Analysis of high density expression microarrays with signed-rank call algorithms

MOTIVATION

We consider the detection of expressed genes and the comparison of them in different experiments with the high-density oligonucleotide microarrays. The results are summarized as the detection calls and comparison calls, and they should be robust against data outliers over a wide target concentration range. It is also helpful to provide parameters that can be adjusted by the user to balance specificity and sensitivity under various experimental conditions.

RESULTS

We present rank-based algorithms for making detection and comparison calls on expression microarrays. The detection call algorithm utilizes the discrimination scores. The comparison call algorithm utilizes intensity differences. Both algorithms are based on Wilcoxon's signed-rank test. Several parameters in the algorithms can be adjusted by the user to alter levels of specificity and sensitivity. The algorithms were developed and analyzed using spiked-in genes arrayed in a Latin square format. In the call process, p-values are calculated to give a confidence level for the pertinent hypotheses. For comparison calls made between two arrays, two primary normalization factors are defined. To overcome the difficulty that constant normalization factors do not fit all probe sets, we perturb these primary normalization factors and make increasing or decreasing calls only if all resulting p-values fall within a defined critical region. Our algorithms also automatically handle scanner saturation.

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

The External RNA Controls Consortium: a progress report

Standard controls and best practice guidelines advance acceptance of data from research, preclinical and clinical laboratories by providing a means for evaluating data quality. The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control.

Extension of a pilot study: impact from the cytochrome P450 2D6 polymorphism on outcome and costs associated with severe mental illness

The influence of cytochrome P450 2D6 (CYP2D6) genetic variability was examined in psychiatric inpatients by evaluating adverse drug events (ADEs), hospital stays, and total costs over a 1-year period in an extension of a previously published brief report. One hundred consecutive psychiatric patients from Eastern State Hospital in Lexington, Kentucky, were genotyped for CYP2D6 expression. ADEs were evaluated by a neurologic rating scale, modified Udvalg for Kliniske Undersogelser Side Effect Rating Scale, or chart review. Information on total hospitalization days and total costs were gathered for a 1-year period. Forty-five percent of the patients received medications that were primarily dependent on the CYP2D6 enzyme for their elimination. When the analysis was restricted to just those patients in each group receiving medication heavily dependent on the CYP2D6 enzyme, the following were observed: (1) a trend toward greater numbers of ADEs from medications as one moved from the group with ultrarapid CYP2D6 activity (UM) to the group with absent CYP2D6 activity (PM); (2) the cost of treating patients with extremes in CYP2D6 activity (UM and PM) was on average $4,000 to $6,000 per year greater than the cost of treating patients in the efficient metabolizer (EM) and intermediate metabolizer (IM) groups; and (3) total duration of hospital stay was more pronounced for those in CYP2D6 PM group. Variance of hospital stays and costs calculated from these preliminary data suggests that 1,500 to 2,000 patients must be evaluated over at least a 1-year period to determine whether the CYP2D6 genetic variation significantly alters the duration of hospital stay and costs.

Elicitor rapidly induces chalcone synthase mRNA in Phaseolus vulgaris cells at the onset of the phytoalexin defense response

DNAs complementary to poly(A)(+) RNA present in elicitor-treated cells of Phaseolus vulgaris L. were inserted into pBR325 and used to transform Escherichia coli strain JA221. A clone was identified that contained sequences complementary to mRNA encoding chalcone synthase, a regulatory enzyme of phenylpropanoid biosynthesis, which catalyzes the first reaction of a branch pathway specific to flavonoid and isoflavonoid biosynthesis. Rapid, marked but transient increases in chalcone synthase mRNA in response to elicitor treatment were observed by RNA blot hybridization with (32)P-labeled chalcone synthase cDNA sequences. Induction of chalcone synthase mRNA governs the rate of enzyme synthesis throughout the phase of rapid increase in enzyme activity at the onset of accumulation of isoflavonoid-derived phytoalexins. The data are consistent with the hypothesis that elicitor causes a rapid transient stimulation of transcription of chalcone synthase gene(s) as an early event in the expression of the phytoalexin defense response.

Organization and differential activation of a gene family encoding the plant defense enzyme chalcone synthase in Phaseolus vulgaris

Chalcone synthase (CHS) catalyzes the first and key regulatory step in the branch pathway of phenylpropanoid biosynthesis specific for synthesis of ubiquitous flavonoid pigments and UV protectants. In bean (Phaseolus vulgaris L.) and other members of the Leguminoseae, chalcone synthase is also involved in the synthesis of the isoflavonoid-derived phytoalexin antibiotics characteristic of this family. We have demonstrated that the haploid genome of bean contains a family of about six to eight CHS genes, some of which are tightly clustered. Treatment of bean cells with fungal elicitor activates several of these genes leading to the accumulation of at least five and probably as many as nine distinct CHS transcripts encoding a set of CHS isopolypeptides of Mr 42-43 kDa but with differing pI in the range pH 6-7. In elicited cells specific transcripts and encoded polypeptides are differentially induced with respect to both the extent and kinetics of accumulation. Wounding or infection of hypocotyl tissue also activates several CHS genes with marked differences in the pattern of accumulation of specific transcripts and encoded polypeptides in wounded compared to infected tissue or elicited cells, indicating operation of more than one cue for defense gene activation. Illumination induces accumulation of a different set of CHS transcripts including only one of the set hitherto demonstrated to be induced by biological stress. The organization and differential regulation of the CHS gene family in bean are discussed in relation to the functions of this enzyme in adaptative and protective responses to diverse environmental stresses.

Comparison of two CYP2D6 genotyping methods and assessment of genotype-phenotype relationships

BACKGROUND

There have been no published reports comparing the CYP450 GeneChip microarray assay with more standard methods of genetic testing.

METHODS

We collected 20-mL blood samples from 236 volunteers for DNA isolation and testing before each individual ingested 60 mg of dextromethorphan, and collected their urine. CYP2D6 alleles *3 to *7, *9, *17, and *41, and multiple CYP2D6 gene copies were tested by allele-specific PCR (AS-PCR), whereas alleles *2 to *4 and *6 to *11 were tested by the Affymetrix CYP450 GeneChip assay. Five of the CYP2D6 alleles (*3, *4, *6, *7, and *9) were tested by both AS-PCR and the CYP450 GeneChip assay in an independent and blinded fashion in 232 of the 236 healthy volunteers. The combined CYP2D6 genotype from both methods was used to divide the population into four subgroups, poor metabolizers (PMs), intermediate metabolizers (IMs), extensive metabolizers (EMs), and ultrarapid metabolizers (UMs), based on their relative function and ability to express the CYP2D6 gene. The urinary elimination of dextromethorphan was assessed in each of these CYP2D6 subgroups.

RESULTS

The CYP2D6*3, *4, *6, *7, and *9 alleles showed a high degree of concordance between the CYP450 GeneChip and AS-PCR methods (>99% concordance). The mean (SD) of the log[dextromethorphan metabolic ratio (MR)] in the four CYP2D6 subgroups was PM = 0.49 (0.38); IM = -1.24 (0.53); EM = -2.35 (0.61); and UM = -2.43 (0.38).

CONCLUSIONS

Oligonucleotide microarray technology is an efficient and reliable way to test for CYP2D6 gene variation based on five alleles compared by separate methods. The methodology is influenced by the quality and amount of DNA present. The log(dextromethorphan MR) is a highly variable index that appears to reflect the crude nature of the dextromethorphan MR as an indicator of CYP2D6 in vivo enzyme activity.

Algorithms for large-scale genotyping microarrays

MOTIVATION

Analysis of many thousands of single nucleotide polymorphisms (SNPs) across whole genome is crucial to efficiently map disease genes and understanding susceptibility to diseases, drug efficacy and side effects for different populations and individuals. High density oligonucleotide microarrays provide the possibility for such analysis with reasonable cost. Such analysis requires accurate, reliable methods for feature extraction, classification, statistical modeling and filtering.

RESULTS

We propose the modified partitioning around medoids as a classification method for relative allele signals. We use the average silhouette width, separation and other quantities as quality measures for genotyping classification. We form robust statistical models based on the classification results and use these models to make genotype calls and calculate quality measures of calls. We apply our algorithms to several different genotyping microarrays. We use reference types, informative Mendelian relationship in families, and leave-one-out cross validation to verify our results. The concordance rates with the single base extension reference types are 99.36% for the SNPs on autosomes and 99.64% for the SNPs on sex chromosomes. The concordance of the leave-one-out test is over 99.5% and is 99.9% higher for AA, AB and BB cells. We also provide a method to determine the gender of a sample based on the heterozygous call rate of SNPs on the X chromosome. See http://www.affymetrix.com for further information. The microarray data will also be available from the Affymetrix web site.

AVAILABILITY

The algorithms will be available commercially in the Affymetrix software package.

Co-ordinated synthesis of phytoalexin biosynthetic enzymes in biologically-stressed cells of bean (Phaseolus vulgaris L.)

Changes in the rates of synthesis of three enzymes of phenyl-propanoid biosynthesis in Phaseolus vulgaris L. (dwarf French bean) have been investigated by immunoprecipitation of [S]methionine-labeled enzyme subunits with mono-specific antisera. Elicitor causes marked, rapid but transient co-ordinated increases in the rate of synthesis of phenyl-alanine ammonia-lyase, chalcone synthase and chalcone isomerase concomitant with the phase of rapid increase in enzyme activity at the onset of accumulation of phenyl-propanoid-derived phytoalexin antibiotics in suspension cultures of P. vulgaris. Co-ordinate induction of enzyme synthesis is also observed in hypocotyl tissue during race:cultivar-specific interactions with Colletotrichum lindemuthianum, causal agent of anthracnose. In an incompatible interaction (host resistant) there are early increases apparently localized to the initial site of infection prior to the onset of phytoalexin accumulation and expression of hypersensitive resistance. In contrast, in a compatible interaction (host susceptible) there is no induction of synthesis in the early stages of infection, but a delayed widespread response at the onset of lesion formation associated with attempted lesion limitation. It is concluded that expression of the phytoalexin defense response in biologically stressed cells of P. vulgaris characteristically involves co-ordinate induction of synthesis of phytoalexin biosynthetic enzymes.

It takes two to tango: reproductive skew and social correlates of male mating success in a lek-breeding bird

Variance in reproductive success among individuals is a defining characteristic of many social vertebrates. Yet, our understanding of which male attributes contribute to reproductive success is still fragmentary in most cases. Male-male reproductive coalitions, where males jointly display to attract females, are of particular interest to evolutionary biologists because one male appears to forego reproduction to assist the social partner. By examining the relationship between social behaviour and reproductive success, we can elucidate the proximate function of coalitions in the context of mate choice. Here, we use data from a 4-year study of wire-tailed manakins (Pipra filicauda) to provide molecular estimates of reproductive skew and to test the hypothesis that male-male social interactions, in the context of coordinated displays, positively influence a male's reproductive success. More specifically, we quantify male-male social interactions using network metrics and predict that greater connectivity will result in higher relative reproductive success. Our data show that four out of six leks studied had significant reproductive skew, with success apportioned to very few individuals in each lek. Metrics of male social affiliations derived from our network analysis, especially male connectivity, measured as the number of males with whom the focal male has extended interactions, were strong predictors of the number of offspring sired. Thus, network connectivity is associated with male fitness in wire-tailed manakins. This pattern may be the result of shared cues used by both sexes to assess male quality, or the result of strict female choice for coordinated display behaviour.

Social networks in the lek-mating wire-tailed manakin (Pipra filicauda)

How social structure interacts with individual behaviour and fitness remains understudied despite its potential importance to the evolution of cooperation. Recent applications of network theory to social behaviour advance our understanding of the role of social interactions in various contexts. Here we applied network theory to the social system of lek-mating wire-tailed manakins (Pipra filicauda, Pipridae, Aves). We analysed the network of interactions among males in order to begin building a comparative framework to understand where coordinated display behaviour lies along the continuum from solitary to obligately cooperative dual-male displays in the family Pipridae. Network degree (the number of links from a male to others) ranged from 1 to 10, with low mean and high variance, consistent with the theory for the evolution of cooperation within social networks. We also assessed factors that could predict social and reproductive success of males. Four network metrics, degree, eigenvector centrality, information centrality and reach, some of which assess circuitous as well as the shortest (geodesic) paths of male connectivity, predicted male social rise. The duration of a male's territorial tenure during the 4 years of the study predicted his probability of siring offspring.

Spatial and temporal drivers of avian population dynamics across the annual cycle

Untangling the spatial and temporal processes that influence population dynamics of migratory species is challenging, because changes in abundance are shaped by variation in vital rates across heterogeneous habitats and throughout the annual cycle. We developed a full-annual-cycle, integrated, population model and used demographic data collected between 2011 and 2014 in southern Indiana and Belize to estimate stage-specific vital rates of a declining migratory songbird, the Wood Thrush (Hylocichla mustelina). Our primary objective was to understand how spatial and temporal variation in demography contributes to local and regional population growth. Our full-annual-cycle model allowed us to estimate (1) age-specific, seasonal survival probabilities, including latent survival during both spring and autumn migration, and (2) how the relative contribution of vital rates to population growth differed among habitats. Wood Thrushes in our study populations experienced the lowest apparent survival rates during migration and apparent survival was lower during spring migration than during fall migration. Both mortality and high dispersal likely contributed to low apparent survival during spring migration. Population growth in high-quality habitat was most sensitive to variation in fecundity and apparent survival of juveniles during spring migration, whereas population growth in low-quality sites was most sensitive to adult apparent breeding-season survival. These results elucidate how full-annual-cycle vital rates, particularly apparent survival during migration, interact with spatial variation in habitat quality to influence population dynamics in migratory species.

Quantifying drivers of population dynamics for a migratory bird throughout the annual cycle

Worldwide, migratory species are undergoing rapid declines but understanding the factors driving these declines is hindered by missing information about migratory connectivity and the lack of data to quantify environmental processes across the annual cycle. Here, we combined range-wide information about migratory connectivity with global remote-sensing data to quantify the relative importance of breeding and non-breeding environmental processes to persistent long-term population declines of a migratory songbird, the wood thrush (Hylocichla mustelina). Consistent with theoretical predictions about population limitation of migratory birds, our results suggest that habitat loss and climate have contributed to the observed declines in wood thrush breeding abundance, yet the relative importance of breeding versus non-breeding factors is population-specific. For example, high-abundance core breeding populations appear to be more limited by habitat loss, whereas low-abundance, peripheral populations appear to be limited by climate-driven seasonal interactions. Further, our analysis indicates that the relative impact of breeding habitat loss is at least three to six times greater than the impact of equivalent non-breeding habitat loss and therefore the steepest regional declines have likely been driven by the loss of breeding habitat. These results underscore the need for population-specific conservation strategies implemented throughout the annual cycle to reverse long-term declines.

Analysis of plasmid genome evolution based on nucleotide-sequence comparison of two related plasmids of Escherichia coli

Plasmid Rsc13, a small derivative of the plasmid R1, contains a region necessary for replication as well as a complete copy (4957 bp) of the ampicillin resistance transposon, Tn3. We determined the nucleotide sequence of the replication region of Rsc13 to be 2937 bp and then compared this region (designated the 2.9-kb region) to the analogous region of pSM1, a small derivative of the plasmid R100 which has common ancestry with R1. Rsc13 and pSM1 were 96% homologous in this 2.9-kb region except for a discrete region of about 250 bp which showed only 44% homology. The sequence and distribution of nucleotide substitutions between Rsc13 and pSM1 supported a map of possible genes and sites which have previously been seen in the replication region of Rsc13 and pSM1 which showed only 44% homology. Analysis of the amino acid sequence and predicted conformation of the two RepA2 polypeptides, however, suggested that they were very similar. We proposed that the repA2 region of R1 and R100 was replaced by a substitution of a short DNA segment from another plasmid which was evolutionarily related to R1 and R100 but had more divergence. This event may have been mediated by a mechanism similar to that of gene conversion as described in eukaryotic systems.

Decay of interspecific avian flock networks along a disturbance gradient in Amazonia

Our understanding of how anthropogenic habitat change shapes species interactions is in its infancy. This is in large part because analytical approaches such as network theory have only recently been applied to characterize complex community dynamics. Network models are a powerful tool for quantifying how ecological interactions are affected by habitat modification because they provide metrics that quantify community structure and function. Here, we examine how large-scale habitat alteration has affected ecological interactions among mixed-species flocking birds in Amazonian rainforest. These flocks provide a model system for investigating how habitat heterogeneity influences non-trophic interactions and the subsequent social structure of forest-dependent mixed-species bird flocks. We analyse 21 flock interaction networks throughout a mosaic of primary forest, fragments of varying sizes and secondary forest (SF) at the Biological Dynamics of Forest Fragments Project in central Amazonian Brazil. Habitat type had a strong effect on network structure at the levels of both species and flock. Frequency of associations among species, as summarized by weighted degree, declined with increasing levels of forest fragmentation and SF. At the flock level, clustering coefficients and overall attendance positively correlated with mean vegetation height, indicating a strong effect of habitat structure on flock cohesion and stability. Prior research has shown that trophic interactions are often resilient to large-scale changes in habitat structure because species are ecologically redundant. By contrast, our results suggest that behavioural interactions and the structure of non-trophic networks are highly sensitive to environmental change. Thus, a more nuanced, system-by-system approach may be needed when thinking about the resiliency of ecological networks.

Rapid and quantitative detection of enzymatically amplified HIV-1 DNA using chemiluminescent oligonucleotide probes

A hybridization protection assay (HPA) that uses acridinium ester (AE) labeled oligonucleotide probes which are specific for a conserved gag gene region of human immunodeficiency virus type 1 (HIV-1) was developed to measure the amount of HIV-1 nucleic acid. Hybridization of the single-stranded probes with their target HIV-1 sequences protected the chemiluminescent AE group from subsequent alkaline hydrolysis. The chemiluminescence from the residual AE could be easily quantitated in a luminometer. The entire process comprising template dissociation, hybridization, alkaline hydrolysis, and chemiluminescence measurement can be completed in less than one hour and does not require the separation of hybridized probe from unhybridized probe. We demonstrated that HPA could quantitatively measure the amount of DNA amplified by polymerase chain reaction. A comparative study using amplified DNA from the peripheral blood mononuclear cells (PBMC) of HIV seropositive and seronegative persons showed that HPA was as sensitive as the previous methods using 32P-labeled DNA probes.

Proximity data-loggers increase the quantity and quality of social network data

Social network analysis is an ideal quantitative tool for advancing our understanding of complex social behaviour. However, this approach is often limited by the challenges of accurately characterizing social structure and measuring network heterogeneity. Technological advances have facilitated the study of social networks, but to date, all such work has focused on large vertebrates. Here, we provide proof of concept for using proximity data-logging to quantify the frequency of social interactions, construct weighted networks and characterize variation in the social behaviour of a lek-breeding bird, the wire-tailed manakin, Pipra filicauda. Our results highlight how this approach can ameliorate the challenges of social network data collection and analysis by concurrently improving data quality and quantity.

Differential accumulation of plant defense gene transcripts in a compatible and an incompatible plant-pathogen interaction

Phenylalanine ammonia-lyase and chalcone synthase catalyze the first reaction of phenylpropanoid biosynthesis and the first reaction of a branch pathway specific for flavonoid-isoflavonoid biosynthesis, respectively. These enzymes are key control elements in the synthesis of kievitone, phaseollin, and related isoflavonoid-derived phytoalexins. RNA blot hybridization with 32P-labeled cDNA sequences was used to demonstrate marked accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs in excision-wounded hypocotyls of Phaseolus vulgaris L. (dwarf French bean) and during race-cultivar-specific interactions between hypocotyls of P. vulgaris and the partially biotrophic fungus Colletotrichum lindemuthianum, the causal agent of anthracnose. In an incompatible interaction (host resistant), early concomitant accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs, localized mainly but not entirely in tissue adjacent to the site of infection, was observed prior to the onset of phytoalexin accumulation and expression of localized, hypersensitive resistance. In contrast, in a compatible interaction (host susceptible) there was no early accumulation of these transcripts; instead, there was a delayed widespread response associated with phytoalexin accumulation during attempted lesion limitation. Two-dimensional gel electrophoresis of [35S]methionine-labeled polypeptides synthesized in vitro by translation of isolated polysomal RNA demonstrated stimulation of the synthesis of characteristic sets of phenylalanine ammonia-lyase and chalcone synthase isopolypeptides in directly infected tissue and distant, hitherto uninfected tissue in both compatible and incompatible interactions. Our data show that specific accumulation of plant defense gene transcripts is a key early component in the sequence of events leading to expression of defense responses in wounded tissue and in infected tissue during race-cultivar-specific interactions and that an elicitation signal is transmitted intercellularly in response to infection.

Quantifying avian nest survival along an urbanization gradient using citizen- and scientist-generated data

Despite the increasing pace of urbanization little is known about the factors that limit bird populations (i.e., population-level processes) within the urban/suburban land-use matrix. Here, we report rates of nest survival within the matrix of an urban land-use gradient in the greater Washington, D.C., USA, area for five common songbirds using data collected by scientists and citizens as part of a project called Neighborhood Nestwatch. Using program MARK, we modeled the effects of species, urbanization at multiple spatial scales (canopy cover and impervious surface), and observer (citizen vs. scientist) on nest survival of four open-cup and one cavity-nesting species. In addition, artificial nests were used to determine the relative impacts of specific predators along the land-use gradient. Our results suggest that predation on nests within the land-use matrix declines with urbanization but that there are species-specific differences. Moreover, variation in nest survival among species was best explained by urbanization metrics measured at larger "neighborhood" spatial scales (e.g., 1000 m). Trends were supported by data from artificial nests and suggest that variable predator communities (avian vs. mammalian) are one possible mechanism to explain differential nest survival. In addition, we assessed the quality of citizen science data and show that citizens had no negative effect on nest survival and provided estimates of nest survival comparable to Smithsonian biologists. Although birds nesting within the urban matrix experienced higher nest survival, individuals also faced a multitude of other challenges such as contaminants and invasive species, all of which could reduce adult survival.

Assessing migratory connectivity for a long-distance migratory bird using multiple intrinsic markers

Patterns of migratory connectivity are a vital yet poorly understood component of the ecology and evolution of migratory birds. Our ability to accurately characterize patterns of migratory connectivity is often limited by the spatial resolution of the data, but recent advances in probabilistic assignment approaches have begun pairing stable isotopes with other sources of data (e.g., genetic and mark-recapture) to improve the accuracy and precision of inferences based on a single marker. Here, we combine stable isotopes and geographic variation in morphology (wing length) to probabilistically assign Wood Thrush (Hylocichla mustilena) captured on the wintering grounds to breeding locations. In addition, we use known-origin samples to validate our model and assess potentially important impacts of isotopic and morphological covariates (age, sex, and breeding location). Our results show that despite relatively high levels of mixing across their breeding and nonbreeding ranges, moderate levels of migratory connectivity exist along an east-west gradient. In addition, combining stable isotopes with geographic variation in wing length improved the precision of breeding assignments by 10% and 37% compared to assignments based on isotopes alone or wing length alone, respectively. These results demonstrate that geographical variation in morphological traits can greatly improve estimates of migratory connectivity when combined with other intrinsic markers (e.g., stable isotopes or genetic data). The wealth of morphological data available from museum specimens across the world represents a tremendously valuable, but largely untapped, resource that is widely applicable for quantifying patterns of migratory connectivity.

Climate, demography and lek stability in an Amazonian bird

Lekking is a rare, but iconic mating system where polygynous males aggregate and perform group displays to attract females. Existing theory postulates that demographic and environmental stability are required for lekking to be an evolutionarily viable reproductive strategy. However, we lack empirical tests for the hypotheses that lek stability is facilitated by age-specific variation in demographic rates, and by predictable, abundant resources. To address this knowledge gap, we use multistate models to examine how two demographic elements of lek stability-male survival and recruitment-vary with age, social status and phase of the El Niño Southern Oscillation (ENSO) in a Neotropical frugivorous bird, the wire-tailed manakin (Pipra filicauda). Our results show that demographic and environmental conditions were related to lek stability in the Ecuadorean Amazon. Apparent annual survival probability of territorial males was higher than that of non-territorial floaters, and recruitment probability increased as males progressed in an age-graded queue. Moreover, annual survival of territorial males and body condition of both floaters and territory holders were higher following years with El Niño conditions, associated with reduced rainfall and probably higher fruit production in the northern Neotropics, and lower after years with wet, La Niña conditions that predominated our study. Recruitment probabilities varied annually, independent of ENSO phase, and increased over our study period, but the annual mean number of territorial males per lek declined. Our results provide empirical support for hypothesized demographic and environmental drivers of lek dynamics. This study also suggests that climate-mediated changes in resource availability can affect demography and subsequent lek stability in a relatively buffered, lowland rainforest.

The ecological-evolutionary interplay: density-dependent sexual selection in a migratory songbird

Little is understood about how environmental heterogeneity influences the spatial dynamics of sexual selection. Within human-dominated systems, habitat modification creates environmental heterogeneity that could influence the adaptive value of individual phenotypes. Here, we used the gray catbird to examine if the ecological conditions experienced in the suburban matrix (SM) and embedded suburban parks (SP) influence reproductive strategies and the strength of sexual selection. Our results show that these habitats varied in a key ecological factor, breeding density. Moreover, this ecological factor was closely tied to reproductive strategies such that local breeding density predicted the probability that a nest would contain extra-pair offspring. Partitioning reproductive variance showed that while within-pair success was more important in both habitats, extra-pair success increased the opportunity for sexual selection by 39% at higher breeding densities. Body size was a strong predictor of relative reproductive success and was under directional selection in both habitats. Importantly, our results show that the strength of sexual selection did not differ among habitats at the landscape scale but rather that fine-scale variation in an ecological factor, breeding density, influenced sexual selection on male phenotypes. Here, we document density-dependent sexual selection in a migratory bird and hypothesize that coarse-scale environmental heterogeneity, in this case generated by anthropogenic habitat modification, changed the fine-scale ecological conditions that drove the spatial dynamics of sexual selection.