Molecular and ecological signatures of an expanding hybrid zone

Many species are currently changing their distributions and subsequently form sympatric zones with hybridization between formerly allopatric species as one possible consequence. The damselfly Ischnura elegans has recently expanded south into the range of its ecologically and morphologically similar sister species Ischnura graellsii. Molecular work shows ongoing introgression between these species, but the extent to which this species mixing is modulated by ecological niche use is not known. Here, we (1) conduct a detailed population genetic analysis based on molecular markers and (2) model the ecological niche use of both species in allopatric and sympatric regions. Population genetic analyses showed chronic introgression between I. elegans and I. graellsii across a wide part of Spain, and admixture analysis corroborated this, showing that the majority of I. elegans from the sympatric zone could not be assigned to either the I. elegans or I. graellsii species cluster. Niche modeling demonstrated that I. elegans has modified its environmental niche following hybridization and genetic introgression with I. graellsii, making niche space of introgressed I. elegans populations more similar to I. graellsii. Taken together, this corroborates the view that adaptive introgression has moved genes from I. graellsii into I. elegans and that this process is enabling Spanish I. elegans to occupy a novel niche, further facilitating its expansion. Our results add to the growing evidence that hybridization can play an important and creative role in the adaptive evolution of animals.     

introgress: a software package for mapping components of isolation in hybrids

A new software package (introgress) provides functions for analysing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. The software works with co-dominant, dominant and haploid marker data, and does not require fixed allelic differences between parental populations for the sampled genetic markers. Permutation and parametric procedures generate neutral expectations for introgression and provide a basis for significance tests of observed genomic clines. The software also implements maximum likelihood estimates of hybrid index from genotypic data and a number of graphical analyses. The package is an extension of the R statistical software, is written in the R language and is freely available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/). In this study, we describe introgress and demonstrate its use with a sample data set.     

Wolbachia effects in natural populations of Chorthippus parallelus from the Pyrenean hybrid zone

We evaluate for the first time the effect of Wolbachia infection, involving two different supergroups, on the structure and dynamics of the hybrid zone between two subspecies of Chorthippus parallelus (Orthoptera) in the Pyrenees. Wolbachia infection showed no effects on female fecundity or a slight increment in females infected by F supergroup, although in the last case it has to be well established. Cytoplasmic incompatibility (CI) is confirmed in crosses carried out in the field between individuals from a natural hybrid population. This CI, registered as the relative reduction in embryo production (s_h), was of s_h = 0.355 and s_h = 0.286 in unidirectional crosses involving B and F supergroups, respectively. CI also occurred in bidirectional crosses (s_h = 0.147) but with a weaker intensity. The transmission rates of the two Wolbachia strains (B and F) were estimated by the optimization of a theoretical model to reach the infection frequencies observed in certain population. To fit this scenario, both supergroups should present transmission rates close to 1. Further, we have simulated the infection dynamics, and hence, the capacity of Wolbachia to structure the population of the host insects and to affect to reproduction and genetic introgression in the hybrid zone. This represents a first example of the influence of Wolbachia in an insect natural hybrid zone.     

Testing an hypothesis of hybrid zone movement for toads in France

Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.     

Sexual selection on plumage and behavior in an avian hybrid zone: experimental tests of male-male interactions

In western Panama, an unusual hybrid zone exists between white-collared manakins, Manacus candei, and golden-collared manakins, M. vitellinus. Unidirectional introgression of plumage traits from vitellinus into candei has created a region in which all definitively plumaged males have a collar that is lemon-colored. These males are nearly indistinguishable from white-collared candei genetically and morphometrically, but strongly resemble golden-collared vitellinus due to the introgression of secondary sexual plumage traits, particularly the lemon-colored collar. The introgression could be explained by sexual selection for golden-collared traits or by a series of mechanisms that do not invoke sexual selection (e.g., neutral diffusion, dominant allele). Sexual selection on male-male interactions implies behavioral differences among the plumage forms--specifically that golden- and lemon-collared males should be more aggressive than white-collared males. In contrast, the nonsexual hypotheses predict behavioral similarity between lemon- and white-collared males, based on their nearly identical genetics. We tested the sexual selection hypothesis experimentally, by presenting males with taxidermic mounts of the three forms. As response variables, we monitored vocalizations and attacks on the mounts by replicate subject males. Both golden-collared and lemon-collared males were more likely to attack than were white-collared males, as predicted under sexual selection but not by the nonsexual hypotheses. Lemon-collared males were more vocally reactive than either parental form, contrary to the prediction of the nonsexual hypotheses. Our study demonstrates that sexual selection on male-male interactions may play an important role in the dynamics of character evolution and hybrid zones.     

Multiple forms of selection shape reproductive isolation in a primate hybrid zone

Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by‐product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced‐representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus‐specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by‐product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.     

MPAgenomics: an R package for multi-patient analysis of genomic markers

Background

Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures.

Results

MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic markers from multi-patient copy number and SNP data profiles. It provides wrappers from commonly used packages to streamline their repeated (sometimes difficult) manipulation, offering an easy-to-use pipeline for beginners in R.The segmentation of successive multiple profiles (finding losses and gains) is performed with an automatic choice of parameters involved in the wrapped packages. Considering multiple profiles in the same time, MPAgenomics wraps efficient penalized regression methods to select relevant markers associated with a given outcome.

Conclusions

MPAgenomics provides an easy tool to analyze data from SNP arrays in R. The R-package MPAgenomics is available on CRAN.     

Inferences from a rapidly moving hybrid zone

Anartia fatima and Anartia amathea (Lepidoptera: Nymphalidae) are sister taxa whose ranges abut in a narrow hybrid zone in eastern Panama. At the center of the zone, hybrids are abundant, although deviations from Hardy-Weinberg and linkage disequilibria are strong, due in part to assortative mating. We measured differences across the zone in four wing color-pattern characters, three allozyme loci, and mitochondrial haplotype. Wing pattern, allozyme, and mitochondrial clines were coincident (i.e., had the same positions) and concordant (i.e.. all markers had similar cline shapes, about 28 km wide). Repeated samples demonstrated that the hybrid zone has been moving eastwards at an average rate of 2.5 km/year over the past 20 years, accompanied by an equivalent movement of the mtDNA cline. No introgression of mtDNA haplotypes were found in the 'wake" of the moving cline, as might be expected for a neutral marker. The concordance of morphological and mtDNA clines between 1994 and 2000, in spite of hybrid zone movement, suggests strong epistasis between the mitochondrial genome and nuclear loci. Cline movement is achieved mainly by pure fatima immigrating into amathea populations; hybrids had little effect, and were presumably outcompeted by fitter pure fatima genotypes. This movement can be explained if random dispersal of 7-19 km x gen(1/2) is coupled with a competitive advantage to A. fatima genomes of 2-5%. Hybrid zone motion is equivalent to Phase III of Wright's shifting balance. Hybrid zone movement has rarely been considered likely in the past, but our results show that it may be more important in biogeography and evolution than generally realized.     

Sharp acoustic boundaries across an altitudinal avian hybrid zone despite asymmetric introgression

Birdsong is a sexually selected trait that could play an important evolutionary role when related taxa come into secondary contact. Many songbird species, however, learn their songs through copying one or more tutors, which complicates the evolutionary outcome of such contact. Two subspecies of a presumed vocal learner, the grey‐breasted wood‐wren (Henicorhina leucophrys), replace each other altitudinally across the western slope of the Ecuadorian Andes. These subspecies are morphologically very similar, but show striking differences in their song. We examined variation in acoustic traits and genetic composition across the altitudinal range covered by both subspecies and between two allopatric populations. The acoustic boundary between the subspecies was found to be highly abrupt across a narrow elevational range with virtually no evidence of song convergence. Mixed singing and use of hetero‐subspecific song occurred in the contact zone and was biased towards the use of leucophrys song types. Hetero‐subspecific song copying by hilaris and not by leucophrys reflected a previously found asymmetric pattern of response to song playback. Using amplified fragment length polymorphisms (AFLP) markers, we detected hybridization in the contact zone and asymmetric introgression in parapatric populations, with more leucophrys alleles present in hilaris populations than vice versa. This pattern may be a trail of introgression due to upslope displacement of leucophrys by hilaris. Our data suggest that song learning may impact speciation and hybridization in contrasting ways at different spatial scales: although learning may speed up population divergence in songs, thereby enhancing assortative mating and reducing gene flow, it may at a local level also lead to the copying of heterospecific songs, therefore allowing some level of hybridization and introgression.     

Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Dispersal is a key factor in invasion and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of the parent–offspring distance distribution, of the western corn rootworm, Diabrotica virgifera virgifera, one of the most destructive pests of maize. This species is currently invading Europe, and the two largest invasive outbreaks, in northern Italy and Central Europe, have recently formed a secondary contact zone in northern Italy. We identified vanishing clines at 12 microsatellite loci throughout the contact zone. By analysing both the rate of change of cline slope and the spatial variation of linkage disequilibrium at these markers, we obtained two σ estimates of about 20 km/generation^1/2. Simulations indicated that these estimates were robust to changes in dispersal kernels and differences in population density between the two outbreaks, despite a systematic weak bias. These estimates are consistent with the results of direct methods for measuring dispersal applied to the same species. We conclude that secondary contact resulting from multiple introductions is very useful for the inference of dispersal parameters and should be more widely used in other species.     

Movement of a Heliconius hybrid zone over 30 years: A Bayesian approach

Hybrid zones have long been of interest to biologists as natural laboratories where we can gain insight into the processes of adaptation and speciation. Repeated sampling of individual hybrid zones has been particularly useful in elucidating the dynamic balance between selection and dispersal that maintains most hybrid zones. Here, we revisit a hybrid zone between Heliconius erato butterflies in Panamá for a third time over more than 30 years. We combine a novel Bayesian extension of stepped‐cline hybrid zone models with environmental data to understand the genetic and environmental causes of cline dynamics in this species. The cline has continued to move west, likely due to dominance drive, but has slowed and broadened. Environmental analyses suggest that widespread deforestation in Panamá could be leading to decreased avian predation and relaxed selection, causing the observed changes in cline dynamics.     

How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels

The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.     

related: an R package for analysing pairwise relatedness from codominant molecular markers

Analyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system. This has the undesirable outcome of making choice of relatedness estimator limited by operating system preference, rather than being based on scientific rationale. Here, we present a new R package, called related, that can calculate relatedness based on seven estimators, can account for genotyping errors, missing data and inbreeding, and can estimate 95% confidence intervals. Moreover, simulation functions are provided that allow for easy comparison of the performance of different estimators and for analyses of how much resolution to expect from a given data set. Because this package works in R, it is platform independent. Combined, this functionality should allow for more appropriate analyses and interpretation of pairwise relatedness and will also allow for the integration of relatedness data into larger R workflows.     

strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence

strap (Stratigraphic Tree Analysis for Palaeontology) is a new package for the freely available statistical programming language R designed to perform three main tasks: (1) to time‐scale phylogenies of fossil taxa; (2) to plot those time‐scaled trees against stratigraphy; and (3) to assess congruence between phylogenies and stratigraphy. Time‐scaling is performed with the DatePhylo function, with three approaches offered. Plotting trees against a choice of five different geological time scaless is possible using the geoscalePhylo function. Finally, the function StratPhyloCongruence calculates stratigraphic congruence measures for one or more input phylogenies, with no taxon limit. All three major congruence measures are offered: Stratigraphic Consistency Index (SCI), Manhattan Stratigraphic Measure (MSM*) and the gap excess ratio (GER; including GERt and GER*), as well as the pseudocongruence measure, the Relative Completeness Index (RCI). Each measure has an accompanying significance test that works by comparing the input trees against a user‐defined number of randomly generated topologies with the same taxon set and age ranges. Additional options for generating these random topologies allow the user to fix the outgroup or retain the input tree shape to make fairer comparisons. A tutorial that assumes no prior knowledge of R showcases all three functions using two different example data sets.     

MicroWeaR: A new R package for dental microwear analysis

Mastication of dietary items with different mechanical properties leaves distinctive microscopic marks on the surface of tooth enamel. The inspection of such marks (dental microwear analysis) is informative about the dietary habitus in fossil as well as in modern species. Dental microwear analysis relies on the morphology, abundance, direction, and distribution of these microscopic marks. We present a new freely available software implementation, MicroWeaR, that, compared to traditional dental microwear tools, allows more rapid, observer error free, and inexpensive quantification and classification of all the microscopic marks (also including for the first time different subtypes of scars). Classification parameters and graphical rendering of the output are fully settable by the user. MicroWeaR includes functions to (a) sample the marks, (b) classify features into categories as pits or scratches and then into their respective subcategories (large pits, coarse scratches, etc.), (c) generate an output table with summary information, and (d) obtain a visual surface‐map where marks are highlighted. We provide a tutorial to reproduce the steps required to perform microwear analysis and to test tool functionalities. Then, we present two case studies to illustrate how MicroWeaR works. The first regards a Miocene great ape obtained from through environmental scanning electron microscope, and other a Pleistocene cervid acquired by a stereomicroscope.     

StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations

Statistical Analysis of Mixed‐Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed‐ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise F_ST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed‐ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high‐throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.     

Genomic variation in cline shape across a hybrid zone

Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome‐scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well‐defined categories of locus types (e.g., neutral vs. highly selected). Our multi‐locus analysis reveals cross‐genomic variation in selective constraints on gene flow and locus‐specific flexibility in the permeability of the interspecies membrane.     

Testing parasite ‘intimacy’: the whipworm Trichuris muris in the European house mouse hybrid zone

Host‐parasite interaction studies across hybrid zones often focus on host genetic variation, treating parasites as homogeneous. ‘Intimately’ associated hosts and parasites might be expected to show similar patterns of genetic structure. In the literature, factors such as no intermediate host and no free‐living stage have been proposed as ‘intimacy’ factors likely constraining parasites to closely follow the evolutionary history of their hosts. To test whether the whipworm, Trichuris muris, is intimately associated with its house mouse host, we studied its population genetics across the European house mouse hybrid zone (HMHZ) which has a strong central barrier to gene flow between mouse taxa. T. muris has a direct life cycle and nonmobile free stage: if these traits constrain the parasite to an intimate association with its host we expect a geographic break in the parasite genetic structure across the HMHZ. We genotyped 205 worms from 56 localities across the HMHZ and additionally T. muris collected from sympatric woodmice (Apodemus spp.) and allopatric murine species, using mt‐COX1, ITS1‐5.8S‐ITS2 rDNA and 10 microsatellites. We show four haplogroups of mt‐COX1 and three clear ITS1‐5.8S‐ITS2 clades in the HMHZ suggesting a complex demographic/phylogeographic history. Microsatellites show strong structure between groups of localities. However, no marker type shows a break across the HMHZ. Whipworms from Apodemus in the HMHZ cluster, and share mitochondrial haplotypes, with those from house mice. We conclude Trichuris should not be regarded as an ‘intimate’ parasite of the house mouse: while its life history might suggest intimacy, passage through alternate hosts is sufficiently common to erase signal of genetic structure associated with any particular host taxon.     

Sharp genetic discontinuity across a unimodal Heliconius hybrid zone

Hybrid zones are powerful natural systems to study evolutionary processes to gain an understanding of adaptation and speciation. In the Cauca Valley (Colombia), two butterfly races, Heliconius cydno cydnides and Heliconius cydno weymeri, meet and hybridize. We characterized this hybrid zone using a combination of mitochondrial DNA (mtDNA) sequences, amplified fragment length polymorphisms (AFLPs), microsatellites and sequences for nuclear loci within and outside of the genomic regions that cause differences in wing colour pattern. The hybrid zone is largely composed of individuals of mixed ancestry. However, there is strong genetic discontinuity between the hybridizing races in mtDNA and, to a lesser extent, in all nuclear markers surveyed. The mtDNA clustering of H. c. cydnides with the H. cydno race from the Magdalena Valley and H. c. weymeri with the H. cydno race from the pacific coast suggests that H. c. cydnides colonized the Cauca Valley from the north, whereas H. c. weymeri did so by crossing the Andes in the southern part, implying a secondary contact origin. Colonization of the valley by H. cydno was accompanied by mimicry shift. Strong ecological isolation, driven by locally adaptive differences in mimetic wing patterns, is playing an important role in maintaining the hybrid zone. However, selection on wing pattern alone is not sufficient to explain the genetic discontinuity observed. There is evidence for differences in male mating preference, but the contribution of additional barriers needs further investigation. Overall, our results support the idea that speciation is a cumulative process, where the combination of multiple isolation barriers, combined with major phenotypic differences, facilitates population divergence in face of gene flow.