Karyotypic polymorphism of the zebra finch Z chromosome

We describe a karyotypic polymorphism on the zebra finch Z chromosome. This polymorphism was discovered because of a difference in the position of the centromere and because it occurs at varying frequencies in domesticated colonies in the USA and Germany and among two zebra finch subspecies. Using DNA fluorescent in situ hybridization to map specific Z genes and measurements of DNA replication, we show that this polymorphism is the result of a large pericentric inversion involving the majority of the chromosome. We sequenced a likely breakpoint for the inversion and found many repetitive sequences. Around the breakpoint, there are numerous repetitive sequences and several copies of PAK3 (p21-activated kinase 3)-related sequences (PAK3Z) which showed testes-specific expression by RT-PCR. Our findings further suggest that the sequenced genome of the zebra finch may be derived from a male heterozygote for the Z chromosome polymorphism. This finding, in combination with regional differences in the frequency of the polymorphism, has important consequences for future studies using zebra finches.     

Gene duplication and fragmentation in the zebra finch major histocompatibility complex

Background

Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines.

Results

The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes.

Conclusion

The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.     

Histone modifications related to chromosome silencing and elimination during male meiosis in Bengalese finch

We report here that a germline-restricted chromosome (GRC) is regularly present in males and females of the Bengalese finch (Lonchura domestica). While the GRC is euchromatic in oocytes, in spermatocytes this chromosome is cytologically seen as entirely heterochromatic and presumably inactive. The GRC is observed in the cytoplasm of secondary spermatocytes, indicating that its elimination from the nucleus occurs during the first meiotic division. By immunofluorescence on microspreads, we investigated the presence of histone H3 modifications throughout male meiosis, as well as in postmeiotic stages. We found that the GRC is highly enriched in di- and trimethylated histone H3 at lysine 9 during prophase I, in agreement with the presumed inactive state of this chromosome. At metaphase I, dimethylated histone H3 is no longer detectable on the GRC and its chromatin is more faintly stained with DAPI. The condensed GRC is underphosphorylated at serine 10 compared to the regular chromosomes during metaphase I, being phosphorylated later at this site after the first meiotic division. From these results, we proposed that trimethylation of histone H3 at lysine 9 on the GRC chromatin increases during metaphase I. This hypermethylated state at lysine 9 may preclude the phosphorylation of the adjacent serine 10 residue, providing an example of cross-talk of histone H3 modifications as described in experimental systems. The differential underphosphorylation of the GRC chromatin before elimination is interpreted as a cytologically detectable byproduct of deficient activity of Aurora B kinase, which is responsible for the phosphorylation of H3 at serine 10 during mitosis and meiosis.     

Molecular cloning and characterization of the germline-restricted chromosome sequence in the zebra finch

The zebra finch (Taeniopygia guttata) germline-restricted chromosome (GRC) is the largest chromosome and has a unique system of transmission in germ cells. In the male, the GRC exists as a single heterochromatic chromosome in the germline and is eliminated from nuclei in late spermatogenesis. In the female, the GRC is bivalent and euchromatic and experiences recombination. These characteristics suggest a female-specific or female-beneficial function of the GRC. To shed light on the function of GRC, we cloned a portion of the GRC using random amplified polymorphic DNA–polymerase chain reaction and analyzed it using molecular genetic and cytogenetic methods. The GRC clone hybridized strongly to testis but not blood DNA in genomic Southern blots. In fluorescent in situ hybridization analysis on meiotic chromosomes from synaptonemal complex spreads, the probe showed hybridization across a large area of the GRC, suggesting that it contains repetitive sequences. We isolated a sequence homologous to the GRC from zebra finch chromosome 3 and a region of chicken chromosome 1 that is homologous to zebra finch chromosome 3; the phylogenetic analysis of these three sequences suggested that the GRC sequence and the zebra finch chromosome 3 sequence are most closely related. Thus, the GRC sequences likely originated from autosomal DNA and have evolved after the galliform–passeriform split. The present study provides a foundation for further study of the intriguing GRC.     

The germ-line-restricted chromosome in the zebra finch: recombination in females and elimination in males

In the zebra finch (Taeniopygia guttata), there is a germ-line-restricted chromosome regularly present in males and females. A reexamination of male and female meiosis in the zebra finch showed that this element forms a euchromatic bivalent in oocytes, but it is always a single, heterochromatic element in spermatocytes. Immunostaining with anti-MLH1 showed that the bivalent in oocytes has two or three foci with a localized pattern, indicating the regular occurrence of recombination. In male meiosis, the single restricted chromosome forms an axis that contains the cohesin subunit SMC3, and the associated chromatin is densely packed until late pachytene. Electron microscopy of thin-sectioned seminiferous tubules shows that the restricted chromosome is eliminated in postmeiotic stages in the form of packed chromatin inside a micronucleus, visible in the cytoplasm of young spermatids. The selective condensation of the restricted chromosome during early meiotic prophase in males is interpreted as a strategy to avoid the triggering of asynaptic checkpoints, but this condensation is reversed prior to the final condensation that leads to its (ulterior) elimination. Recombination during female meiosis may prevent the genetic attrition of the restricted chromosome and, along with the elimination in male germ cells, ensures its regular transmission through females.     

Molecular cloning of zebra finch W chromosome repetitive sequences: evolution of the avian W chromosome

The zebra finch (Taeniopygia guttata) has a large Z chromosome and highly condensed W chromosome. We used the random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) technique to isolate female-specific sequences ZBM1 and ZBM2. Southern blot hybridization to male and female zebra finch genomic DNA suggested that these sequences were located on the W chromosome, although homologous sequences appeared to be autosomal or Z-linked. Fluorescent in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones corresponding to ZBM sequences showed hybridization to the whole W chromosome, suggesting that the BACs encode sequences that are repeated across the entire W chromosome. Based on the sequencing of a ZBM repetitive sequence and Z chromosome derived BAC clones, we demonstrate a random distribution of repeat sequences that are specific to the W chromosome or encoded by both Z and W. The positions of ZW-common repeat sequences mapped to a noncoding region of a Z chromosome BAC clone containing the CHD1Z gene. The apparent lineage-specificity of W chromosome repeat sequences in passerines and galliform birds suggest that the W chromosome had not differentiated well from the Z at the time of divergence of these lineages. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Changes in the behaviour of the male zebra finch during a 12-hr day

Isolated male zebra finches show a daily cycle of locomotion similar to that of other birds. During a 12-hr day (07.00 to 19.00 hours) approximately 75 per cent of movement between perches occurs between 08.00 and 14.00 hours. Trends are also apparent in other behaviours, as assessed by the number of 30-s time units in which they are recorded. Soft call notes, singing, drinking and taking of sand and cuttlefish bone all decline during the day. Sitting still and preening rise. Despite these changes the associations between acts are similar at different times of day. In general the behaviours previously found to be associated with locomotion during the morning decline with it during the day, whereas those not associated with it rise.     

Maternal effects due to male attractiveness affect offspring development in the zebra finch

Maternal effects occur when offspring phenotype is influenced by environmental factors experienced by the mother. Mothers are predicted to invest differentially in offspring in ways that will maximize offspring fitness depending on the environment she expects them to encounter. Here, we test for maternal effects in response to mate attractiveness on offspring developmental traits in the zebra finch Taeniopygia guttata. We controlled for parental genetic quality by manipulating male attractiveness using coloured leg rings and by randomly assigning mating pairs. The potential confounding effect of differential nestling care was controlled for by cross-fostering clutches and by allowing for variance due to foster father attractiveness in general linear models. We found a difference in egg mass investment between attractiveness groups and, importantly, we found that all of the offspring traits we measured varied with the attractiveness of the father. This provides strong evidence for maternal effects in response to mate attractiveness. Furthermore, due to the experiment design, we can conclude that these effects were mediated by differential investment of egg resources and not due to genetic differences or differences in nestling care.     

Development of the catecholaminergic innervation of the song system of the male zebra finch

Catecholamines (CA) have been proposed to have neuromodulatory actions, particularly on attention and learning, in a number of neural systems. Because several of the interconnected brain nuclei that mediate song learning and production in the adult male zebra finch (Taeniopygia guttata) contain these neurotransmitters, we investigated the appearance of the catecholaminergic innervation of the song nuclei of male zebra finches during posthatch development, specifically during the period in which song learning occurs. We studied the development of immunoreactivity for tyrosine hydroxylase (TH) in the song nuclei HVc, RA, NIf, LMAN, and Area X in young males aged 20, 35, and 60 days as well as in adults (>90 days). We also visualized catecholamines directly in Area X using CA histofluorescence. Both TH immunoreactivity and CA histofluorescence were initially low in Area X relative to their levels in the surrounding parolfactory lobe (LPO), and then increased during development to become more intense than in LPO by days 60–90. Similarly, TH immunoreactivity in HVc was initially low relative to that in the surrounding neostriatum, then increased during development to become more intense than that in the surround by day 60. TH immunostaining also increased markedly in NIf, RA, and LMAN over the same period. These results show that the levels of catecholamines and their major synthetic enzyme increase in song nuclei during development and thus raise the possibility that these transmitters contribute to the development of the song system or to song learning. © 1996 John Wiley & Sons, Inc.     

State-dependent incubation behaviour in the zebra finch

State dependence is thought to be an important factor in resource allocation decisions, particularly in those decisions relating to parental care. Incubation behaviour is a costly part of avian parental care, and therefore likely to depend on the parent's body condition. We manipulated the body condition of zebra finches, Taeniopygia guttata, during incubation by using prelaying diets of different protein content, and induced birds to lay a similar number of eggs. We tested the hypothesis that birds in better body condition would invest more in incubation than birds in poorer condition when incubating on the same diet. Females that had received a high-protein prelaying diet lost more body mass than those that had received a low-protein diet. They also increased the length of their incubation bouts between early and middle incubation, whereas females that had received a low-protein prelaying diet increased bout length only between middle and late incubation. There were no differences between males from the two diet groups, and males were responsible for a lesser proportion of incubation than females. These results indicate that incubation behaviour is state dependent in female zebra finches, and that birds of different body condition adopt different incubation strategies. We found no differences in incubation duration and hatching success between the two incubation strategies in captivity, but the potential risk of nest predation in the wild may differ. We suggest that only females in good condition can afford to adopt a strategy of increasing bout length early in incubation; females in poorer condition first have to recover their body condition after having produced a clutch. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour       

Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata

Zebra finches are a ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 h. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication.     

Meiotic Cas9 expression mediates gene conversion in the male and female mouse germline

Highly efficient gene conversion systems have the potential to facilitate the study of complex genetic traits using laboratory mice and, if implemented as a “gene drive,” to limit loss of biodiversity and disease transmission caused by wild rodent populations. We previously showed that such a system of gene conversion from heterozygous to homozygous after a sequence targeted CRISPR/Cas9 double-strand DNA break (DSB) is feasible in the female mouse germline. In the male germline, however, all DSBs were instead repaired by end joining (EJ) mechanisms to form an “insertion/deletion” (indel) mutation. These observations suggested that timing Cas9 expression to coincide with meiosis I is critical to favor conditions when homologous chromosomes are aligned and interchromosomal homology-directed repair (HDR) mechanisms predominate. Here, using a Cas9 knock-in allele at the Spo11 locus, we show that meiotic expression of Cas9 does indeed mediate gene conversion in the male as well as in the female germline. However, the low frequency of both HDR and indel mutation in both male and female germlines suggests that Cas9 may be expressed from the Spo11 locus at levels too low for efficient DSB formation. We suggest that more robust Cas9 expression initiated during early meiosis I may improve the efficiency of gene conversion and further increase the rate of “super-mendelian” inheritance from both male and female mice.

This study shows that while Cas9 expression during meiosis I promotes genotype conversion - the mechanism underlying CRISPR ’gene drive’ - in both male and female mice, timing and high levels of Cas9 protein are critical to achieve robust efficiency.     

Single-cell responses in the ectostriatum of the zebra finch

The responses of single cells to computer-generated spots, bars, gratings, and motion-in-depth stimuli were studied in the ectostriatum and the adjacent neostriatum of the zebra finch, Taeniopygia guttata. No differences in neuronal properties could be detected between ectostriatum and neostriatum. The receptive fields of ectostriatal neurons are large, often extending over the entire visual field of the contralateral eye, and have oddly defined borders. The centers of the receptive fields, located in the foveal region, generally yielded better responses than the periphery, and exhibited different subdivisions. Neurons responded selectively to moving bars, preferring those moving parallel to their longest axis. An SDO (sensitivity, direction, orientation) analysis of responses to sinusoidal gratings showed that all orientations were equally represented by ectostriatal neurons, while there was a slight preference for forward and upward movements. The neurons also showed preferences for gratings of a particular spatial frequency, and responded vigorously to stimuli moving towards the eye (looming). Our results indicate that the ectostriatum is involved in both detecting displacement of the surround and in stimulus identification. By comparison with results obtained in the extrastriate cortex of mammals, it is concluded that the homology of the ectostriatum with the extrastriate cortex of mammals, which was proposed on the basis of hodological findings, is supported by our study.Abbreviations Di index of directionality - HW HH half-width at half-height - PLLS posterolateral lateral suprasylvian cortex - PMLS posterior medial lateral suprasylvian area - PSTH poststimulus time histogram - SDO sensitivity, direction, orientation     

Towards quantification of vocal imitation in the zebra finch

The transition from an amorphous subsong into mature song requires a series of vocal changes. By tracing song elements during development, we have shown that the imitation trajectory to the target could not be predicted based on monotonic progression of vocal changes, indicating an internal component that imposes constraints on song development. Here we further examine the nature of constraints on song imitation in the zebra finch. We first present techniques for identifying and tracing distinctive vocal changes, and then we examine how sequences of vocal change are expressed and coordinated. Examples suggest two types of constraints on song imitation, based on the nature of the temporal context. Developmentally diachronic constraints are imposed by sequential dependencies between vocal changes as a function of developmental time, whereas developmentally synchronic constraints are given by the acoustic context of notes within the song. Finally, we show that the tendency of birds to copy certain sounds in the song model before others might be related to such constraints. We suggest that documenting the full range of distinctive vocal changes and the coordination of their expression would be useful for testing mechanisms of vocal imitation.     

The temporal pattern of feeding in the zebra finch

Feeding in zebra finches occurs in clearly defined bouts, but strong individual differences have been found in the finer details of its pattern. Some birds showed a constant probability of starting feeding with passage of time between meals and a constant probability of stopping during a meal. In these cases meal length (number of pecks at seed) tended to correlate with the length of the preceding gap. By contrast, in most individuals both meals and gaps tended to be of a typical length, and in some of these autocorrelation showed feeding to follow a cycle approximately 24 to 30 min long. Meal length in most of these birds correlated strongly with the length of the succeeding gap. The individual differences found are discussed and hypotheses put forward for their causation.     

Beak gape dynamics during song in the zebra finch

Bird song is a complex communication behavior that requires the coordination of several motor systems. Sound is produced in the syrinx and then modified by the upper vocal tract, but the specific nature and dynamics of this modification are not well understood. To determine the contribution of beak movements to sound modification, we studied the beak gape patterns in zebra finches (Taeniopygia guttata). Subsyringeal air sac pressure and song were recorded together with changes in beak gape, which were monitored with a magneto-sensitive transducer. Beak gape was positively correlated with fundamental frequency, peak frequency, and subsyringeal air sac pressure in all but one bird. For harmonic stacks, peak frequency increased with increasing beak gape, and the relationship between fundamental frequency and beak gape was no longer significant. Experimentally holding the beak open or closed had acoustic consequences consistent with the model in which beak movements change upper vocal tract length and, thus, the filter properties. Beak gape was positively correlated with sound amplitude in all but two birds. The relationship between beak aperture and amplitude may, however, be indirect because air sac pressure is correlated with amplitude and beak gape. The beak is opened quickly and to its widest aperture immediately prior to the onset of sound and at rapid transitions in sound, suggesting that beak movements may affect vibratory behavior of the labia.