Finch Species Research Articles

The Complete Genome Sequences of 23 Finch Species (Fringillidae, Passeriformes).

We present complete genome sequences of 23 species of finches from 6 genera.

Bird species richness and diversity responses to land use change in the Lake Victoria Basin, Kenya

The increasing demand for cultivated lands driven by human population growth, escalating consumption and activities, combined with the vast area of uncultivated land, highlight the pressing need to better understand the biodiversity conservation implications of land use change in Sub-Saharan Africa. Land use change alters natural wildlife habitats with fundamental consequences for biodiversity. Consequently, species richness and diversity typically decline as land use changes from natural to disturbed. We assess how richness and diversity of avian species, grouped into feeding guilds, responded to land use changes, primarily expansion of settlements and cultivation at three sites in the Lake Victoria Basin in western Kenya, following tsetse control interventions. Each site consisted of a matched pair of spatially adjacent natural/semi-natural and settled/cultivated landscapes. Significant changes occurred in bird species richness and diversity in the disturbed relative to the natural landscape. Disturbed areas had fewer guilds and all guilds in disturbed areas also occurred in natural areas. Guilds had significantly more species in natural than in disturbed areas. The insectivore/granivore and insectivore/wax feeder guilds occurred only in natural areas. Whilst species diversity was far lower, a few species of estrildid finches were more common in the disturbed landscapes and were often observed on the scrubby edges of modified habitats. In contrast, the natural and less disturbed wooded areas had relatively fewer estrildid species and were completely devoid of several other species. In aggregate, land use changes significantly reduced bird species richness and diversity on the disturbed landscapes regardless of their breeding range size or foraging style (migratory or non-migratory) and posed greater risks to non-migratory species. Accordingly, land use planning should integrate conservation principles that preserve salient habitat qualities required by different bird species, such as adequate patch size and habitat connectivity, conserve viable bird populations and restore degraded habitats to alleviate adverse impacts of land use change on avian species richness and diversity.

From microcosm to macrocosm: adaptive radiation of Darwin’s finches

Abstract In this Perspective we show the value of studying living organisms in the field to understand their history. Darwin’s finches are an iconic example of the early stages of speciation in a young adaptive radiation that produced 18 species in little more than a million years. The question they pose is how and why so many species originated and diversified rapidly. A long-term study of four species of finches on the small island of Daphne Major, combined with genomic investigations, provide some answers in terms of extrinsic and intrinsic factors. Beak size and shape, as well as body size, are key heritable features involved in both ecological and reproductive isolation, and their evolution by natural selection was caused by competitor species during prolonged droughts. Introgressive hybridization of related species is rare but recurring, apparently widespread, increases genetic variation, and does not incur a fitness cost. Hybridization can produce a new species. We use a phylogeny based on whole genome sequences of the four finches to infer morphological transitions in their radiation. Several lines of evidence indicate that some species are missing from the early phase of the radiation due to extinction. Combining these results, we re-cast the classical allopatry-then-sympatry theory of adaptive radiation as a competition-selection-hybridization process that generates a diversity of species.

Pre-existing visual preference for white dot patterns in estrildid finches: a comparative study of a multi-species experiment.

The diverse characteristics of animal signal designs can be explained by the sensory bias hypothesis, which suggests that natural selection shapes sensory bias and preferences associated with signal design. Traditionally, this hypothesis has focused on female sensory biases and male sexual traits. However, considering shared sensory systems between males and females in non-sexual contexts, existing sensory bias possibly contributes to the evolution of shared social and sexual traits. Our previous studies on the family Estrildidae supported this idea. An evolutionary relationship probably existed between diet and white dot plumage, and a species of estrildid finches showed a visual preference for white dot patterns. To investigate this further, we examined hunger-related visual preferences using phylogenetic comparative methods and behavioural experiments. Specifically, we compared the gazing responses of 12 species of estrildids to monochromatic printed white dot and stripe patterns, considering their phylogenetic relationships. The results support our idea that the common estrildid ancestor had a hunger-related visual preference for white dot patterns. Subject species generally preferred white dots to stripes. Furthermore, males and females showed a similar preference towards dots. Our findings provide insights into the role of sensory bias in the evolution of mutual ornamentation.

Evolutionary divergence of body size and wing and leg structure in relation to foraging mode in Darwin’s Galapagos finches

Abstract The wings, legs, and tail in Darwin’s finches show many clear adaptations to different types of locomotion used during foraging. We use size scaling to analyse how various characters vary with body mass to clarify dimensional relationships. The selective advantage of a character is judged in terms of energy savings. The wing aspect ratio (4.6–4.9) is very low, so the energy costs for flight are high. Low body mass, low wing loading, and short arm wings in the warbler finch, small tree finch, and small ground finch promote agility and manoeuvrability among vegetation, along with short wings in the warbler finch. Evolution towards a shorter arm wing seems to be favoured in the smaller finch species. Long legs, long toes, and long curved claws are adaptations for climbing/clinging locomotion without tail support (woodpecker finch, small and large tree finches, cactus finch but having short legs). Selection for longer legs seems to act towards a lengthening of the tarsometatarsus. The climbing technique in the woodpecker finch is described. We discuss how the diversification in the beaks relates to the locomotion organs.

Song system neuroanatomy, and immediate early gene expression in a finch species with extensive male and female song.

Birdsong is a relatively well-studied behavior, both due to its importance as a model for vocal production learning and as an intriguing complex social behavior. Until the last few decades, work on birdsong focused almost exclusively on males. However, it is now widely accepted that female song not only exists, but is fairly common throughout the oscine passerines. Despite this, and the large number of researchers who have begun exploring female song in the field, researchers in the lab have been slow to adopt model species with female song. Studying female song in the lab is critical for our understanding of sex-specific factors in the physiology controlling this fascinating behavior. Additionally, as a model for vocal production learning in humans, understanding the mechanistic and neuroendocrine control of female song is clearly important. In this study, we examined the red-cheeked cordon bleu (RCCB), an Estrildid finch species with extensive female song. Specifically, we found that there were no significant sex differences in circulating levels of testosterone and progesterone, nor in song production rate. There were no significant differences in cell densities in the three nuclei of the song control system we examined. Additionally, the volume of the robust nucleus of the arcopallium was not significantly different and we report the smallest sex difference in HVC yet published in a songbird. Finally, we demonstrated similar levels of motor driven immediate early gene expression in both males and females after song production.

Front Cover: The Wild‐Type tRNA Adenosine Deaminase Enzyme TadA Is Capable of Sequence‐Specific DNA Base Editing (ChemBioChem 16/2023)

The directed evolution of the adenosine deaminase enzyme TadA from an RNA-editing enzyme to an efficient DNA-editing enzyme was crucial for the development of the adenine base editor (ABE). Previous experiments showed no detectable DNA-editing activity by an ABE utilizing wild-type TadA (ABE0.1), but here we show ABE0.1 is able to edit DNA strictly within TACG motifs. This sequence requirement is partially governed by the C-terminal α5 helix of TadA, which accumulated many mutations during the directed evolution of TadA. The evolution of TadA to better access adenines within a diverse range of sequences is reflective of the Galapagos finches, which evolved different beak shapes in order to better access the food that was available to them. This cover art shows the protein structures of ecTadA (PDB: 1Z3A) and the evolved TadA8e (PDB: 6VCA), along with two species of Galapagos finches using the different α5 helix structures to access a target adenine within different sequence contexts. More information can be found in the Research Article by A. C. Komor et al.

Olfactory sex preferences in six Estrildid Finch species

Avian courtship behaviour is essential to attract potential mating partners. Courtship behaviours can involve displays of different sensory modes. Sex discrimination is a crucial step and in many bird species, sexes differ in acoustic and visual traits, allowing sex discrimination. It has been shown only recently that in some species of Estrildid Finches, chemical cues are involved in social communication. Here, we investigated whether olfaction also plays a role in sex discrimination in Estrildid Finches. Investigating olfactory sex preferences as an indicator behaviour in six different Estrildid Finch species, we aimed to understand whether sex- and/or species-specific differences in olfactory preferences exists and whether olfactory sex preferences correspond to species-specific differences in sex-specific acoustic and visual displays, e.g., singing, plumage dimorphisms and courtship dance. Olfactory sex preferences were tested in a Y-Maze test. We found differences in scent preferences among the different species of Estrildid Finches. We discussed the behavioural pattern with respect to other species-specific traits. And their potential implications in a broader mate choice context.

Poleward shifts and altered periodicity in boreal bird irruptions over six decades.

Range boundaries are long-term biogeographic features of species distributions and abundance. However, many species demonstrate dynamic range boundaries, reflecting strong seasonal and annual variability in migratory behaviour. As a form of facultative migration, irruptions involve the movement of many individuals outside of their resident range in response to climate variability, resource availability, and demographic processes. Many species have experienced range shifts and altered phenology in response to modern climate change, but spatiotemporal changes in irruption dynamics are less well known. We quantified changes in the geography and periodicity of boreal bird irruptions across eastern North America from 1960 to 2021. Using data from Audubon's Christmas Bird Count for nine finch species, including several exhibiting recent population declines, we evaluated latitudinal trends in southern range and irruption boundaries and characterized irruption periodicity using spectral wavelet analysis. Six boreal birds exhibited significant northward shifts in their southern range boundaries and three species displayed shifts in their southern irruption boundaries. Irruption periodicity across multiple species was consistent across the 1960s and 1970s, culminating in frequent and synchronized irruptions of multiple species (superflights) during earlier decades. Coherence between species dampened beginning in the early 1980s as superflight periodicity became increasingly unstructured, finally reforming in recent decades, after 2000. Boreal birds are considered important sentinels of the boreal forests, and northward shifts and altered periodicity of irruptions may indicate broad-scale changes in climate- and resource-associated drivers operating across the boreal forests.

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Endogenous retroviruses (ERVs) are inherited remnants of retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. Here, we utilize the strength of Darwin’s finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin’s finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We find shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin’s finches’ radiation. Unexpected ERV variation in finch species on different islands suggests historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, and across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin’s finches.

Intrinsically disordered BMP4 morphogen and the beak of the finch: Co-option of an ancient axial patterning system

Darwin's finches, with the primary diversity in the shape and size of their beaks, represent an excellent model system to study speciation and adaptive evolution. It is generally held that evolution depends on the natural selection of heritable phenotypic variations originating from the genetic mutations. However, it is now increasingly evident that epigenetic transgenerational inheritance of phenotypic variation can also guide evolutionary change. Several studies have shown that the bone morphogenetic protein BMP4 is a major driver of beak morphology. A recent study explored variability of the morphological, genetic, and epigenetic differences in the adjacent “urban” and “rural” populations of two species of Darwin's finches on the Galápagos Islands and revealed significant changes in methylation patterns in several genes including those involved in the BMP/TGFß pathway in the sperm DNA compared to erythrocyte DNA. These observations indicated that epigenetic changes caused by environmental fluctuations can be passed on to the offspring. Nonetheless, the mechanism by which dysregulated expression of BMP4 impacts beak morphology remains poorly understood. Here, we show that BMP4 is an intrinsically disordered protein and present a causal a link between epigenetic changes, BMP4 dysregulation and the evolution of the beak of the finch by natural selection.

Sympatric finches increase trophic and spatiotemporal partitioning to enable coexistence through periods of low resource availability

Abstract Ecological niche theory dictates that sympatric species cannot occupy the same ecological niche at the same time. Sympatric granivorous finch species in tropical savannas appear to contradict this theory by moving in mixed‐species flocks and feeding together upon the same resources. Here, we explored this contradiction by tracking individuals from three finch species (Gouldian—Chloebia gouldiae, long‐tailed—Poephila acuticauda and masked finch—P. personata) often seen feeding together, while simultaneously determining the dietary composition during periods of high and low resource abundance. Dietary composition was characterised using stable isotope ratios of δ13C and δ15N within the blood, and foraging areas were determined from continuous detection using passive VHF radio telemetry. Individuals were sampled early in the dry season when grass seeds were abundant, in the middle of the dry season and at the end when seeds were very scarce. The results showed plasticity in ecological niche overlap among the three finch species depending on grass seed availability within the landscape. In the early dry season, the species foraged together on the abundant grass seed. As the dry season progressed and grass seed availability declined, masked and long‐tailed finches exhibited greater spatial partitioning, masked and Gouldian finches increased dietary partitioning, and long‐tailed and Gouldian finches increased both dietary and spatial partitioning. Our study showed that sympatric granivorous finches utilise trophic and spatiotemporal partitioning to enable coexistence through periods of low resource availability in tropical savannas. Gouldian finches increased activity and ranging behaviour, while long‐tailed and masked finches diversified their diet. Read the free Plain Language Summary for this article on the Journal blog.

Germline-restricted chromosome shows remarkable variation in size among closely related passerine species.

Passerine birds have a supernumerary chromosome in their germ cells called the germline-restricted chromosome (GRC). The GRC was first discovered more than two decades ago in zebra finch but recent studies have suggested that it is likely present in all passerines, the most species rich avian order, encompassing more than half of all modern bird species. Despite its wide taxonomic distribution, studies on this chromosome are still scarce and limited to a few species. Here, we cytogenetically analyzed the GRC in five closely related estrildid finch species of the genus Lonchura. We show that the GRC varies enormously in size, ranging from a tiny micro-chromosome to one of the largest macro-chromosomes in the cell, not only among recently diverged species but also within species andsometimes even between germ cells of a single individual. In Lonchura atricapilla, we also observed variation in GRC copy number among male germ cells of a single individual. Finally, our analysis of hybrids between two Lonchura species with noticeably different GRC size directly supported maternal inheritance of the GRC. Our results reveal the extraordinarily dynamic nature of the GRC, which might be caused by frequent gains and losses of sequences on this chromosome leading to substantial differences in genetic composition of the GRC between and even within species. Such differences might theoretically contribute to reproductive isolation between species and thus accelerate the speciation rate of passerine birds compared to other bird lineages.

Automated annotation of birdsong with a neural network that segments spectrograms

Songbirds provide a powerful model system for studying sensory-motor learning. However, many analyses of birdsong require time-consuming, manual annotation of its elements, called syllables. Automated methods for annotation have been proposed, but these methods assume that audio can be cleanly segmented into syllables, or they require carefully tuning multiple statistical models. Here, we present TweetyNet: a single neural network model that learns how to segment spectrograms of birdsong into annotated syllables. We show that TweetyNet mitigates limitations of methods that rely on segmented audio. We also show that TweetyNet performs well across multiple individuals from two species of songbirds, Bengalese finches and canaries. Lastly, we demonstrate that using TweetyNet we can accurately annotate very large datasets containing multiple days of song, and that these predicted annotations replicate key findings from behavioral studies. In addition, we provide open-source software to assist other researchers, and a large dataset of annotated canary song that can serve as a benchmark. We conclude that TweetyNet makes it possible to address a wide range of new questions about birdsong.

Female in-nest attendance predicts the number of ectoparasites in Darwin's finch species.

Selection should act on parental care and favour parental investment decisions that optimize the number of offspring produced. Such predictions have been robustly tested in predation risk contexts, but less is known about alternative functions of parental care under conditions of parasitism. The avian vampire fly (Philornis downsi) is a myasis-causing ectoparasite accidentally introduced to the Galápagos Islands, and one of the major mortality causes in Darwin's finch nests. With an 11-year dataset spanning 21 years, we examine the relationship between parental care behaviours and number of fly larvae and pupae in Darwin's finch nests. We do so across three host species (Camarhynchus parvulus, C. pauper, Geospiza fuliginosa) and one hybrid Camarhynchus group. Nests with longer female brooding duration (minutes per hour spent sitting on hatchlings to provide warmth) had fewer parasites, and this effect depended on male food delivery to chicks. Neither male age nor number of nest provisioning visits were directly associated with number of parasites. While the causal mechanisms remain unknown, we provide the first empirical study showing that female brooding duration is negatively related to the number of ectoparasites in nests. We predict selection for coordinated host male and female behaviour to reduce gaps in nest attendance, especially under conditions of novel and introduced ectoparasites.

Germline-Restricted Chromosome (GRC) in Female and Male Meiosis of the Great Tit (Parus major, Linnaeus, 1758).

All songbirds studied so far have a germline-restricted chromosome (GRC), which is present in the germ cells and absent in the somatic cells. It shows a wide variation in size, morphology, and genetic content between the songbird species. In this paper, we analyzed GRC behavior in female and male meiosis of the great tit, using immunolocalization of meiotic proteins and FISH with GRC-derived DNA probes. We found that, despite dozens of million years of independent evolution, the great tit GRC displays a striking similarity with the GRCs of two species of martins and two species of estrildid finches examined earlier. It was usually present in two copies in females forming recombining bivalent and in one copy in males forming a condensed heterochromatic body with dotted-like axial elements of the synaptonemal complex. We observed mosaicism for the GRC copy number in the female and male great tit. This indicates that one of the GRC copies might be passively lost during premeiotic germ cell divisions. After the meiotic prophase, the GRC was ejected from most male germ cells. The reverse and interspecies FISH with GRC-specific microdissected DNA probes indicates that GRCs of the great tit, pale martin, and zebra finch differ substantially in their genetic content despite similarities in the meiotic behavior.

Highly variable sperm morphology in the masked finch (Poephila personata) and other estrildid finches

Abstract Spermatozoa exhibit remarkable levels of morphological diversification among and within species. Among the passerine birds, the zebra finch (Taeniopygia guttata) has become a model system for studies of sperm biology, yet studies of closely related Estrildidae finches remain scarce. Here, we examine sperm morphology in the masked finch (Poephila personata) and place the data into the broader context of passerine sperm morphology using data for an additional 189 species. The masked finch exhibited high levels of within- and among-male variation in total sperm length and in specific sperm components. Furthermore, among-male variance in sperm length was significantly greater in estrildid (N = 12) compared with non-estrildid species (N = 178). We suggest that the high variation in sperm morphology in the masked finch and other estrildid species is likely to be linked to low levels of sperm competition, hence relaxed or weak selection on sperm length, in the clade. Our findings highlight that the highly variable sperm of the masked finch and widely studied zebra finch are ‘typical’ for estrildid species and stress the relevance of studying groups of closely related species. Finally, we suggest that further studies of Estrildidae will enhance our understanding of sperm diversity and avian diversity more generally.

Darwin’s finches habitually anoint their feathers with leaves of the endemic tree Psidium galapageium during the non‐breeding season

AbstractBirds host a wide range of ectoparasites and have developed behavioural strategies to combat them, such as preening, dust bathing and water bathing. In addition, a wide range of avian taxa anoint their feathers with insects or plants that have pharmaceutical properties, though most observations on anointing are anecdotal. Darwin's finches preen with leaves of an endemic tree (Psidium galapageium) and a previous laboratory study has shown that this plant has compounds that repel both mosquitoes and the invasive parasitic fly Philornis downsi, whose larvae suck blood from nestlings and incubating females and cause high nestling mortality. In the current study, we tested the hypothesis that preening with P. galapageium leaves serves to repel these parasites with an indirect approach. Mosquitoes and P. downsi affect their hosts mainly during the bird breeding season and P. downsi only affects breeding females, but not adult males. To test our hypothesis, we gathered quantitative data on leaf‐preening behaviour in Darwin's finches during their breeding and non‐breeding season and also investigated the influence of time of day and humidity, as humid conditions facilitate the release of volatile organic compounds. Contrary to our predictions, anointing occurred significantly more often during the non‐breeding season when mosquito and P. downsi numbers are lower. Four Darwin's finch species anointed their feathers habitually, and during the non‐breeding season, 56% of all preening events were with leaves. We found no effect of sex, but preening with leaves occurred predominately in the morning when leaves were wet. Our study is the first to provide quantitative data on anointing behaviour in birds and the high percentage of preening with leaves in the non‐breeding season suggests that the behaviour has an adaptive value. However, further studies are needed to test whether it reduces the negative impact of parasites other than mosquitoes and P. downsi.

Urban living influences the nesting success of Darwin's finches in the Galápagos Islands.

Urbanization is expanding worldwide with major consequences for organisms. Anthropogenic factors can reduce the fitness of animals but may have benefits, such as consistent human food availability. Understanding anthropogenic trade‐offs is critical in environments with variable levels of natural food availability, such as the Galápagos Islands, an area of rapid urbanization. For example, during dry years, the reproductive success of bird species, such as Darwin's finches, is low because reduced precipitation impacts food availability. Urban areas provide supplemental human food to finches, which could improve their reproductive success during years with low natural food availability. However, urban finches might face trade‐offs, such as the incorporation of anthropogenic debris (e.g., string, plastic) into their nests, which may increase mortality. In our study, we determined the effect of urbanization on the nesting success of small ground finches (Geospiza fuliginosa; a species of Darwin's finch) during a dry year on San Cristóbal Island. We quantified nest building, egg laying and hatching, and fledging in an urban and nonurban area and characterized the anthropogenic debris in nests. We also documented mortalities including nest trash‐related deaths and whether anthropogenic materials directly led to entanglement‐ or ingestion‐related nest mortalities. Overall, urban finches built more nests, laid more eggs, and produced more fledglings than nonurban finches. However, every nest in the urban area contained anthropogenic material, which resulted in 18% nestling mortality while nonurban nests had no anthropogenic debris. Our study showed that urban living has trade‐offs: urban birds have overall higher nesting success during a dry year than nonurban birds, but urban birds can suffer mortality from anthropogenic‐related nest‐materials. These results suggest that despite potential costs, finches benefit overall from urban living and urbanization may buffer the effects of limited resource availability in the Galápagos Islands.

Sex identification in embryos and adults of Darwin's finches.

Darwin's finches are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwin's finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol to extract DNA from Darwin's finch embryos. In addition, we applied minor modifications to two of the previously reported PCR primer sets for CHD1, a gene used for sexing adult passerine birds. The sex of all 29 tested embryos of six species of Darwin's finches was determined successfully by PCR, using both primer sets. Next to embryos, hatchlings and fledglings are also impossible to distinguish visually. This extends to juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwin's finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwin's finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR: individuals sexed based on marginal sex specific morphological traits; and birds which were impossible to classify in the field. PCR revealed that for birds with marginal sex specific traits, sexing in the field produced a 13% error rate. This demonstrates that PCR based sexing can improve field studies on Darwin's finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwin's finches throughout ontogeny, from embryos to adults.