Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population

Behaviour and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behaviour of the hybridizing taxa can also impact the incidence and outcome of hybridization events. Hybridization between yellow baboons and anubis baboons has been well documented in the Amboseli basin of Kenya, where more anubis-like individuals tend to experience maturational and reproductive advantages. However, it is unknown whether these advantages are reflected in the genetic structure of populations surrounding this area. Here, we used microsatellite genotype data to evaluate the structure and composition of baboon populations in southern Kenya. Our results indicate that, unlike for mitochondrial DNA, microsatellite-based measures of genetic structure concord with phenotypically based taxonomic distinctions and that the currently active hybrid zone is relatively narrow. Isolation with migration analysis revealed asymmetric gene flow in this region from anubis populations into yellow populations, in support of the anubis-biased phenotypic advantages observed in Amboseli. Populations that are primarily yellow but that receive anubis gene flow exhibit higher levels of genetic diversity than yellow populations far from the introgression front. Our results support previous work that indicates a long history of hybridization and introgression among East African baboons. Specifically, it suggests that anubis baboons are in the process of gradual range expansion into the range of yellow baboons, a pattern potentially explained by behavioural and life history advantages that correlate with anubis ancestry.     

Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites

Although growing numbers of single nucleotide polymorphisms (SNPs) and microsatellites (short tandem repeat polymorphisms or STRPs) are used to infer population structure, their relative properties in this context remain poorly understood. SNPs and STRPs mutate differently, suggesting multi-locus genotypes at these loci might differ in ability to detect population structure. Here, we use coalescent simulations to measure the power of sets of SNPs and STRPs to identify population structure. To maximize the applicability of our results to empirical studies, we focus on the popular STRUCTURE analysis and evaluate the role of several biological and practical factors in the detection of population structure. We find that: (1) fewer unlinked STRPs than SNPs are needed to detect structure at recent divergence times <0.3 N_e generations; (2) accurate estimation of the number of populations requires many fewer STRPs than SNPs; (3) for both marker types, declines in power due to modest gene flow (N_em=1.0) are largely negated by increasing marker number; (4) variation in the STRP mutational model affects power modestly; (5) SNP haplotypes (θ=1, no recombination) provide power comparable with STRP loci (θ=10); (6) ascertainment schemes that select highly variable STRP or SNP loci increase power to detect structure, though ascertained data may not be suitable to other inference; and (7) when samples are drawn from an admixed population and one of its parent populations, the reduction in power to detect two populations is greater for STRPs than SNPs. These results should assist the design of multi-locus studies to detect population structure in nature.     

Inferences of selection and migration in the Danish house mouse hybrid zone

We analysed the patterns of allele frequency change for ten diagnostic autosomal allozyme loci in the hybrid zone between the house mouse subspecies Mus musculus domesticus and M. m. musculus in central Jutland. After determining the general orientation of the clines of allele frequencies, we analysed the cline shapes along the direction of maximum gradient. Eight of the ten clines are best described by steep central steps with coincident positions and an average width of 8.9 km (support limits 7.6–12.4) flanked by tails of introgression, indicating the existence of a barrier to gene flow and only weak selection on the loci studied. We derived estimates of migration from linkage disequilibrium in the centre of the zone, and by applying isolation by distance methods to microsatellite data from some of these populations. These give concordant estimates of σ =  0.5–0.8 km generation     . The barrier to gene flow is of the order of 20 km (support limits 14–28), and could be explained by selection of a few per cent at 43–120 underdominant loci that reduces the mean fitness in the central populations to 0.45. Some of the clines appear symmetrical, whereas others are strongly asymmetrical, and two loci appear to have escaped the central barrier to gene flow, reflecting the differential action of selection on different parts of the genome. Asymmetry is always in the direction of more introgression into musculus , indicating either a general progression of domesticus into the musculus territory, possibly mediated by differential behaviour, or past movement of the hybrid zone in the opposite direction, impeded by potential geographical barriers to migration in domesticus territory.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 593–616.     

Ascertainment bias in spatially structured populations: a case study in the eastern fence lizard

Despite increased interest in applying single nucleotide polymorphism (SNP) data to questions in natural systems, one unresolved issue is to what extent the ascertainment bias induced during the SNP discovery phase will impact available analysis methods. Although most studies addressing ascertainment bias have focused on human populations, it is not clear whether existing methods will work when applied to other species with more complex demographic histories and more significant levels of population structure. Here we present findings from an empirical approach to exploring the effect of population structure on issues of ascertainment bias in the Eastern Fence Lizard, Sceloporus undulatus. We find that frequency spectra and summary statistics were highly sensitive to SNP discovery strategy, necessitating careful selection of the initial ascertainment panel. Randomly selected ascertainment panels performed equally well as ascertainment panels chosen to jointly sample geographic, phenotypic, and genetic diversity. Geographically restricted panels resulted in larger biases. Additionally, we found existing ascertainment bias correction methods, which were not developed for geographically structured data sets, were largely effective at reducing the impact of ascertainment bias. Because bias correction methods performed well even when underlying assumptions were violated, our results suggest tools are currently available to analyze SNP data in structured populations.     

Density-dependent migration and human population structure in historical Massachusetts

Studies of population structure often focus on the effects of population size and migration rates on genetic variation. Few studies, however, have investigated the relationship between these two factors. The purpose of this paper is to determine the extent to which migration (and gene flow) is density-dependent (that is, affected by population size) for populations in historical Massachusetts. Data from 4,859 marriage records were analyzed from four populations in north-central Massachusetts during the time period 1741 to 1849. These data were placed into 29 samples defined in terms of population and time cohort. Within each cohort the overall exogamy rate was computed along with three estimates of gene flow based on marital migration: local migration (k), long-distance migration (m), and effective migration rate (me). Three samples show unusually low rates that reflect the history of settlement. Regression analyses were used with the remaining samples, and they show nonlinear density-dependent migration that is unrelated to temporal trends. Migration is highest in samples with small population sizes (less than 800) and large population sizes (greater than 1,600). Migration is lowest in medium-sized populations. Two processes are suggested to explain this curvilinear relationship of migration and population size. In small populations, the lack of suitable potential mates and/or availability of settled land leads to an increase in migration into the population. As population size increases, this migration decreases. After populations reach a certain size, migration increases again, most likely reflecting the economic pull of larger populations. These patterns could act to enhance, or counter, genetic drift, depending on the direction of density dependence.     

Genetic population structure and neighbourhood population size estimates of the caddisfly Plectrocnemia conspersa

1. We used both genetic and ecological methods to evaluate the role of history and the scale of colonisation in structuring populations of the caddisfly Plectrocnemia conspersa. There was no genetic differentiation between sites up to 20 km apart, despite population sizes suggesting that genetic drift could create substantial variation at this scale. 2. Genetic differentiation between populations separated by more than 20 km was greater than expected given the contrasting short‐range trend, and implied a neighbourhood population size that is implausibly small. Therefore, the evolutionary processes that affect the short‐range trend do not explain differentiation over greater distances. 3. At small scales (<20 km), relatively short flights by winged adults spread over a number of generations could account for the spread of genes. For instance, dispersing individuals could found small (often temporary) populations, which may then grow and exchange genes with larger and more permanent local populations, amplifying the effects of the initial gene flow. 4. Over larger scales (20–500 km), substantial gaps between regions containing suitable habitat patches could reduce the number of colonisation events. Genetic patterns at this scale may date from the time they were last colonised. Previous ecological studies have rarely examined the dynamics of aquatic insect populations over these larger geographical scales, yet these processes may be central to their persistence and spread.     

Mating system structure and population density in a polygynous lizard, Sauromalus obesus (= ater)

Increases in population density often are associated with achange in mating system structure in numerous taxa. Typically,male interactions are minimal in extremely low density populations.As density increases, males exhibit territoriality but if densitybecomes too high, the energetic cost of defending a territorywill eventually outweigh the reproductive benefits associatedwith territoriality. Consequently, males in high density populationsmay abandon territoriality and adopt dominance polygyny, lekking behavior, or scramble competition. We investigated the relationshipbetween population density and mating system structure in threepopulations of the chuckwalla, Sauromalus obesus (= ater),near Phoenix, Arizona. Densities in the Phoenix Mountains (2.7chuckwallas/ha) were lower than any population previously studied.In the Santan Mountains (10.9 chuckwallas/ha), densities weresimilar to populations studied in the Mojave Desert, and inthe South Mountains (65 chuckwallas/ha), densities were the highest yet recorded. Male mating behavior was examined by determininghome range overlap and by making direct behavioral observations.Male home range size decreased with increasing population density.There was little overlap in home ranges among males in allthree populations, whereas home ranges of males and femalesconsistently overlapped, indicating that males were strictly territorial. This conclusion was supported by behavioral observationsof interactions among individuals in a natural setting. Thenumber of females wihin male territories was correlated withfood resources (plants) in all three populations. Female homerange size appeard to be related to food resources whereasmale home ranges appeared to be related to female distribution,population density, and geology. The retention of territoriality in spite of high population densities raises new questions aboutthe relationship between density and resource defense.     

Temporal cline in a hybrid zone population between Fraxinus excelsior L. and Fraxinus angustifolia Vahl

The two closely related ash species Fraxinus excelsior L. (common ash) and Fraxinus angustifolia Vahl (narrow-leaved ash) have a broad contact zone in France where they hybridize. However, little is known about the local structure of hybrid zone populations and the isolation mechanisms. We assessed the potential effect of floral phenology on the structure of a riparian ash hybrid zone population in central France. The distribution of flowering times was unimodal and lay between the flowering periods of the two species. Using microsatellite markers, we detected isolation by time, which has possibly originated from assortative mating. Multivariate analyses indicated that morphological variation is not distributed at random with respect to flowering times. Spatial autocorrelation analyses showed that temporal and spatial patterns were tightly linked. Interestingly, despite the fact that the population shows isolation by time, neighbourhood size and historical dispersal variance (sigma = 63 m) are similar to those detected in pure stands of F. excelsior where individuals flower rather synchronously and hermaphrodites are not the most frequent sexual type. Trees flowering at intermediate dates, which comprised the majority of the population, produced on average more flowers and fruits. We detected no significant differences in floral parasite infections relative to reproductive timing, although there was a tendency for late flowering trees to suffer from more gall attack. We discuss the impact of temporal variation in fitness traits and their possible role in the maintenance of the hybrid zone.     

Assortative mating and differential male mating success in an ash hybrid zone population

Background  

The structure and evolution of hybrid zones depend mainly on the relative importance of dispersal and local adaptation, and on the strength of assortative mating. Here, we study the influence of dispersal, temporal isolation, variability in phenotypic traits and parasite attacks on the male mating success of two parental species and hybrids by real-time pollen flow analysis. We focus on a hybrid zone population between the two closely related ash species Fraxinus excelsior L. (common ash) and F. angustifolia Vahl (narrow-leaved ash), which is composed of individuals of the two species and several hybrid types. This population is structured by flowering time: the F. excelsior individuals flower later than the F. angustifolia individuals, and the hybrid types flower in-between. Hybrids are scattered throughout the population, suggesting favorable conditions for their local adaptation. We estimate jointly the best-fitting dispersal kernel, the differences in male fecundity due to variation in phenotypic traits and level of parasite attack, and the strength of assortative mating due to differences in flowering phenology. In addition, we assess the effect of accounting for genotyping error on these estimations.     

Characterization of the marriage structure and migration in Chuvash population]

Parameters of the marriage structure and migration were analyzed on the basis of marriage records in the Kanash, Cheboksary, and Morgaushi raions of the Chuvash Republic. Ethnic assortiveness was not detected in Chuvashes and was 4.16-18.05 in Russians. Gene flow between Chuvashes and Russians was 5.1-8.3%; the degree of endogamy was 0.61-0.70.     

Marital and migration structure and inbreeding in the Adyg population]

Endogamy and gametic indices for both Russian and Adyg populations living in the Adyg autonomous region of Krasnodar district were determined on different levels of territorial units: village, rural, community (a group of villagers) and rural region. Inbreeding coefficient was estimated for Adyg population and its structure analysed: a random component contributes mostly to the inbreeding coefficient (Fst = 0.00991), non-random component of the inbreeding coefficient being Fis = 0.010009, which testifies to negative marital assortativity among Adygs. Local inbreeding "a" and decline in the inbreeding "phi" coefficient at a distance from 0 to 500 km were calculated using the Malecot's formula: the coefficient "a" was found to be 0.00397, which is in good accordance with the Fst.     

Behavioral asymmetries in a moving hybrid zone

Three narrow hybrid zones exist between hermit and Townsend'swarblers in the Pacific Northwest. Character transition curvessuggest that these zones are moving and that Townsend's warblershave a selective advantage over hermit warblers. This studycompares year-to-year return rates, male persistence on territories,pairing success, pairing patterns, and territory quality of hermitand Townsend's warblers and their hybrids in the WashingtonCascades hybrid zone. There was no difference in the year-to-yearreturn rate between the parental species. Townsend's males weremore successful in maintaining territories and attracting matesthan hermit males. Among mated pairs there were few hermit malescompared to females, independently supporting the inferiorityof hermit males in competition for territories or female mate choicefor Townsend's-like males. I found no difference in the qualityof hermit and Townsend's territories; however, in poor habitatsTownsend's males were more successful at attracting mates, suggestingfemale preference for Townsend's-like males. In high-qualityhabitats, there was no difference in pairing success betweenthe parental species. The fitness of hybrids relative to parentalsaffects the width and movement of the zone. Hybrids were intermediatein their ability to maintain territories and to attract mates, whichshould increase the width of the zone and accelerate its movement.Fewer hybrid males returned to from one year to the next, andamong mated pairs there were few hybrid females relative tomales, suggesting hybrid inferiority, which should narrow thehybrid zone and slow its movement.     

Malarial parasitism and male competition for mates in the western fence lizard,Sceloporus occidentalis

Summary The effect of malarial parasitism on the ability of male western fence lizards, Sceloporus occidentalis, to compete for access to females was assessed experimentally. Pairs of male lizards, one infected with the malarial parasite, Plasmodium mexicanum, and the other not infected, were matched by size and color and placed in large seminatural outdoor enclosures along with an adult female lizard. Infected males displayed to females and to other males less often than did noninfected male lizards. Noninfected lizards were dominant in social interactions more often than malarious animals, based on duration and intensity of agonistic encounters toward the other male, and time spent with the female. Thus, malarial infection hinders the ability of male fence lizards to compete for mates.     

Individual and population energetics of a lizard on a Mediterranean islet

Summary Population density in the lacertid lizardPodarcis lilfordi on the Mediterranean islet of Nitge, Menorca, Balearic Islands, was found to be 12 190 ind · ha^-1 (SE, ±2135), exceeding densities reported for other island or mainland lizard populations. Field metabolic rates inP. lilfordi were measured by the doubly labeled water method, allowing estimation of a population metabolizable energy demand of 13.86 MJ · ha^-1 · day^-1-only 9.8% of that for a theoretical mammal population of the same body mass and density. Energy demand was considerably higher than that estimated for other lizard populations, primarily due to high population density but also because of high individual daily energy expenditure (1255 KJ · day^-1; body mass=5.13 g). Field metabolic rates were partitioned into maintenance and activity components by respirometry of captive animals at field body temperatures. Activity metabolism formed the main component (77.4%) of total respiratory metabolism resulting from a combination of long daily activity periods (ca. 12 h), and greatly elevated metabolism during activity (5.7 times greater than resting levels). It is hypothesized that low food availability per individual constrains the time-energy budget of this species, obligating long periods of intense foraging.     

Spatio-temporal changes in the genetic structure of the Passerina bunting hybrid zone

Although theoretical models predict that the structure of a hybrid zone can change under a variety of scenarios, only a few empirical studies of hybrid zones have unequivocally demonstrated zone movement. These studies are rare because few data sets exist that include repeated, temporally spaced, samples of the same hybrid zone. We analysed mitochondrial DNA haplotype data from samples separated by 40-45 years from across the Passerina amoena (Lazuli Bunting) and Passerina cyanea (Indigo Bunting) hybrid zone to investigate whether the genetic structure of this zone has changed during that interval. Both cline and generalized linear mixed modelling analyses uncovered a significant narrowing and a substantial westward shift of the Passerina bunting hybrid zone, clearly illustrating hybrid zone movement. The cause of the change may be due to a combination of ecological, demographic and behavioural factors. Our results predict that the width of the hybrid zone will continue to narrow over time, a finding consistent with reinforcement theory.     

Genetic structure of natural populations of Castanea sativa in Turkey: evidence of a hybrid zone

This study points out the evidence of a hybrid zone between two groups of genetically differentiated populations of chestnut (Castanea sativa Mill.) in Turkey. Genetic structure, gene flow and introgression levels, based on 16 allozyme loci, were investigated on 34 population samples spanning the entire C. sativa distribution area in this country. The occurrence of the hybrid zone, located in the Bithynian region, was inferred in a group of populations showing the following genetic characteristics: (i) enhanced genetic variability and intermediate allelic frequencies between those of the Western and Eastern groups of populations; (ii) sharp and concordant changes in allele frequencies; (iii) decreased gene flow with the Western and Eastern populations. Starting from the cline width estimated to be 324 km, strength of selection was evaluated from the gene flow distance, as indicated from the degree of genetic structuring outside the hybrid zone. Evolutionary processes shaping the observed genetic differentiation and introgression are discussed on the basis of palynological data, palaeoclimatic events and evidence of hybridization found in other plant and animal species in the same region.     

Divergent character clines across a recent secondary contact zone in a Hispaniolan lizard

Studies of genetic contact zones provide valuable information regarding the processes of population divergence, adaptation and speciation. In this paper, I examine transitions in morphology, mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) haplotypes across a recent secondary contact zone in a Hispaniolan lizard Ameiva chrysolaema . Maximum likelihood cline fitting analyses suggest non-coincidence of cline centers and that the mtDNA cline is significantly displaced to the west of the remaining clines. nDNA and morphological clines are coincident and tend to be associated with the prevailing environmental gradient. The lack of cytonuclear disequilibrium near the center of the contact zone and the non-coincidence of character clines suggest that this zone does not conform to a tension zone model of hybridization; thus, gene flow across the zone does not seem to be impeded. The extremely narrow width of the dorsal scale size cline and the close association of this cline with the steepness of the environmental (precipitation) gradient suggest that this character may be under environmental selection. Taken together, this contact zone appears to be structured by a combination of mtDNA introgression, possibly associated with eastward movement of the zone, and environmental selection on some characters.