It is often claimed that pair bonds preferentially form between individuals that resemble one another. Such assortative mating appears to be widespread throughout the animal kingdom. Yet it is unclear whether the apparent ubiquity of assortative mating arises primarily from mate choice (‘like attracts like’) which can be constrained by same-sex competition for mates, from spatial or temporal separation, or from observer, reporting, publication or search bias. Here, based on a conventional literature search, we find compelling meta-analytical evidence for size-assortative mating in birds (r = 0.178, 95% CI: 0.142 – 0.215, 83 species, 35,591 pairs). However, our analyses reveal that this effect vanishes gradually with increased control of confounding factors. Specifically, the effect size decreased by 42% when we used unpublished data from nine long-term field studies, i.e. data free of reporting and publication bias (r = 0.103, 95% CI: 0.074 – 0.132, eight species, 16,611 pairs). Moreover, in those data assortative mating effectively disappeared when both partners were measured by independent observers or separately in space and time (mean r = 0.018, 95% CI: -0.016 – 0.057). Likewise, we also found no evidence for assortative mating in a direct experimental test for mutual mate choice in captive populations of zebra finches (r = -0.020, 95% CI: -0.148 – 0.107, 1,414 pairs). These results highlight the importance of unpublished data in generating unbiased meta-analytical conclusions, and suggest that the apparent ubiquity of assortative mating reported in the literature is overestimated and may not be driven by mate choice or mating competition for preferred mates.

The sperm mid-piece has traditionally been considered to be the engine that powers sperm. Larger mid-pieces have therefore been assumed to provide greater energetic capacity. However, in the zebra finch Taeniopygia guttata, a recent study showed a surprising negative relationship between mid-piece length and sperm energy content. Using a multidimensional approach to study mid-piece structure, we tested whether this unexpected relationship can be explained by a trade-off between mid-piece length and mid-piece thickness and/or cristae density inside the mitochondrial helix. We used selective plane illumination microscopy to study mid-piece structure from three-dimensional images of zebra finch sperm and used high-resolution transmission electron microscopy to quantify mitochondrial density. Contrary to the assumption that longer mid-pieces are larger and therefore produce or contain a greater amount of energy, our results indicate that the amount of mitochondrial material is consistent across mid-pieces of varying lengths, and longer mid-pieces are simply proportionately ‘thinner’.

Many fields of science currently experience a heated debate about the extent of publication bias against null-findings. Here, we show a case where putatively well-established text-book knowledge cannot be confirmed. Across four decades, zebra finch (Taeniopygia guttata) studies have reported effects of bands of certain colors on male or female attractiveness and further on behavior, physiology, life-history and fitness. Only 8 out of 39 publications presented exclusively null-findings. Here, we analyze the results of eight experiments in which we quantified the fitness of 730 color-banded individuals from four captive populations (two domesticated and two recently wild-derived). This sample size exceeds the combined sample size of all 23 publications that clearly support the “color-band effect” hypothesis. In our populations, band color explained no variance in fitness and there were no context- or population-specific band color effects. Analysis of unpublished data from three other laboratories strengthens our null finding. Finally, a meta-analysis of previously published results is indicative of selective reporting and suggests that the effect size approaches zero when sample size is large. We argue that our field would benefit from more effective means to counter confirmation bias and publication bias.

Colourful plumage ornaments may evolve because they play a role in mate choice or in intrasexual competition, acting as signals of species identity or of individual quality. The zebra finch (Taeniopygia guttata) is a model organism for the study of mate choice and its colourful plumage ornaments are thought to be used in both of these contexts. Numerous genetic colour variants have been described for this species, but they are rare in the wild. This raises the question whether discrimination against deviant phenotypes maintains the species’ uniform plumage colour (rare mate disadvantage). Further, comparison to closely related species suggests that the lack of colourful ornaments in female zebra finches is a derived condition. Male preferences for less ornamented females may have led to sexual dichromatism in the zebra finch. Here, we test the role of plumage ornaments experimentally by altering male and female colouration to mimic two types of naturally occurring genetic colour variants. We estimated effects on social dominance and reproductive success in large breeding aviaries in one domesticated and two recently wild-derived populations. Hypotheses, methods and analyses were preregistered to ensure maximal objectivity of the results presented. Despite a fairly drastic manipulation and a powerful experimental design, we found no effect of the treatment on social dominance or on reproductive success. Our results suggest that mate choice is not the mechanism that maintains homogeneity of zebra finch plumage colouration, or that can explain the loss of ornaments in females.

Studies of mate choice typically assume that individuals prefer high quality mates and select them based on condition-dependent indicator traits. In species with bi-parental care, mutual mate choice is expected to result in assortative mating for quality. When assortment is not perfect, the lower quality pair members are expected to compensate by increased parental investment to secure their partner (positive differential allocation). This framework has been assumed to hold for monogamous species like the zebra finch (Taeniopygia guttata), but progress has been hampered by the difficulty to define individual quality. By combining multiple measures of causes (inbreeding, early nutrition) and consequences (ornaments, displays, fitness components) of variation in quality into a single principal component, we here show that quality variation can be quantified successfully. We further show that variation in quality indeed predicts individual pairing success, presumably because it reflects an individual's vigor or ability to invest in reproduction. However, despite high statistical power, we found no evidence for either assortative mating or for positive differential allocation. We suggest that zebra finch ornaments and displays are not sufficiently reliable for the benefits of choosiness to exceed the costs of competition for the putative best partner. To assess the generality of these findings unbiased quantification of signal honesty and preference strength is required, rather than selective reporting of significant results.

The phenotype-linked fertility hypothesis suggests that females can judge male fertility by inspecting male phenotypic traits. This is because male sexually selected traits might correlate with sperm quality if both are sensitive to factors that influence male condition. A recent meta-analysis found little support for this hypothesis, suggesting little or no shared condition dependence. However, we recently reported that in captive zebra finches (Taeniopygia guttata) inbreeding had detrimental effects both on phenotypic traits and on measures of sperm quality, implying that variation in inbreeding could induce positive covariance between indicator traits and sperm quality. Therefore, we here assess empirically the average strength of correlations between phenotypic traits (courtship rate, beak colour, tarsus length) and measures of sperm quality (proportion of functional sperm, sperm velocity, sperm length) in populations of only outbred individuals and in mixed populations consisting of inbreds (F = 0.25) and outbreds (F = 0). As expected, phenotype sperm-trait correlations were stronger when the population contained a mix of inbred and outbred individuals. We also found unexpected heterogeneity between our two study populations, with correlations being considerably stronger in a domesticated population than in a recently wild-derived population. Correlations ranged from essentially zero among outbred-only wild-derived birds (mean Fisher's Zr ± SE = 0.03 ± 0.10) to moderately strong among domesticated birds of mixed inbreeding status (Zr ± SE = 0.38 ± 0.08). Our results suggest that, under some conditions, the phenotype-linked fertility hypothesis might apply.

Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches. Then, we validated the most promising SNP-phenotype associations (n = 25 SNPs) in 5,228 birds from four populations. Genotype-phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP-effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in non-model organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.

Inbreeding depression, or the reduction in fitness due to mating between close relatives, is a key issue in biology today. Inbreeding negatively affects many fitness-related traits, including survival and reproductive success. Despite this, very few studies have quantified the effects of inbreeding on vertebrate gamete traits under controlled breeding conditions using a full-sib mating approach. Here, we provide comprehensive evidence for the negative effect of inbreeding on sperm traits in a bird, the zebra finch Taeniopygia guttata. We compared sperm characteristics of both inbred (pedigree F = 0.25) and outbred (pedigree F = 0) individuals from two captive populations, one domesticated and one recently wild-derived, raised under standardized conditions. As normal spermatozoa morphology did not differ consistently between inbred and outbred individuals, our study confirms the hypothesis that sperm morphology is not particularly susceptible to inbreeding depression. Inbreeding did, however, lead to significantly lower sperm motility and a substantially higher percentage of abnormal spermatozoa in ejaculate. These results were consistent across both study populations, confirming the generality and reliability of our findings.

The proportion of an individual’s genome that is identical-by-descent (GWIBD) can be estimated from pedigrees (inbreeding coefficient “Pedigree F”) or molecular markers (“Marker F”), but both estimators come with error. Assuming unrelated pedigree founders, Pedigree F is the expected proportion of GWIBD given a specific inbreeding constellation. Meiotic recombination introduces variation around that expectation (Mendelian noise) and related pedigree founders systematically bias Pedigree F downwards. Marker F is an estimate of the actual proportion of GWIBD but it suffers from the sampling error of markers plus the error that occurs when a marker is homozygous without reflecting common ancestry (identical-by-state). We here show via simulation of a zebra finch and a human linkage map that three aspects of meiotic recombination (independent assortment of chromosomes, number of cross-overs and their distribution along chromosomes) contribute to variation in GWIBD and thus the precision of Pedigree and Marker F. In zebra finches, where the genome contains large blocks which are rarely broken up by recombination, the Mendelian noise was large (nearly twofold larger standard deviations compared to humans) and Pedigree F thus less precise than in humans, where cross-overs are distributed more uniformly along chromosomes. Effects of meiotic recombination on Marker F were reversed, such that the same number of molecular markers yielded more precise estimates of GWIBD in zebra finches than in humans. As a consequence, in species inheriting large blocks that rarely recombine, even small numbers of microsatellite markers will often be more informative about inbreeding and fitness than large pedigrees.

The two parental alleles at a specific locus are usually inherited with equal probability to the offspring. However, at least three processes can lead to an apparent departure from fair segregation: early viability selection, biased gene conversion and various kinds of segregation distortion. Here, we conduct a genome-wide scan for transmission distortion in a captive population of zebra finches (Taeniopygia guttata) using 1302 single-nucleotide polymorphisms (SNPs) followed by confirmatory analyses on independent samples from the same population. In the initial genome-wide scan, we found significant distortion at three linked loci on chromosome Tgu2 and we were able to replicate this finding in each of two follow-up data sets [overall transmission ratio = 0.567 (95% CI = 0.536–0.600), based on 1101 informative meioses]. Although the driving allele was preferentially transmitted by both heterozygous females [ratio = 0.560 (95% CI = 0.519–0.603)] and heterozygous males [ratio = 0.575 (95% CI = 0.531–0.623)], we could rule out postzygotic viability selection and biased gene conversion as possible mechanisms. Early postzygotic viability selection is unlikely, because it would result in eggs with no visible embryo and hence no opportunity for genotyping, and we confirmed that both females and males heterozygous for the driving allele did not produce a larger proportion of such eggs than homozygous birds. Biased gene conversion is expected to be rather localized, while we could trace transmission distortion in haplotypes of several megabases in a recombination desert. Thus, we here report the rare case of a prezygotically active transmission distorter operating equally effectively in female and male meioses.