Felix Breden

Sex Chromosomes and Sexual Selection in Poeciliid Fishes

We propose that the evolution of female preferences can be strongly influenced by linkage of attractive male traits to the Y chromosome and female preferences to the X chromosome in male heterogametic species. Such linkage patterns are predicted by models of the evolution of sexually antagonistic genes. Subsequent recombination of attractive male characters from the Y to the X would create physical linkage between attractive male trait and preference. A literature survey shows that Y linkage of potentially sexually antagonistic traits is common in poeciliid fishes and other species with sex chromosomes that are not well differentiated, but may also occur in taxa with degenerate Y chromosomes. In the guppy, attractive male traits are primarily Y and X linked; a literature review of the inheritance of sex‐limited attractive male characters suggests that 16 are Y linked, 24 recombine between the X and Y, two are X linked, and two are autosomal. Crosses and backcrosses between high female preference (Endler’s live‐bearers) and low female preference (Rio San Miguel) guppy populations show that this character has a strong additive genetic component and that it will be possible to investigate the physical linkage of male and female sexually selected characters in this species through mapping studies.

Invasion success and genetic diversity of introduced populations of guppies Poecilia reticulata in Australia

High genetic diversity is thought to characterize successful invasive species, as the potential to adapt to new environments is enhanced and inbreeding is reduced. In the last century, guppies, Poecilia reticulata, repeatedly invaded streams in Australia and elsewhere. Quantitative genetic studies of one Australian guppy population have demonstrated high additive genetic variation for autosomal and Y‐linked morphological traits. The combination of colonization success, high heritability of morphological traits, and the possibility of multiple introductions to Australia raised the prediction that neutral genetic diversity is high in introduced populations of guppies. In this study we examine genetic diversity at nine microsatellite and one mitochondrial locus for seven Australian populations. We used mtDNA haplotypes from the natural range of guppies and from domesticated varieties to identify source populations. There were a minimum of two introductions, but there was no haplotype diversity within Australian populations, suggesting a founder effect. This was supported by microsatellite markers, as allelic diversity and heterozygosity were severely reduced compared to one wild source population, and evidence of recent bottlenecks was found. Between Australian populations little differentiation of microsatellite allele frequencies was detected, suggesting that population admixture has occurred historically, perhaps due to male‐biased gene flow followed by bottlenecks. Thus success of invasion of Australia and high additive genetic variance in Australian guppies are not associated with high levels of diversity at molecular loci. This finding is consistent with the release of additive genetic variation by dominance and epistasis following inbreeding, and with disruptive and negative frequency‐dependent selection on fitness traits.

MITOCHONDRIAL DNA SEQUENCE VARIATION AMONG NATURAL POPULATIONS OF THE TRINIDAD GUPPY, POECILIA RETICULATA

Guppies were sampled from eight populations representing four river drainage basins in northern Trinidad, and from one population on the nearby island of Tobago. For each individual, a 465 base pair (bp) segment of the control region of the mitochondrial genome was sequenced. The resulting DNA sequences were subjected to sequence divergence calculations and the populations were linked by maximum parsimony analysis to determine their phylogenetic relationships. Mitochondrial DNA (mtDNA) sequence variation was found both within and between river drainages, correlated with the geographic features of northern Trinidad. The variation observed exists primarily between drainages, particularly between the Oropuche drainage and all other Trinidad drainages examined. Estimates of time of divergence between guppy populations of different drainages, based on mtDNA sequence variation, ranged from 100,000 to 200,000 for the most recently separated populations and from 600,000 to 1.2 million years between the Oropuche populations and all others examined. Examination of fish from northeastern South America will be required to determine whether these populations differentiated in their present locations or were the result of separate invasions of Trinidad from different Venezuelan sources. However, genetic isolation of these populations appears to predate the current physical separation of the island of Trinidad from the Venezuelan mainland.

Genome‐wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies

Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole‐genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome‐wide picture of standing natural variation in populations, genome‐wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor‐net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise FST values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. FST outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome‐wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations

Genetic tools for studying adaptation and the evolution of behavior

The rapid expansion of genomic and molecular genetic techniques in model organisms, and the application of these techniques to organisms that are less well studied genetically, make it possible to understand the genetic control of many behavioral phenotypes. However, many behavioral ecologists are uncertain about the value of including a genetic component in their studies. In this article, we review how genetic analyses of behavior are central to topics ranging from understanding past selection and predicting future evolution to explaining the neural and hormonal control of behavior. Furthermore, we review both new and old techniques for studying evolutionary behavior genetics and highlight how the choice of approach depends on both the question and the organism. Topics discussed include genetic architecture, detecting the past history of selection, and genotype‐by‐environment interactions. We show how these questions are being addressed with techniques including statistical genetics, QTL analyses, transgenic analyses, and microarrays. Many of the techniques were first applied to the behavior of genetic model organisms such as laboratory mice and flies. Two recent developments serve to expand the relevance of such studies to behavioral ecology. The first is to use model organisms for studies of the genetic basis of evolutionarily relevant behavior and the second is to apply methods developed in model genetic systems to species that have not previously been examined genetically. These conceptual advances, along with the rapid diversification of genetic tools and the recognition of widespread genetic homology, suggest a bright outlook for evolutionary genetic studies. This review provides access to tools through references to the recent literature and shows the great promise for evolutionary behavioral genetics.

SPATIAL AND TEMPORAL VARIATION IN GROUP RELATEDNESS: EVIDENCE FROM THE IMPORTED WILLOW LEAF BEETLE

The distribution of genetic variance within and among socially interacting groups, often quantified as the average relatedness or r̄, is an important determinant of the evolution of social behaviors. Models of social evolution often treat this average as a constant characteristic of a species. In this paper, we present data documenting the degree of temporal and spatial variation in the average relatedness of larval groups of imported willow leaf beetles, a species whose immatures display several primitive social behaviors. Collections of groups were made over three generations at three localities in Virginia and three localities in Illinois. Average relatedness was estimated from the distribution of electrophoretically determined genotypic frequencies within and among groups for each collection. Average relatedness ranged from 0.20 at one locality in Illinois to 0.65 at one locality in Virginia. Individual cases of pairwise differences between samples indicated that there were both temporal and locality effects. Further, statistical analysis showed the set of relatedness values to be heterogeneous with significant locality effects. Geographic genetic variance was also partitioned among trees sampled within localities in Illinois, among localities within each state, and between states. Notably, significant gene‐frequency variation among groups of beetles occupying closely spaced trees was detected at several localities.

Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation

The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3-0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested.

Selection Within and between Kin Groups of the Imported Willow Leaf Beetle

Two opposing levels of selection determine the evolution of cannibalism in the imported willow leaf beetle, Plagiodera versicolora. Within kin groups, cannibals exhibit a developmental and survival advantage over non-cannibals. Between groups, individuals in groups with low rates of cannibalism enjoy a survival advantage owing to an increase in survival with larval group size. This effect of the cannibal on group survivorship is not a simple function of group size; rather, the effect of an individuals phenotype on the fitness of the other members of its kin group depends on the array of phenotypes in the group. Two factors determining the evolution of cannibalism vary in space and time: the relative strength of selection within and between groups; and the average degree of relatedness within groups, which determines the evolutionary outcome of selection. This sets up the possibility that the balance between selection for cannibalism within and between groups may vary in a complicated manner across the range of this species.

Comparison of Antibody Repertoires Produced by HIV-1 Infection, Other Chronic and Acute Infections, and Systemic Autoimmune Disease

Background Antibodies (Abs) produced during HIV-1 infection rarely neutralize a broad range of viral isolates; only eight broadly-neutralizing (bNt) monoclonal (M)Abs have been isolated. Yet, to be effective, an HIV-1 vaccine may have to elicit the essential features of these MAbs. The V genes of all of these bNt MAbs are highly somatically mutated, and the VH genes of five of them encode a long (≥20 aa) third complementarity-determining region (CDR-H3). This led us to question whether long CDR-H3s and high levels of somatic mutation (SM) are a preferred feature of anti-HIV bNt MAbs, or if other adaptive immune responses elicit them in general. Methodology and Principal Findings We assembled a VH-gene sequence database from over 700 human MAbs of known antigen specificity isolated from chronic (viral) infections (ChI), acute (bacterial and viral) infections (AcI), and systemic autoimmune diseases (SAD), and compared their CDR-H3 length, number of SMs and germline VH-gene usage. We found that anti-HIV Abs, regardless of their neutralization breadth, tended to have long CDR-H3s and high numbers of SMs. However, these features were also common among Abs associated with other chronic viral infections. In contrast, Abs from acute viral infections (but not bacterial infections) tended to have relatively short CDR-H3s and a low number of SMs, whereas SAD Abs were generally intermediate in CDR-H3 length and number of SMs. Analysis of VH gene usage showed that ChI Abs also tended to favor distal germline VH-genes (particularly VH1-69), especially in Abs bearing long CDR-H3s. Conclusions and Significance The striking difference between the Abs produced during chronic vs. acute viral infection suggests that Abs bearing long CDR-H3s, high levels of SM and VH1-69 gene usage may be preferentially selected during persistent infection.

Opsin gene duplication and diversification in the guppy, a model for sexual selection

Identification of genes that control variation in adaptive characters is a prerequisite for understanding the processes that drive sexual and natural selection. Male coloration and female colour perception play important roles in mate choice of the guppy, a model organism for studies of natural and sexual selection. We examined a potential source for the known variation in colour perception, by analysing genomic and complementary DNA sequences of genes that code for visual pigment proteins. We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. Alleles with non-synonymous changes that suggest dissimilar spectral tuning properties occur in the same population and even in the same individual, and the high frequency of non-synonymous substitutions argues for diversifying selection acting on these proteins. Therefore, variability in tuning amino acids is partitioned within individuals and populations of the guppy, in contrast to variability for LWS at higher taxonomic levels in cichlids, a second model system for differentiation owing to sexual selection. Since opsin variability parallels the extreme male colour polymorphism within guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species.