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Biology subjects

Sin, S. Y. W.

Publications and source records attributed to Sin, S. Y. W..

15 recordsLinked to original sources

Do lovebirds ever forget? Long-term memory retention and adaptive forgetting in rosy-faced lovebirds

Long-term memory has been extensively documented in many animals across a range of ecological contexts. Far less is understood, however, about how long memories persist after active modification or how conflicting memories are adaptively regulated to enable flexible behaviour. Parrots are widely recognized for their high intelligence and cognitive capability, yet the study of memory has focused on only a handful of large parrot species. Here, using a binary choice symbolic system, we conducted three experiments on 28 rosy-faced lovebirds (Agapornis roseicollis) to investigate (1) memory retention of initial associative learning at intervals of two weeks, half a year, and one year; (2) reversal learning, where the rewarded and unrewarded symbols were swapped; and (3) memory retention, following reversal learning at two-week and half-year intervals. We revealed that (a) initial associative learning memory was strikingly persistent, remaining detectable after nearly 600 days; (b) reversal learning performance was comparable to that of large parrot species; and (c) while the post-reversal forgetting curve mirrored the pattern of initial learning, it exhibited a shorter retention duration and a lower retention plateau. These findings suggest that forgetting may serve as an adaptive mechanism that regulates the retrievability of conflicting information, rather than a simple erasure of memory traces. When the environment changes, the retrievability of previously functional but now maladaptive memories is suppressed, but their long-term storage is preserved for potential future use under analogous circumstances. Such dynamic regulations prevent the repetitive overwriting of information in a fluctuating environment, thereby fostering greater behavioural flexibility across dynamic scenarios.

animal behavior and cognition↗

From innovation to integration: Personality, sex, and learning drive recombination of innovative behaviours in lovebirds

Behaviour innovation plays a pivotal role in a species adaptability to dynamic environments. Investigating innovative behaviour and its underlying mechanism is therefore crucial for elucidating the development of cognitive flexibility across animals. Animal personality--which shapes how individuals perceive and engage with their surroundings--could offer insights into individual variation in this process. This study used a three-step foraging puzzle to evaluate the innovation capacity in 28 rosy-faced lovebirds (Agapornis roseicollis), specifically examining their capacity to recombine individually innovated component behaviours into integrated, more sophisticated techniques. We found that nearly half of the individuals spontaneously innovated multiple component behaviours to solve novel puzzles. Crucially, when challenged with a more sophisticated task, they recombined these behaviours into functionally dependent sequences without prior social demonstration. We further identified sex, persistence, and asocial learning capacity as key predictors of innovative problem-solving performance, with females, persistent individuals, and superior asocial learners excelled at problem-solving. Our findings demonstrate that behavioural innovation is not a static event, but a dynamic process--modulated by physical, cognitive, and personality variables--in which behaviours are flexibly transferred and recombined into increasingly complex forms to enable rapid individual adaptation.

animal behavior and cognition↗

Omnivorous diets of sympatric duck species in a subtropical East Asia wetland unveiled by multi-marker DNA metabarcoding

The East Asian-Australasian Flyway (EAAF) is experiencing notable population decreases in its migratory waterbird species. Our understanding of the foraging ecology of these waterbird species, including ducks, is crucial for monitoring and safeguarding their food sources and wetland habitats. Here, we used a DNA metabarcoding approach to analyze the fecal DNA from duck species to elucidate their dietary composition during the wintering period in a subtropical East Asian wetland. By employing multiple markers (18S, COI, and trnL) targeting different taxonomic groups and levels, we offered a comprehensive dietary analysis for omnivores that consume both plants and animals. We revealed the dietary compositions of common migratory duck species and their intraspecific and interspecific variations. While ducks are generally known to be omnivorous, Anas crecca had a more specialized diet and was primarily herbivorous throughout winter. In contrast, the sympatric Mareca penelope and Spatula clypeata exhibited a more omnivorous foraging behavior. Moreover, A. crecca displayed less dietary variation among individuals, while individuals of M. penelope and S. clypeata were highly variable in their diets. Comparing our results with those of studies conducted in different regions, we found that the dietary compositions of these duck species varied to different degrees across geographic locations. This variation underscores the flexibility of these duck species in their diets and their adaptable foraging strategies. Our findings also indicate that grasslands rich in herbaceous plants and aquatic environments abundant in small aquatic invertebrates are vital foraging habitats for duck species during their winter stay.

ecology↗

Food for thought: Rosy-faced lovebirds (Agapornis roseicollis) are capable of associative symbol learning and inference-based quantity discrimination

Cognitive capacity for quantity discrimination is highly adaptive in various ecological contexts and subject to convergent evolution across diverse animal species, yet the underlying mechanism involved is not fully understood. Discrimination accuracy generally increases with the ratio between two quantities; however, this ability is expected to differ across ratio ranges. To test this we presented a novel symbol system to 28 rosy-faced lovebirds (Agapornis roseicollis), associating additive tally marks with symbols representing a one-to-one correspondence with different food quantities. Trained lovebirds could spontaneously infer the relative food quantities represented by other symbols. Lovebirds proved capable of (1) associating symbols (i.e., object-file symbolism); with (2) "more-less" quantity inference, by deducing food quantities based on their knowledge of this symbol-quantity association; and (3) enhancing their performance in relation to disparity ratio (conforming to Webers law) and absolute difference. Furthermore (4), the influence of food ratio and absolute difference varied with different ratio ranges. Within a small ratio range ([≤] 3) discrimination performance improved with increments of ratio or absolute difference, whereas within a higher ratio range (> 3), the effect of these factors diminished. We conclude that rosy-faced lovebirds are capable of advanced numeracy and quantity discrimination, similar to larger parrot species.

animal behavior and cognition↗

Genomic signatures and demographic history of the widespread and critically endangered yellow-breasted bunting

Population declines may have long-term genetic consequences, including genetic erosion and inbreeding depression, which could affect species evolutionary potential and increase their risk of extinction. Small populations are more vulnerable to genetic threats than common species, but even species with large populations can also be at risk of extinction. The yellow-breasted bunting (Emberiza aureola) is a common and widespread songbird in the northern Palearctic regions, but its population has drastically declined by around 90% throughout the past 30 years, leading to an upgrade of its conservation status to critically endangered. In this study, we identified three populations within this species using whole-genome resequencing data, but the genetic differentiation between populations was shallow. These populations underwent similar population fluctuations but differed in the extent of population decline, resulting in lower genetic diversity and more homozygous deleterious mutations in a population comprising individuals on islands. The ancient demographic history was mainly associated with the climate, while recent population declines are likely due to human activities. Our results suggest that the yellow-breasted bunting population before the recent population collapse faced relatively low genetic threats and had high evolutionary potential. However, we should be vigilant about the genetic threats faced by this species as our sampling time occurred at the onset of its recent global population collapse. This study provides valuable genetic information for appropriate conservation management of the yellow-breasted bunting and sheds light on the extinction risks and genetic consequences common species face.

genomics↗

Foraging niche partitioning of three Myotis bat species and marine fish consumption by Myotis pilosus in a subtropical East Asian region

Most bats are insectivorous, but some species have evolved the ability to prey on fish. Although piscivory has been confirmed in the Ricketts big-footed myotis (Myotis pilosus), the extent of piscivory of other cohabiting Myotis species is uncertain. This study aims to explore the dietary niches and fish consumption of three Myotis species in a subtropical East Asian region, and specifically the fish diet of M. pilosus. Our findings reveal, for the first time, that M. pilosus consumes marine fishes, in contrast to previous research conducted in inland regions that suggested year-round consumption of cyprinids in freshwater habitats. We also observed seasonal variation in the diets of M. pilosus. It predominately hunted wide-banded hardyhead silverside, sailfin flying fish, and shorthead anchovy during the wet season, while mainly preying upon mullets during the dry months. In more inland areas, M. pilosus was found to primarily feed on invasive freshwater poeciliids. Furthermore, M. pilosus consumed more fish during the dry season, while there was a greater consumption of insects during the wet months. Most notably among our findings is the consumption of fish by two individuals of Horsfields myotis (M. horsfieldii), indicating that the species is potentially piscivorous. We revealed that both M. horsfieldii and M. pilosus consumed water striders, suggesting that foraging of aquatic insects could be driving the evolution of fishing behavior. Our findings have also shed light on the flexibility of foraging behavior in piscivorous bats.

ecology↗

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can offer insight regarding how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). In contrast to the low variation in mitochondrial genomes, a genome-wide panel of >4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling indicated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are indicative of multiple, isolated glacial refugia that coincide with present-day population structure. This study highlights the power of genome-level sequencing approaches to deepen our understanding of evolutionary processes in nonmodel wild species and to contribute to efforts assessing how historic demographic events and contemporary factors might influence biodiversity.

evolutionary biology↗

Investigating the use of odour and colour foraging cues by rosy-faced lovebirds (Agapornis roseicollis) using deep-learning based behavioural analysis

Olfaction and vision can play important roles in optimizing foraging decisions of birds, enabling them to maximize their net rate of energy intake while searching for, handling, and consuming food. Parrots have been used extensively in avian cognition research, and some species use olfactory cues to find food. Here we pioneered machine learning analysis and pose-estimation with convolutional neural networks (CNNs) to elucidate the relative importance of visual and olfactory cues for informing foraging decisions in the rosy-faced lovebird (Agapornis roseicollis) as a non-typical model species. In a binary choice experiment, we used markerless body pose tracking to analyse bird response behaviours. Rosy-faced lovebirds quickly learnt to discriminate the feeder provisioned with food by forming an association with visual (red/green papers) but not olfactory (banana/almond odour) cues. When visual cues indicated the provisioned and empty feeders, feeder choice was more successful, choice latency shorter, and interest in the empty feeder significantly lower. This demonstrates that visual cues alone are sufficient to inform lovebird foraging decisions without needing to use olfactory cues, suggesting that selection has not driven olfactory-based foraging in lovebird evolution.

animal behavior and cognition↗

Prevalence and genotypes of Chlamydia psittaci in pet birds of Hong Kong

Psittacosis, or parrot fever, is a zoonotic disease caused by Chlamydia species associated with birds. One of the causative agents of the disease is Chlamydia psittaci, which is often carried by psittacine and can be highly pathogenic and virulent to humans. In Hong Kong, a city with high population density, psittacosis is a notifiable disease with over 60% of cases in the last decade resulting in hospitalization. However, the source of transmission of C. psittaci and its prevalence in pet birds in Hong Kong are currently unknown. To evaluate the risks of psittacosis transmission through pet birds, we tested the presence of C. psittaci and determined its genotypes in samples obtained from 516 captive birds from households, pet shops, and a veterinary hospital in Hong Kong. Results revealed that five samples (0.97%), collected from budgerigars and cockatiels, were C. psittaci-positive, while 80% of them were obtained from pet shops. The identified strains belonged to genotype A and were closely related to the strain SP15 that was previously discovered in mainland China. Our study highlights the need for genotyping Chlamydia species in psittacosis patients to understand their source(s) of origin.

zoology↗

Temporal characterization of the viral load of psittacine beak and feather disease virus in rosy-faced lovebirds (Agapornis roseicollis)

Psittacine beak and feather disease virus (PBFDV) is a widespread and highly pathogenic virus in parrots (Psittaciformes), threatening both captive and wild populations over the world. The disease typically presents with feather and beak abnormalities, along with possible immune system suppression. No cure or commercialized vaccine is currently available. Our understanding of the Psittacine beak and feather disease often come from infected individuals with visible symptoms. Limited knowledge exists regarding the pathology and role of asymptomatic individuals in disease transmission. Asymptomatic individuals could shed virus in their crop secretion, feces, or feathers. In this study, we investigated the temporal change in viral load in feather and fecal samples from 17 asymptomatic rosy-faced lovebirds (Agapornis roseicollis). We developed a qPCR assay for PBFDV viral load quantification in the studied lovebirds. Our results showed that most of the individuals had very low viral load, while three individuals with high viral load at the beginning of the experiment were observed to exhibit a decreasing trend in viral load in both fecal and feather samples. Surprisingly, the viral load in an individual can drop from a high level to an undetectable level within three months, which is contrary to the prevailing notion that the disease is highly lethal with few reports of complete recovery. We also showed that viral load in feathers was higher than in feces. Our study provides valuable insights into the infection dynamics of PBFDV in asymptomatic individuals and contribute to the understanding of disease transmission in parrots.

ecology↗

Environmental factors and host sex influence the skin microbiome structure of Hong Kong newt (Paramesotriton hongkongensis) in a coldspot of chytridiomycosis in subtropical East Asia

Chytridiomycosis, an infectious skin disease caused by the chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans, has been threatening global amphibian biodiversity. On the skin of chytrid-resistant amphibians, some antifungal bacteria likely defend them against chytridiomycosis, reducing the mortality of resistant amphibians. The Hong Kong newt (Paramesotriton hongkongensis) inhabits East Asia which is a suspected origin of chytrids. Asymptomatic infection in the newts suggests their long-term coexistence with chytrids. Thus, the skin microbiomes of this resistant species warrant investigation, along with other factors that can affect the microbiome. Among the 149 newts sampled in their natural habitats in Hong Kong, putative antifungal bacteria were found on all newts. There were 314 amplicon sequence variants distributed over 25 genera of putative antifungal bacteria, abundant ones included Acinetobacter, Flavobacterium, and Novosphingobium spp. The skin microbiome compositions were strongly influenced by the inter-site geographical distances. Despite inter-site differences, we identified some core skin microbes across sites, which could be vital to P. hongkongensis. The dominant cores included family Comamonadaceae, family Chitinophagaceae, and class Betaproteobacteria. Moreover, habitat elevation and host sex also exhibited significant effects on skin microbiome compositions. The antifungal bacteria found on these newts offer an important resource for conservation against chytridiomycosis, such as probiotic treatments for susceptible species.

ecology↗

Genetic basis and evolution of structural color polymorphism in an Australian songbird

Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaption under differential selection. Some island birds have melanic plumage differing from the color of mainland conspecifics, a trait proposed as an insular adaptation. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genomes to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. We also detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies, as predicted by earlier work, but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This re-evolution was likely driven by a pre-existing female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.

evolutionary biology↗

De Novo Assembly of the Northern Cardinal (Cardinalis cardinalis) Genome Reveals Candidate Regulatory Regions for Sexually Dichromatic Red Plumage Coloration

Northern cardinals (Cardinalis cardinalis) are common, mid-sized passerines widely distributed in North America. As an iconic species with strong sexual dichromatism, it has been the focus of extensive ecological and evolutionary research, yet genomic studies investigating the evolution of genotype-phenotype association of plumage coloration and dichromatism are lacking. Here we present a new, highly contiguous assembly for C. cardinalis. We generated a 1.1 Gb assembly comprised of 4,762 scaffolds, with a scaffold N50 of 3.6 Mb, a contig N50 of 114.4 kb and a longest scaffold of 19.7 Mb. We identified 93.5% complete and single-copy orthologs from an Aves dataset using BUSCO, demonstrating high completeness of the genome assembly. We annotated the genomic region comprising the CYP2J19 gene, which plays a pivotal role in the red coloration in birds. Comparative analyses demonstrated non-exonic regions unique to the CYP2J19 gene in passerines and a long insertion upstream of the gene in C. cardinalis. Transcription factor binding motifs discovered in the unique insertion region in C. cardinalis suggest potential androgen-regulated mechanisms underlying sexual dichromatism. Pairwise Sequential Markovian Coalescent (PSMC) analysis of the genome reveals fluctuations in historic effective population size between 100,000-250,000 in the last 2 millions years, with declines concordant with the beginning of the Pleistocene epoch and Last Glacial Period. This draft genome of C. cardinalis provides an important resource for future studies of ecological, evolutionary, and functional genomics in cardinals and other birds.

evolutionary biology↗

Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird

Procellariiform seabirds are known for their well-developed olfactory capabilities, reflected by their large olfactory bulb to brain ratio and olfactory-mediated behaviors. Many species in this clade use olfactory cues for foraging and navigation, and some species can recognize individual-specific odors. Their genomes and transcriptomes may yield important clues about how the olfactory receptor (OR) subgenome was shaped by natural and sexual selection. In this study, we assembled a high-quality Leachs storm petrel (Oceanodroma leucorhoa) genome to facilitate characterization of the OR repertoire. We also surveyed expressed OR genes through transcriptome analysis of the olfactory epithelium - to our knowledge, the first avian study to interrogate OR diversity in this way. We detected a large number ([~]61) of intact OR genes, and identified OR genes under positive selection. In addition, we estimated that this species has the lowest proportion ([~]60%) of pseudogenes compared to other waterbirds studied thus far. We show that the traditional annotation-based genome mining method underestimates OR gene number (214) as compared to copy number analysis using depth-of-coverage analysis, which estimated a total of 492 OR genes. By examining OR expression pattern in this species, we identified highly expressed OR genes, and OR genes that were differentially expressed between age groups, providing valuable insight into the development of olfactory capabilities in this and other avian species. Our genomic evidence is consistent with the Leachs storm petrels well-developed olfactory sense, a key sensory foundation for its pelagic lifestyle and behavioral ecology.

evolutionary biology↗

Neo-sex chromosomes and demography shape genetic diversity in the Critically Endangered Raso lark

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for ~500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. It is plausible that these regions might inadvertently and temporarily preserve pre-existing allelic variation in females that would otherwise be lost through genetic drift. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present day diversity can be shaped by ancient demographic events.

genomics↗