Male‐biased gene flow across an avian hybrid zone: evidence from mitochondrial and microsatellite DNA

Mating pattern and gene flow were studied in the contact zone between two morphologically very similar Chiffchaff taxa (Phylloscopus collybita, P. brehmii) in SW France and northern Spain. Mating was assortative in brehmii, but not in collybita. Mixed matings were strongly asymmetric (excess of collybita male × brehmii female pairs), but did produce viable offspring in some cases. Sequence divergence of the mitochondrial cytochrome b gene was 4.6%. Haplotypes segregated significantly with phenotype (only five ‘mismatches’ among 94 individuals), demonstrating that mitochondrial gene flow was very restricted. The estimated proportion of F₁ hybrids in the reproductive population was significantly lower than expected under a closed population model, indicating strong selection against hybrids. Genetic typing of 101 individuals at four microsatellite loci also showed significant population differentiation, but nuclear gene flow was estimated to be 75 times higher than mitochondrial gene flow. This strong discrepancy is probably due to unisexual hybrid sterility (Haldane’s rule). Thus, there is a strong, but incomplete, reproductive barrier between these taxa.     

Differential high‐altitude adaptation and restricted gene flow across a mid‐elevation hybrid zone in Andean tit‐tyrant flycatchers

The tropical Andes are a global hotspot of avian diversity that is characterized by dramatic elevational shifts in community composition and a preponderance of recently evolved species. Bird habitats in the Andes span a nearly twofold range of atmospheric pressure that poses challenges for respiration, thermoregulation, water balance and powered flight, but the extent to which physiological constraints limit species' elevational distributions is poorly understood. We report a previously unknown hybrid zone between recently diverged flycatchers (Aves, Tyrannidae) with partially overlapping elevational ranges. The southern Anairetes reguloides has a broad elevational range (0–4200 m), while the northern Anairetes nigrocristatus is restricted to high elevations (>2200 m). We found hybrids in central Peru at elevations between ~3100 and 3800 m, with A. nigrocristatus above this elevation and A. reguloides below. We analysed variation in haematology, heart mass, morphometrics, plumage and one mitochondrial and three nuclear loci across an elevational transect that encompasses the hybrid zone. Phenotypic traits and genetic markers all showed steep clines across the hybrid zone. Haemoglobin concentration, haematocrit, mean cellular haemoglobin concentration and relative heart mass each increased at altitude more strongly in A. reguloides than in A. nigrocristatus. These findings suggest that A. nigrocristatus is more resistant than A. reguloides to high‐altitude hypoxic respiratory stress. Considering that the ancestor of the genus is suggested to have been restricted to high elevations, A. reguloides may be secondarily adapted to low altitude. We conclude that differential respiratory specialization on atmospheric pressure combined with competitive exclusion maintains replacement along an elevational contour, despite interbreeding.     

Divergence and gene flow in the globally distributed blue‐winged ducks

The ability to disperse over long distances can result in a high propensity for colonizing new geographic regions, including uninhabited continents, and lead to lineage diversification via allopatric speciation. However, high vagility can also result in gene flow between otherwise allopatric populations, and in some cases, parapatric or divergence‐with‐gene‐flow models might be more applicable to widely distributed lineages. Here, we use five nuclear introns and the mitochondrial control region along with Bayesian models of isolation with migration to examine divergence, gene flow, and phylogenetic relationships within a cosmopolitan lineage comprising six species, the blue‐winged ducks (genus Anas), which inhabit all continents except Antarctica. We found two primary sub‐lineages, the globally‐distributed shoveler group and the New World blue‐winged/cinnamon teal group. The blue‐winged/cinnamon sub‐lineage is composed of sister taxa from North America and South America, and taxa with parapatric distributions are characterized by low to moderate levels of gene flow. In contrast, our data support strict allopatry for most comparisons within the shovelers. However, we found evidence of gene flow from the migratory, Holarctic northern shoveler A. clypeata and the more sedentary, African Cape shoveler A. smithii into the Australasian shoveler A. rhynchotis, although we could not reject strict allopatry. Given the diverse mechanisms of speciation within this complex, the shovelers and blue‐winged/cinnamon teals can serve as an effective model system for examining how the genome diverges under different evolutionary processes and how genetic variation is partitioned among highly dispersive taxa.     

Gene‐flow across the European crow hybrid zone – a spatial simulation

In hybrid zones populations that are otherwise allopatric meet and produce hybrids. One of the most well‐known hybrid zones occurs throughout much of Europe between the hooded and carrion crows. Even though these species (or subspecies) of crows look very different, genetic differentiation is weak, and introgression seems to be common. In a spatial simulation that was based on empirically estimated values, we investigated how introgressing alleles that would confer some fitness advantage would flow across the zone. The advantage was assumed to be some unknown factor that enhanced survival for carriers relative to non‐carriers. We varied the yearly survival advantage between 0 to 10% and recorded how this would affect zone shape and position. In the simulation we cycled ‘yearly’ events such as reproduction, mortality and juvenile dispersal. We started the simulation by equipping all individuals of one crow type outside the zone with a homozygotic set of the beneficial allele. At all levels of advantage the allele first rapidly became fixed in the donator crow type, then transgressed into the receiving type more slowly and finally became fixed in all individuals. The time until fixation varied from around 176 yr for a 10% advantage to around 20 000 yr for 0% advantage. An exciting discovery was that the position of the zone would move during the introgression but then stop. The reason is that the beneficial allele would be common in the donating type but not in the receiving type during the introgression event. At large the crow hybrid zone appears to have been stable for a long time but there have been small recent northward movements of carrion crows in both Scotland and Denmark. We suggest that introgression by itself is a factor that should be considered as an explanation for why hybrid zones move temporarily.     

Differences in dietary composition and preference maintained despite gene flow across a woodrat hybrid zone

1. Ecotones, characterized by adjacent yet distinct biotic communities, provide natural laboratories in which to investigate how environmental selection influences the ecology and evolution of organisms. For wild herbivores, differential plant availability across sharp ecotones may be an important source of dietary‐based selection.
2. We studied small herbivore diet composition across a sharp ecotone where two species of woodrat, Neotoma bryanti and N. lepida, come into secondary contact with one another and hybridize. We quantified woodrat dietary preference through trnL metabarcoding of field‐collected fecal pellets and experimental choice trials. Despite gene flow, parental N. bryanti and N. lepida maintain distinct diets across this fine spatial scale, and across temporal scales that span both wet and dry conditions.
3. Neotoma bryanti maintained a more diverse diet, with Frangula californica (California coffeeberry) making up a large portion of its diet. Neotoma lepida maintains a less diverse diet, with Prunus fasciculata (desert almond) comprising more than half of its diet. Both F. californica and P. fasciculata are known to produce potentially toxic plant secondary compounds (PSCs), which should deter herbivory, yet these plants have relatively high nutritional value as measured by crude protein content.
4. Neotoma bryanti and N. lepida consumed F. californica and P. fasciculata, respectively, in greater abundance than these plants are available on the landscape—indicating dietary selection. Finally, experimental preference trials revealed that N. bryanti exhibited a preference for F. californica, while N. lepida exhibited a relatively stronger preference for P. fasciculata. We find that N. bryanti exhibit a generalist herbivore strategy relative to N. lepida, which exhibit a more specialized feeding strategy in this study system.
5. Our results suggest that woodrats respond to fine‐scale environmental differences in plant availability that may require different metabolic strategies in order to balance nutrient acquisition while minimizing exposure to potentially toxic PSCs.

     

Evolutionary responses of tree phenology to the combined effects of assortative mating,gene flow and divergent selection

The timing of bud burst (TBB) in temperate trees is a key adaptive trait, the expression of which is triggered by temperature gradients across the landscape. TBB is strongly correlated with flowering time and is therefore probably mediated by assortative mating. We derived theoretical predictions and realized numerical simulations of evolutionary changes in TBB in response to divergent selection and gene flow in a metapopulation. We showed that the combination of the environmental gradient of TBB and assortative mating creates contrasting genetic clines, depending on the direction of divergent selection. If divergent selection acts in the same direction as the environmental gradient (cogradient settings), genetic clines are established and inflated by assortative mating. Conversely, under divergent selection of the same strength but acting in the opposite direction (countergradient selection), genetic clines are slightly constrained. We explored the consequences of these dynamics for population maladaptation, by monitoring pollen swamping. Depending on the direction of divergent selection with respect to the environmental gradient, pollen filtering owing to assortative mating either facilitates or impedes adaptation in peripheral populations.     

No evidence for size‐assortative mating in the wild despite mutual mate choice in sex‐role‐reversed pipefishes

Size‐assortative mating is a nonrandom association of body size between members of mating pairs and is expected to be common in species with mutual preferences for body size. In this study, we investigated whether there is direct evidence for size‐assortative mating in two species of pipefishes, Syngnathus floridae and S. typhle, that share the characteristics of male pregnancy, sex‐role reversal, and a polygynandrous mating system. We take advantage of microsatellite‐based “genetic‐capture” techniques to match wild‐caught females with female genotypes reconstructed from broods of pregnant males and use these data to explore patterns of size‐assortative mating in these species. We also develop a simulation model to explore how positive, negative, and antagonistic preferences of each sex for body size affect size‐assortative mating. Contrary to expectations, we were unable to find any evidence of size‐assortative mating in either species at different geographic locations or at different sampling times. Furthermore, two traits that potentially confer a fitness advantage in terms of reproductive success, female mating order and number of eggs transferred per female, do not affect pairing patterns in the wild. Results from model simulations demonstrate that strong mating preferences are unlikely to explain the observed patterns of mating in the studied populations. Our study shows that individual mating preferences, as ascertained by laboratory‐based mating trials, can be decoupled from realized patterns of mating in the wild, and therefore, field studies are also necessary to determine actual patterns of mate choice in nature. We conclude that this disconnect between preferences and assortative mating is likely due to ecological constraints and multiple mating that may limit mate choice in natural populations.     

Evidence for type assortative mating between the freshwater and Omono types of nine-spined stickleback in natural fresh water

A total of 123 adult specimens of the nine-spined stickleback Pungitius pungitius were identified as either the freshwater or Omono types, based on diagnostic allozyme loci, and their allozyme patterns compared with restriction fragment length polymorphism patterns of polymerase chain reaction-amplified mtDNA segments (mtDNA PCR-RFLP pattern). All specimens of the two types were clearly identified by the mtDNA PCR-RFLP patterns, except for a single putative hybrid progeny. The mtDNA PCR-RFLP patterns of 133 clutches from 21 nests were also compared with those of their parental males, and 126 out of 127 clutches were found to be consistent with the parental male pattern, the remaining six clutches being guarded by an F₁ hybrid male. The results demonstrated that type assortative mating had occurred between the two types in nature, indicating the existence of a premating isolating mechanism between them.     

Chromosome differentiation,hybrid breakdown and the maintenance of a narrow hybrid zone in Caledia

The protein D1 was obtained from nuclei of Drosophila melanogaster embryos and purified by perchloric acid fractionation and preparative gel electrophoresis. In nuclei its amount is approximately 1% of the amount of DNA by weight. D1 is soluble in 5% perchloric acid and extractable from nuclei by solutions of moderate ionic strength (0.35 M NaCl). Amino acid analysis shows that it is rich in both basic (20%) and acidic (27%) aminoacids. In all these properties D1 resembles HMG proteins (high mobility group; Johns et al., 1975) of vertebrates; however, its apparent molecular weight (50,000) is much higher. The distribution of D1 in salivary gland polytene chromosomes was investigated by immunofluorescence. Two levels of fluorescence intensity were observed: 1) Very bright fluorescence at chromosomal positions 81F, 83E, 101F, 102C and 102F; these sites are shown, by double labeling techniques, to coincide with quinacrine bright sites. 2) Medium to low fluorescence at many sites widely distributed throughout all chromosomes. In order to interpret these results and to relate them to the in vivo distribution of D1, we have investigated the pattern of immunofluorescence staining as a function of the methods of chromosome preparation and salivary gland fixation. The immunological specificity of the anti-D1 serum was studied by comparing its reactivity with D. melanogaster and D. virilis chromosome spreads and whole salivary glands, and by using reagents that minimize non-specific antibody interactions. We conclude that Dl is widely distributed throughout cytoplasm and nucleus, present in many chromomeres but most abundant in chromosomal sites that contain the AT-rich satellite DNA of density 1.672. This distribution, together with available evidence about the nucleotide sequences present in this satellite, suggests that D1 binds preferentially to chromatin containing sequences AATAT and/or AATATAT.     

Spatial variation in gene flow across a hybrid zone reveals causes of reproductive isolation and asymmetric introgression in wall lizards*

Hybrid zones provide insights into the evolution of reproductive isolation. Sexual selection can contribute to the evolution of reproductive barriers, but it remains poorly understood how sexual traits impact gene flow in secondary contact. Here, we show that a recently evolved suite of sexual traits that function in male-male competition mediates gene flow between two lineages of wall lizards (Podarcis muralis). Gene flow was relatively low and asymmetric in the presence of exaggerated male morphology and coloration compared to when the lineages share the ancestral phenotype. Putative barrier loci were enriched in genomic regions that were highly differentiated between the two lineages and showed low concordance between the transects. The exception was a consistently low genetic exchange around ATXN1, a gene that modulates social behavior. We suggest that this gene may contribute to the male mate preferences that are known to cause lineage-assortative mating in this species. Although female choice modulates the degree of reproductive isolation in a variety of taxa, wall lizards demonstrate that both male-male competition and male mate choice can contribute to the extent of gene flow between lineages.     

Female polyandry and size‐assortative mating in isolated local populations of the Japanese common toad Bufo japonicus

In anurans, female polyandry under male harassment is distributed across taxa because of external aquatic fertilization. According to the sexual selection theory, male–male competition for access to females is affected by the operational sex ratio (OSR) and population density. The Japanese common toad, Bufo japonicus, is widespread in mainland Japan, and like the European common toad, B. bufo, it engages in explosive breeding. In this study, we observed the breeding behaviour of B. japonicus in isolated local populations for over four years in two breeding ponds with different population sizes and densities: large‐low (L‐pond) and small‐high (S‐pond). We analysed the relative polyandry ratio in egg clutches laid by females and estimated the size‐assortative mating pattern to be an indicator of male–male competition in the two ponds. Both ponds tended to exhibit a size‐assortative mating pattern; however, the frequency of polyandry was different in the two ponds (L‐pond = 20% and S‐pond = 90%). Our results showed that polyandry could occur without multiple amplexus with a high population density, i.e. eggs were often fertilized by free‐swimming sperm in the small shallow pond. We propose that high female polyandry ratios without continuous male harassment are generated because of a male‐biased OSR and a high population density in the small pond. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 236–242.     

Fitness consequences of potential assortative mating inside and outside a hybrid zone in Chorthippus parallelus (Orthoptera: Acrididae): implications for reinforcement and sexual selection theory

We have examined the fitness consequences of random and potentially non-random matings within two populations taken from inside, and two from outside a hybrid zone in Chorthippus parallelus. When given the opportunity to mate non-randomly, females from all populations laid egg pods more quickly than females obliged to mate at random. A range of fitness parameters measured on the offspring did not show increased fitness following potential non-random mating for any population. However, in non-hybrid populations, the sons of non-randomly mated females had about twice the mating success of the sons of those females forced to mate at random, suggesting the existence of heritable variation for male reproductive success. Hybrid dysfunction did not occur amongst the offspring of randomly mated hybrid females, demonstrating that the lack of dysfunction within these populations is not due to the evolution of assortative mating within them.     

Evidence of phenotypic and social assortative mating for anthropometric and physiological traits in couples from the Basque country (Spain)

This study examined 28 anthropometrical and physiological traits in 107 married couples living in the province of Biscay (Basque Country, Spain). The aim was to verify the existence of a phenotypic and/or social preference when choosing a mate. For this, correlations between pairs of spouses were estimated by maximum likelihood, and a model of familial transmission (path analysis) was applied in order to test if social homogamy between mates existed. The results provide significant evidence of phenotypic as well as social homogamy in several of the studied traits. Even if an assortment existed when choosing a mate for bony traits such as height, the effect of cohabitation cannot be discounted as the main causal factor for the high phenotypic resemblance observed between spouses for body composition traits. In addition, with the social homogeneity of the studied sample, significant evidence of the existence of social homogamy between mates was only found for 20% of the studied variables.     

Assortative mating,sexual selection,and their consequences for gene flow in Littorina

When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.     

Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.     

Evidence for demographic bottlenecks and limited gene flow leading to low genetic diversity in a rare thistle

European calcareous grasslands have decreased dramatically in area and number during the last two centuries. As a result, many populations of calcareous grassland species are confined to small and isolated fragments, where their long-term survival is to some extent uncertain. Recently, several restoration projects have been initiated to enlarge the current grassland area in order to maintain the exceptionally high species richness. However, from a genetic point of view, the success of these restoration measures is not necessarily guaranteed, as strong historical decreases in population size and limited gene flow may have led to low genetic diversity through genetic bottlenecks and drift. In this study, we investigated genetic diversity and structure of 16 populations of the calcareous grassland specialist Cirsium acaule in a severely fragmented landscape in south-western Belgium. The overall distribution of this species in the study area was significantly and positively related to patch area, suggesting that small patches do not allow survival of this species. Both allelic richness and genetic diversity were significantly and positively related to population size. Estimation of observed and expected gene diversity provided evidence for population bottlenecks in the history of not less than 31% of all sampled populations. Reconstruction of the historical land use showed that patch area decline in populations that went through a recent bottleneck was significantly larger than that in populations that showed no evidence of a bottleneck. Assignment analyses showed low migration rates, suggesting that replenishment of lost alleles through gene flow is highly unlikely. Overall, our results indicate that in the absence of gene flow strong decreases in calcareous grassland area may have long-lasting effects on genetic diversity of plant populations and may hamper the success of restoration projects that simply aim at restoring initial habitat conditions or enlarging population fragments, as indicated by the fact that none of the recently restored areas has been occupied by C. acaule.     

The scale‐of‐choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples

The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134 trait correlations found that positive estimates of assortative mating were more frequent and larger in magnitude than negative estimates. Here, we describe the scale‐of‐choice effect (SCE), which occurs when mate choice exists at a smaller scale than that of the investigator's sampling, while simultaneously the trait is heterogeneously distributed at the true scale‐of‐choice. We demonstrate the SCE by Monte Carlo simulations and estimate it in two organisms showing positive (Littorina saxatilis) and negative (L. fabalis) assortative mating. Our results show that both positive and negative estimates are biased by the SCE by different magnitudes, typically toward positive values. Therefore, the low frequency of negative assortative mating observed in the literature may be due to the SCE's impact on correlation estimates, which demands new experimental evaluation.