Easy-to-use R functions to separate reduced-representation genomic datasets into sex-linked and autosomal loci, and conduct sex assignment

Identifying sex-linked markers in genomic datasets is important because their presence in supposedly neutral autosomal datasets can result in incorrect estimates of genetic diversity, population structure and parentage. However, detecting sex-linked loci can be challenging, and available scripts neglect some categories of sex-linked variation. Here, we present new R functions to (1) identify and separate sex-linked loci in ZW and XY sex determination systems and (2) infer the genetic sex of individuals based on these loci. We tested these functions on genomic data for two bird and one mammal species and compared the biological inferences made before and after removing sex-linked loci using our function. We found that our function identified autosomal loci with ≥98.8% accuracy and sex-linked loci with an average accuracy of 87.8%. We showed that standard filters, such as low read depth and call rate, failed to remove up to 54.7% of sex-linked loci. This led to (i) overestimation of population F_IS by up to 24%, and the number of private alleles by up to 8%; (ii) wrongly inferring significant sex differences in heterozygosity; (iii) obscuring genetic population structure and (iv) inferring ~11% fewer correct parentages. We discuss how failure to remove sex-linked markers can lead to incorrect biological inferences (e.g. sex-biased dispersal and cryptic population structure) and misleading management recommendations. For reduced-representation datasets with at least 15 known-sex individuals of each sex, our functions offer convenient resources to remove sex-linked loci and to sex the remaining individuals (freely available at https://github.com/drobledoruiz/conservation_genomics).

Genome of the Lord Howe Island stick insect reveals a highly conserved Phasmid X chromosome

We present a chromosome scale genome assembly for Dryococelus australis, a critically endangered Australian phasmid. The assembly, constructed with Pacific Biosciences continuous long reads and chromatin conformation capture (Omni-C) data, is 3.42 Gbp in length with a scaffold N50 of 262.27 Mbp and L50 of 5. Over 99% of the assembly is contained in 17 major scaffolds which corresponds to the species' karyotype. The assembly contains 96.3% of insect BUSCO genes in single copy. A custom repeat library identified 63.29% of the genome covered by repetitive elements; most were not identifiable based on similarity to sequences in existing databases. A total of 33,793 putative protein coding genes were annotated. Despite the high contiguity and single copy BUSCO content of the assembly, over 1 Gbp of the flow cytometry estimated genome size is not represented, likely due to the large and repetitive nature of the genome. We identified the X chromosome with a coverage based analysis and searched for homologs of genes known to be X linked across the genus Timema. We found 59% of these genes on the putative X chromosome, indicating strong conservation of X chromosomal content across 120 million years of phasmid evolution.

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Background

The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required.

Results

We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene.

Conclusions

The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater.

A Comprehensive Overview of Technologies for Species and Habitat Monitoring and Conservation

The range of technologies currently used in biodiversity conservation is staggering, with innovative uses often adopted from other disciplines and being trialed in the field. We provide the first comprehensive overview of the current (2020) landscape of conservation technology, encompassing technologies for monitoring wildlife and habitats, as well as for on-the-ground conservation management (e.g., fighting illegal activities). We cover both established technologies (routinely deployed in conservation, backed by substantial field experience and scientific literature) and novel technologies or technology applications (typically at trial stage, only recently used in conservation), providing examples of conservation applications for both types. We describe technologies that deploy sensors that are fixed or portable, attached to vehicles (terrestrial, aquatic, or airborne) or to animals (biologging), complemented with a section on wildlife tracking. The last two sections cover actuators and computing (including web platforms, algorithms, and artificial intelligence).

A novel framework for evaluating in situ breeding management strategies in endangered populations

Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.

Beak and feather disease virus (BFDV) prevalence, load and excretion in seven species of wild caught common Australian parrots

Pathogens pose a major risk to wild host populations, especially in the face of ongoing biodiversity declines. Beak and feather disease virus (BFDV) can affect most if not all members of one of the largest and most threatened bird orders world-wide, the Psittaciformes. Signs of disease can be severe and mortality rates high. Its broad host range makes it a risk to threatened species in particular, because infection can occur via spill-over from abundant hosts. Despite these risks, surveillance of BFDV in locally abundant wild host species has been lacking. We used qPCR and haemagglutination assays to investigate BFDV prevalence, load and shedding in seven abundant host species in the wild in south-east Australia: Crimson Rosellas (Platycercus elegans), Eastern Rosellas (Platycercus eximius), Galahs (Eolophus roseicapillus), Sulphur-crested Cockatoos (Cacatua galerita), Blue-winged Parrots (Neophema chrysostoma), Rainbow Lorikeets (Trichoglossus moluccanus) and Red-rumped Parrots (Psephotus haematonotus). We found BFDV infection in clinically normal birds in six of the seven species sampled. We focused our analysis on the four most commonly caught species, namely Crimson Rosellas (BFDV prevalence in blood samples: 41.8%), Sulphur-crested Cockatoos (20.0%), Blue-winged Parrots (11.8%) and Galahs (8.8%). Species, but not sex, was a significant predictor for BFDV prevalence and load. 56.1% of BFDV positive individuals were excreting BFDV antigen into their feathers, indicative of active viral replication with shedding. Being BFDV positive in blood samples predicted shedding in Crimson Rosellas. Our study confirms that BFDV is endemic in our study region, and can inform targeted disease management by providing comparative data on interspecies variation in virus prevalence, load and shedding.

Warmer temperature and provision of natural substrate enable earlier metamorphosis in the critically endangered Baw Baw frog

Temperature and food availability are known to independently trigger phenotypic change in ectotherms, but the interactive effects between these factors have rarely been considered. This study investigates the independent and interactive effects of water temperature and food availability on larval growth and development of the critically endangered Baw Baw frog, Philoria frosti. Larvae were reared at low (12°C) or high (17°C) water temperature in the absence or presence of substrate that controlled food availability, and body size and time to metamorphosis were quantified. Growth and development of larvae was influenced by the individual effects of temperature and food availability; time to metamorphosis was shorter in warm water treatment groups and in the presence of substrate and increased food. Unexpectedly, however, water temperature and food availability did not have an interactive effect on either time to metamorphose or body size at metamorphosis. Under all treatment groups, metamorphic onset occurred once a developmental size threshold was reached, indicating that growth rate and body size are key factors controlling the metamorphic process in Baw Baw frogs (consistent with the Wilbur-Collins model for ectotherm development). From an applied perspective, our findings have implications for amphibian conservation because they indicate that simple manipulations of temperature and food availability can be used to increase the rate of frog production in conservation breeding programs.

A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes

Indirect transmission of pathogens can pose major risks to wildlife, yet the presence and persistence of wildlife pathogens in the environment has been little studied. Beak and feather disease virus (BFDV) is of global conservation concern: it can infect all members of the Psittaciformes, one of the most threatened bird orders, with infection often being lethal. Indirect transmission of BFDV through contaminated nest hollows has been proposed as a major infection source. However, data on whether and for how long nest sites in the wild remain contaminated have been absent. We determined the BFDV status of birds (parents and nestlings) for 82 nests of Crimson Rosellas, Platycercus elegans and Eastern Rosellas, Platycercus eximius. In 11 of these nests (13.4%, 95% confidence interval 6.9-22.7), we found an infected parent or nestling. Using nest swabs, we then compared BFDV presence at three points in time (before, during and after breeding) in three groups of nest boxes. These were nest boxes occupied by infected birds, and two control groups (nest boxes occupied by uninfected birds, and unoccupied nest boxes). Detection of BFDV on nest swabs was strongly associated with the infection status of parents in each nest box and with the timing of breeding. During breeding, boxes occupied by BFDV-positive birds were significantly more likely to have BFDV-positive nest swabs than boxes occupied by BFDV-negative birds; nest swabs tested BFDV-positive in 80% (28.4-99.5) of nests with parental antigen excretion, 66.7% (9.4-99.2) of nests occupied by parents with BFDV-positive cloacal swabs and 66.7% (22.3-95.7) of nests occupied by parents with BFDV-positive blood. 0% (0-52.2) of nests with BFDV-positive nestlings had BFDV-positive nest swabs. Across all boxes occupied by BFDV-positive birds (parents or nestlings), no nest swabs were BFDV-positive before breeding, 36.4% (95% CI 10.9-69.2) were positive during breeding and 9.1% (0.2-41.3) remained positive after breeding. BFDV was present on nest swabs for up to 3.7 months. Our study provides novel insights into the potential role of nest cavities and other fomites in indirect transmission of BFDV, and possibly other pathogens, and offers a non-invasive method for surveillance of pathogens in wild bird populations.

Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies

Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (N(e) < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.

Assortative mating among animals of captive and wild origin following experimental conservation releases

Captive breeding is a high profile management tool used for conserving threatened species. However, the inevitable consequence of generations in captivity is broad scale and often-rapid phenotypic divergence between captive and wild individuals, through environmental differences and genetic processes. Although poorly understood, mate choice preference is one of the changes that may occur in captivity that could have important implications for the reintroduction success of captive-bred animals. We bred wild-caught house mice for three generations to examine mating patterns and reproductive outcomes when these animals were simultaneously released into multiple outdoor enclosures with wild conspecifics. At release, there were significant differences in phenotypic (e.g. body mass) and genetic measures (e.g. Gst and F) between captive-bred and wild adult mice. Furthermore, 83% of offspring produced post-release were of same source parentage, inferring pronounced assortative mating. Our findings suggest that captive breeding may affect mating preferences, with potentially adverse implications for the success of threatened species reintroduction programmes.

Impacts of visitor number on Kangaroos housed in free-range exhibits

Free range exhibits are becoming increasingly popular in zoos as a means to enhance interaction between visitors and animals. However very little research exists on the impacts of visitors on animal behaviour and stress in free range exhibits. We investigated the effects of visitor number on the behaviour and stress physiology of Kangaroo Island (KI) Kangaroos, Macropus fuliginosus fuliginosus, and Red Kangaroos, Macropus rufus, housed in two free range exhibits in Australian zoos. Behavioural observations were conducted on individual kangaroos at each site using instantaneous scan sampling to record activity (e.g., vigilance, foraging, resting) and distance from the visitor pathway. Individually identifiable faecal samples were collected at the end of each study day and analysed for faecal glucocorticoid metabolite (FGM) concentration. When visitor number increased, both KI Kangaroos and Red Kangaroos increased the time spent engaged in visitor-directed vigilance and KI Kangaroos also increased the time spent engaged in locomotion and decreased the time spent resting. There was no effect of visitor number on the distance kangaroos positioned themselves from the visitor pathway or FGM concentration in either species. While there are limitations in interpreting these results in terms of fear of visitors, there was no evidence of adverse effects animal welfare in these study groups based on avoidance behaviour or stress physiology under the range of visitor numbers that we studied.

Evaluating physiological stress in Sumatran tigers (Panthera tigris ssp. sumatrae) managed in Australian zoos

Glucocorticoid quantification using non-invasive methods provides a powerful tool for assessing the health and welfare of wildlife in zoo-based programmes. In this study, we provide baseline data on faecal-based glucocorticoid (cortisol) monitoring of Sumatran tigers (Panthera tigris ssp. sumatrae) managed at the Melbourne Zoo in Victoria, Australia. We sampled five tigers daily for 60 days. Faecal cortisol metabolites (FCMs) in tiger faecal extracts were quantified using enzyme immunoassays that were successfully validated using parallelism and accuracy recovery checks. Two female tigers had significantly higher mean FCM levels than the two males and another female, suggesting that females may have higher FCM levels. A significant elevation was noted in the FCM levels for one female 2 days after she was darted and anaesthetized; however, the FCM levels returned to baseline levels within 3 days after the event. Comparative analysis of FCM levels of tigers sampled at Melbourne Zoo with tigers sampled earlier at two other Australian Zoos (Dreamworld Themepark and Australia Zoo) showed that FCM levels varied between zoos. Differences in the enclosure characteristics, timing of sampling, size and composition of groupings and training procedures could all contribute to this variation. Overall, we recommend the use of non-invasive sampling for the assessment of adrenocortical activity of felids managed in zoos in Australia and internationally in order to improve the welfare of these charismatic big cats.

Covariance of paternity and sex with laying order explains male bias in extra-pair offspring in a wild bird population

It has been hypothesized that parents increase their fitness by biasing the sex ratio of extra-pair offspring (EPO) towards males. Here, we report a male bias among EPO in a wild population of blue tits (Cyanistes caeruleus). This resulted from a decline in both the proportion of males and EPO over the laying order of eggs in the clutch. However, previous studies suggest that, unlike the decline in EPO with laying order, the relationship between offspring sex ratio and laying order is not consistent between years and populations in this species. Hence, we caution against treating the decline in proportion of males with laying order, and the resulting male bias among EPO, as support for the above hypothesis. Variable patterns of offspring sex and paternity over the laying order may explain inconsistent associations between offspring sex and paternity, between and within species.

Declining extra-pair paternity with laying order associated with initial incubation behavior, but independent of final clutch size in the blue tit

Although functional explanations for female engagement in extra-pair copulation have been studied extensively in birds, little is known about how extra-pair paternity is linked to other fundamental aspects of avian reproduction. However, recent studies indicate that the occurrence of extra-pair offspring may generally decline with laying order, possibly because stimulation by eggs induces incubation, which may suppress female motivation to acquire extra-pair paternity. Here we tested whether experimental inhibition of incubation during the laying phase, induced by the temporary removal of eggs, resulted in increased extra-pair paternity, in concert with a later cessation of laying, in blue tits (Cyanistes caeruleus). As expected, experimental females showed a more gradual increase in nocturnal incubation duration over the laying phase and produced larger clutches than controls. Moreover, incubation duration on the night after the first egg was laid predicted how extra-pair paternity declined with laying order, with less incubation being associated with more extra-pair offspring among the earliest eggs in the clutch. However, incubation duration on this first night was unrelated to our experimental treatment and independent of final clutch size. Consequently, the observed decline in extra-pair paternity with laying order was unaffected by our manipulation and larger clutches included proportionally fewer extra-pair offspring. We suggest that female physiological state prior to laying, associated with incubation at the onset of laying, determines motivation to acquire extra-pair paternity independent of final clutch size. This decline in proportion of extra-pair offspring with clutch size may be a general pattern within bird species.

Characterization of MHC-I in the blue tit (Cyanistes caeruleus) reveals low levels of genetic diversity and trans-population evolution across European populations

The major histcompatibility complex (MHC) is a vital component of the adaptive immune system in all vertebrates. This study is the first to characterize MHC class I (MHC-I) in blue tits (Cyanistes caeruleus), and we use MHC-I exon 3 sequence data from individuals originating from three locations across Europe: Spain, the Netherlands to Sweden. Our phylogeny of the 17 blue tit MHC-I alleles contains one allele cluster with low nucleotide diversity compared to the remaining more diverse alleles. We found a significant evidence for balancing selection in the peptide-binding region in the diverse allele group only. No separation according to geographic location was found in the phylogeny of alleles. Although the number of MHC-I loci of the blue tit is comparable to that of other passerine species, the nucleotide diversity of MHC-I appears to be much lower than that of other passerine species, including the closely related great tit (Parus major) and the severely inbred Seychelles warbler (Acrocephalus sechellensis). We believe that this initial MHC-I characterization in blue tits provides an important step towards understanding the mechanisms shaping MHC-I diversity in natural populations.

Factors affecting germline mutations in a hypervariable microsatellite: a comparative analysis of six species of swallows (Aves: Hirundinidae)

Microsatellites mutate frequently by replication slippage. Empirical evidence shows that the probability of such slippage mutations may increase with the length of the repeat region as well as exposure to environmental mutagens, but the mutation rate can also differ between the male and female germline. It has been hypothesized that more intense sexual selection or sperm competition can also lead to elevated mutation rates, but the empirical evidence is inconclusive. Here, we analyzed the occurrence of germline slippage mutations in the hypervariable pentanucleotide microsatellite locus HrU10 across six species of swallow (Aves: Hirundinidae). These species exhibit marked differences in the length range of the microsatellite, as well as differences in the intensity of sperm competition. We found a strong effect of microsatellite length on the probability of mutation, but no residual effect of species or their level of sperm competition when the length effect was accounted for. Neither could we detect any difference in mutation rate between tree swallows (Tachycineta bicolor) breeding in Hamilton Harbour, Ontario, an industrial site with previous documentation of elevated mutation rates for minisatellite DNA, and a rural reference population. However, our cross-species analysis revealed two significant patterns of sex differences in HrU10 germline mutations: (1) mutations in longer alleles occurred typically in the male germline, those in shorter alleles in the female germline, and (2) male germline mutations were more often expansions than contractions, whereas no directional bias was evident in the female germline. These results indicate some fundamental differences in male and female gametogenesis affecting the probability of slippage mutations. Our study also reflects the value of a comparative, multi-species approach for locus-specific mutation analyses, through which a wider range of influential factors can be assessed than in single-species studies.

Polygyny and extra-pair paternity enhance the opportunity for sexual selection in blue tits

Polygyny and extra-pair paternity are generally thought to enhance sexual selection. However, the extent to which these phenomena increase variance in male reproductive success will depend on the covariance between success at these two strategies. We analysed these patterns over four breeding seasons in facultatively polygynous blue tits Cyanistes caeruleus. We found that both polygyny and extra-pair paternity increased variance in male reproductive success and that standardised variance in annual number of genetic fledglings was 2.6 times higher than standardised variance in apparent success when assuming strict monogamy. Nevertheless, male success at securing within-pair paternity was unrelated to success at gaining extra-pair paternity and, when considering the positive effect of age on extra-pair success and attracting a second female, polygynous males were no more likely to sire extra-pair fledglings. Overall, polygynous males fledged more genetic offspring than monogamous males, but first-year polygynous males lost a greater share of within-pair paternity. A literature review suggests that this adverse effect of polygyny on within-pair paternity is frequent among birds, inconsistent with the prediction that females engage in extra-pair copulation with successful males to obtain good genes. Furthermore, a male's share of paternity was repeatable between years, and among females of polygynous males within years, such that a compatibility function of extra-pair copulations was likewise unsupported. Instead, we suggest that the observed patterns are most consistent with a fertility insurance role for extra-pair copulations, which does not exclude the greater opportunity for sexual selection through differential ability of males to gain paternity.

Androgens during development in a bird species with extremely sexually dimorphic growth, the brown songlark, Cinclorhamphus cruralis

In birds, early exposure to androgens has been shown to influence offspring growth and begging behaviour, and has been proposed as a mechanism for the development of sexual size dimorphism (SSD). Sex specific effects during development can occur due to sex-specific allocation of maternal androgens, sensitivity to, or synthesis of, androgens. In addition, maternal hormones have been suggested as a mechanism to skew brood sex ratio. This study uses one of the world's most extreme SSD species, the brown songlark Cinclorhamphus cruralis, to investigate (1) sex-specific differences of androgens in yolk and chick plasma and (2) the relationship between androgens and sex ratio bias. The study reveals no indication of sex-specific maternal allocation, but a modest sex effect during the later stages of incubation when the embryo starts to produce its own androgens. Moreover, there was a strong seasonal sex ratio bias: female-biased early and male-biased later in the season, but yolk testosterone (T) did not show a seasonal trend. Taken together these results suggest that if androgens, from any source, have a significant role in development of SSD in this species it is most likely via sex-specific sensitivity or synthesis rather than differential maternal transfer to the egg.

Nutritional bias as a new mode of adjusting sex allocation

Sex biases in the allocation of resources to offspring occur in a broad range of taxa. Parents have been shown to achieve such biases either by producing numerically more of one sex or by providing the individuals of one sex with a greater quantity of resources. In addition, skews in allocation could occur if the offspring of one sex receive resources of higher quality (greater nutritional or energetic value by weight or volume), although this mode of adjustment has, to our knowledge, never been demonstrated. We compared the types of prey and the metabolizable energy provisioned to male and female nestlings in one of the most sexually size dimorphic of all birds, the brown songlark, Cinclorhamphus cruralis. Within broods, we found that males not only received more prey than their smaller sisters, but also prey of apparently higher quality. This dietary disparity could result either from mothers actively discriminating between the sexes when providing prey or from competition among siblings. We suggest that sex differences in offspring diet quality may occur in a wide range of other taxa and function as an additional mechanism of sex allocation adjustment.

Breeding behaviour and ecology of the sexually size-dimorphic brown songlark, Cinclorhamphus cruralis

The Australian endemic brown songlark, Cinclorhamphus cruralis, is one of the most sexually size-dimorphic of all birds, and yet its breeding ecology remains poorly documented. Here we redress this situation by describing the breeding activities of brown songlarks over three years (1998–2000) in the semi-arid grasslands of south-western New South Wales. Study populations of this nomadic species were selected in late August of each year on the basis of high adult abundance. Adult males at these sites were, on average, 2.3 times heavier than females. Over the three seasons, nesting activities started in early to late August and continued until early November or December. Males were highly polygynous and, on average, occupied territories of about 4.0 ha. Nests were well concealed at the base of small shrubs and grass tussocks or in thick herbage. Clutches ranged in size from 2 to 5 eggs (mean 3.2) and were incubated exclusively by the female for 11–13 days (mean 12.1). Nestlings received a range of invertebrate prey, mainly from the female, for 10–14 days (mean 11.5) before leaving the nest. Only 17% of nesting attempts were estimated to be successful, and each of these nests produced an average of 2.7 fledglings. Predators, including foxes, Vulpes vulpes, and brown snakes, Pseudonaja textilis, were the main cause of nest failure. Some females produced replacement clutches following nest failure, while others laid second clutches after the success of an earlier brood. We speculate that extreme size dimorphism has evolved in this species because (i) males compete physically for breeding territories, and (ii) habitat heterogeneity and excellent visibility of their surroundings allow some males to defend territories of sufficient size to support nesting by multiple females.

Pre-ovulation control of hatchling sex ratio in the Seychelles warbler

Females of some bird species have a high degree of control over the sex ratio of their offspring at laying. Although several mechanisms have been put forward to explain how females might control the sex of their eggs, virtually nothing is known. As females are the heterogametic sex in birds, adjustment of the clutch sex ratio could arise either by pre- or post-ovulation control mechanisms. The Seychelles warbler (Acrocephalus sechellensis) exhibits extreme adaptive egg sex ratio bias. Typically, warblers produce only single-egg clutches, but by translocating pairs to vacant habitat of very high quality, most females were induced to produce two-egg clutches. Overall, females skewed clutch sex ratios strongly towards daughters (86.6%). This bias was evident in the first egg, but critically, also in the second eggs laid a day apart, even when all absent, unhatched, or unsexed second eggs were assumed to be male. Although a bias in the first egg may arise through either pre- or post-ovulation mechanisms, the skew observed in second eggs could only arise through pre-ovulation control. Post-ovulation adjustment may also contribute to skewed hatchling sex ratios, but as sex-biased release of gametes is likely to be a more efficient process of control, pre-ovulation mechanisms may be the sole means of adjustment in this species. High fitness differentials between sons and daughters, as apparent in the Seychelles warblers, may be necessary for primary sex ratio adjustment to evolve.

Breeding ecology of the fairy martin

The breeding biology of the fairy martin, Hirundo ariel, was studied over three years (1992–95) in the Yarra Valley, Victoria. Adult males and females in this population were morphologically similar, though only females acquired a brood patch during the breeding season. Colonies ranged in size from 8 to 29 nests. Birds arrived in the study area in September and usually commenced laying in October, though nesting activities were generally asynchronous both between and within colonies. Most colonies contained active nests until February. At least 16% of adults and 5% of fledglings, on average, returned to the study area in the following year. Returning adults generally nested at the same colony site as the previous year, while most first-year birds nested at sites other than their natal colony. Adult males were more likely to return than adult females. Clutch size ranged from 2 to 5, with a mean of 3.5, and declined over the season. The incubation period varied from 12 to 18 days with a mean of 13.7. A mean of 1.8 chicks fledged per completed clutch, while 60% of clutches produced at least one chick. The period from hatching to fledging varied from 17 to 32 days, with a mean of 22.1, and increased with brood size. Fledging success was highest during the middle of the breeding season. Adverse weather conditions, resulting in the abandonment of clutch and brood, were the most common cause of nest failure, and on several occasions also resulted in adult mortality. Almost half the breeding females produced at least two clutches in the one season. Pairs produced from 0 to 8 fledglings per season, with those that commenced nesting earlier in the season having higher annual productivity. These results are discussed in relation to the breeding ecology of other members of the Hirundinidae.