigated patterns of genetic differentiation within and among three distantly separated populations in South Australia using nine polymorphic microsatellite loci and four regions of mitochondrial DNA (COI, COII, Cytb, lrRNA). We sampled eight subpopulations, one in the Lake Gilles CP, two near Penong and five around Poochera where distances ranged from 360 km to sites separated by 2-10 km. Only little differentiation was found at the local scale (within the assumed dispersal distance of males) using nuclear markers, whereas the three distant locations were moderately differentiated (FST = 0.06). Mitochondrial DNA genetic structure was much more pronounced on all scales (phiST = 0.98), with regular differences in both haplotype composition and frequency even occurring among closely located sites. This lack of congruence between nuclear and mitochondrial markers strongly suggests limited female dispersal and male-biased gene flow among populations. As to the conservation status of the species there is no evidence for severe population reductions in the recent past, which would have left populations genetically depauperate.

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

Characterization of the (GAAA) microsatellite region in the plant parasitic nematode Meloidogyne artiellia

Microsatellites have become one of the most powerful genetic markers in biology. We have used DNA sequencing to characterize a highly variable microsatellite (GAAA) locus in the root-knot nematode Meloidogyne artiellia. The use of microsatellite flanking primers produced four amplification products that are defined as electromorphs, based on conventional length criteria. The sequencing of these four amplification products revealed the presence of new variants in the population due to sequence variability. The sum of electromorphs and sequence polymorphisms resulted in a total of six variants. The high degree of variability in the microsatellite containing region is due not only to variation in the number of tetranucleotide repeats but also to variation (length and site variation) in the flanking regions of the microsatellite. These investigations show that, in spite of the size homoplasy, the variability of the microsatellite flanking sequences of M. artiellia could be used as informative markers for phylogenetic reconstructions.

Global relationships amongst black-browed and grey-headed albatrosses: analysis of population structure using mitochondrial DNA and microsatellites

The population structure of black-browed (Thalassarche melanophris and T. impavida) and grey-headed (T. chrysostoma) albatrosses was examined using both mitochondrial DNA (mtDNA) and microsatellite analyses. mtDNA sequences from 73 black-browed and 50 grey-headed albatrosses were obtained from five island groups in the Southern Ocean. High levels of sequence divergence were found in both taxa (0.55-7.20% in black-browed albatrosses and 2.10-3.90% in grey-headed albatrosses). Black-browed albatrosses form three distinct groups: Falklands, Diego Ramirez/South Georgia/Kerguelen, and Campbell Island (T. impavida). T. melanophris from Campbell Island contain birds from each of the three groups, indicating high levels of mixture and hybridization. In contrast, grey-headed albatrosses form one globally panmictic population. Microsatellite analyses on a larger number of samples using seven highly variable markers found similar population structure to the mtDNA analyses in both black-browed and grey-headed albatrosses. Differences in population structure between these two very similar and closely related species could be the result of differences in foraging and dispersal patterns. Breeding black-browed albatrosses forage mainly over continental shelves and migrate to similar areas when not breeding. Grey-headed albatrosses forage mainly at frontal systems, travelling widely across oceanic habitats outside the breeding season. Genetic analyses support the current classification of T. impavida as being distinct from T. melanophris, but would also suggest splitting T. melanophris into two groups: Falkland Islands, and Diego Ramirez/South Georgia/Kerguelen.

Microsatellite size homoplasy, SSCP, and population structure: a case study in the freshwater snail Bulinus truncatus

The extent of microsatellite size homoplasy, as well as its effect on several population genetics statistics, was investigated in natural populations using the single-strand conformation polymorphism (SSCP) method. The analysis was conducted using 240 individuals from 13 populations of the freshwater snail Bulinus truncatus at a GT(n)CT(m) compound microsatellite locus. We showed that SSCP can be used to uncover, at least partly, size homoplasy in the core sequence of this category of loci. Eight conformers (SSCP variants) were detected among the three size variants (electromorphs). Sequencing revealed that each conformer corresponded to a different combination of repeats in the GT(n) and CT(m) arrays. Part of this additional variability was detected within populations, resulting in a substantial increase in gene diversity in four populations. Additional variability also changed the values of parameters used to analyze population differentiation among populations: pairwise tests of differentiation were significant much more often with conformers than with electromorphs. On the other hand, pairwise estimates of F(st) were either smaller or larger with conformers than with electromorphs, depending on whether or not electromorphs were shared among populations. However, estimates of F(st) (or analogs) over all populations were very similar, ranging between 0.66 and 0.75. Our results were consistent with the theoretical prediction that homoplasy should not always lead to stronger population structure. Finally, conformer sequences and electromorph size distribution suggested that single-point and/or stepwise mutations occurring simultaneously in the different repeated arrays of compound microsatellites produce sequence variation without size variation and hence generate more size homoplasy than expected under a simple stepwise mutation model.

Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids

Recent studies have suggested that size homoplasy is a prevalent feature of microsatellites and is expected to increase with time of divergence among populations and taxa. In this study, we performed sequence analysis of alleles from a complex microsatellite locus (Pzeb4, initially isolated from Pseudotropheus (Maylandia) zebra) from 1 midwater-feeding and 10 rock-dwelling cichlid fish species from Lake Malawi, East Africa, to investigate how widespread size homoplasy is among closely related taxa at this locus. All cichlid fishes endemic to this lake are believed to have originated within the last 700,000 years, and some species may be less than 200 years old. The number of eletromorphs found per species varied from 3 to 13. Sequence analysis of 95 cloned Pzeb4 PCR products (representing 18 electromorphs) revealed 13 new alleles. Ten of the 13 electromorphs (77%) were found to show size homoplasy due to either single nucleotide substitutions/indels or large indels. To investigate how well this locus fits the single-step mutation model (SMM), the minimum number of mutations required to explain the length differences between pairs of alleles was plotted against their size differences. Of the 300 comparisons, 166 (55.3%) corresponded to SMM expectations and 86 (28.7%) required a smaller number of mutations, and for 48 (16.0%) pairwise comparisons, a larger number of mutations were required to explain the length differences as compared with SMM expectations. Finally, a large deletion in the microsatellite sequence observed in the three rock-dwelling species Pseudotropheus lucerna, Pseudotropheus (Tropheops) 'band,' and Pseudotropheus (Tropheops) 'rust' and the midwater-feeding species Copadichromis sp. is believed to represent a shared ancestral polymorphism.