Recent Northward Expansion of a Passerine Bird Species, Brownish-Flanked Bush Warbler (Horornis fortipes).

Northward expansions of bird distributions have been commonly observed in the Northern Hemisphere, likely as a result of climate change. The causes and ecological impacts of such range shifts have received extensive attention, but studies on the process of range shifts are still relatively scarce. The Brownish-flanked Bush Warbler (Horornis fortipes) has expanded northward from 35° N to 40° N during the past decade. In this study, we collated 77 records of the species beyond its traditional distribution during the past ten years from citizen science data. Most of the new records were from northeast of its traditional distribution, including the North China Plain, Taihang Mountains, and Taishan Mountain, and a few records from the northern margin of the Qinling Mountains and Qinghai-Tibet Plateau. We concluded that the Brownish-flanked Bush Warbler has bred in this new area in at least six sites. The newly established populations are assumed to belong to the subspecies H. f. davidianus, which can be divided into eastern and western dialect groups based on differences in songs. Song recordings from 10 males from Beijing and its adjacent areas were collected. Bayesian analysis based on the acoustic traits indicated that these males were most likely from the western dialect area, with a posterior probability of 99.975%. Combining topographical data with the habitat preference of the species, we inferred that these individuals spread northeastward from the Qinling Mountains to Taihang Mountains, and further along the Yanshan Mountains. This study is a case study of the distribution expansion of a bird species, which reflects the dynamics of a species in the early stage of its northward expansion.

The adaptive evolution of cancer driver genes.

BACKGROUND: Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS: Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS: These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.

Assemblages of Plasmodium and Related Parasites in Birds with Different Migration Statuses.

Migratory birds spend several months in their breeding grounds in sympatry with local resident birds and relatively shorter periods of time at stopover sites. During migration, parasites may be transmitted between migratory and resident birds. However, to what extent they share these parasites remains unclear. In this study, we compared the assemblages of haemosporidian parasites in migratory, resident, and passing birds, as well as the correlations between parasite assemblages and host phylogeny. Compared with passing birds, migratory birds were more likely to share parasites with resident birds. Shared lineages showed significantly higher prevalence rates than other lineages, indicating that common parasites are more likely to spill over from the current host to other birds. For shared lineages, the prevalence was significantly higher in resident birds than in migratory birds, suggesting that migratory birds pick up parasites at their breeding ground. Among the shared lineages, almost two-thirds presented no phylogenetic signal in their prevalence, indicating that parasite transmission among host species is weakly or not correlated with host phylogeny. Moreover, similarities between parasite assemblages are not correlated with either migration status or the phylogeny of hosts. Our results show that the prevalence, rather than host phylogeny, plays a central role in parasite transmission between migratory and resident birds in breeding grounds.

An explanation for negligible senescence in animals.

Negligible or negative senescence occurs when mortality risk is stable or decreases with age, and has been observed in some wild animals. Age-independent mortality in animals may lead to an abnormally long maximum individual lifespans and be incompatible with evolutionary theories of senescence. The reason why there is no evidence of senescence in these animals has not been fully understood. Recovery rates are usually very low for wild animals with high dispersal ability and/or small body size (e.g., bats, rodents, and most birds). The only information concerning senescence for most of these species is the reported lifespan when individuals are last seen or caught. We deduced the probability density function of the reported lifespan based on the assumption that the real lifespan corresponding to Weibull or Gompertz distribution. We show that the magnitude of the increase in mortality risk is largely underestimated based on the reported lifespans with low recovery probability. The risk of mortality can aberrantly appear to have a negative correlation with age when it actually increases with increasing lifespan. We demonstrated that the underestimated aging rate for wild animals with low recovery probability can be generalizable to any aging models. Our work provides an explanation for the appearance of negligible senescence in many wild animals. Humans attempt to obtain insights from other creatures to better understand our own biology and its gain insight into how to enhance and extended human health. Our advice is to take a second glance before admiring the negligible senescence in other animals. This ability to escape from senescence is possibly only as beautiful illusion in animals.

A dataset of bird distributions in zoogeographical regions of China.

Background: China, the largest country in Asia, has a land area of approximately 9.6 million square kilometres. There are 1481 bird species (following the taxonomy of IOC World Bird List version 12.1) recorded in two zoogeographical realms, seven regions and 19 subregions in the country. From 1955 to 2017, six authoritative monographs were published, which recorded the distribution area for all bird species in China and were widely quoted by research papers and field guides. This massive amount of data could be used to address many hot topics in ornithology, biogeography and ecology. However, rapid changes in the taxonomic status and different schemes of zoogeographical regionalisation in these six monographs provided limits to the utilisation of these valuable data. New information: By integrating the data from the six monographs, we presented an open-access dataset on the occurrences and residence types of all Chinese bird species in zoogeographical regions over the past 60 years. The taxonomic statuses for these species were determined following the IOC World Bird List version 12.1 and the zoogeographical regions were based on the updated scheme. These data provide valuable information for the research in bird ecology and conservation biology.

Linking the maximum reported life span to the aging rate in wild birds.

Dozens of surrogates have been used to reflect the rate of aging in comparative biology. For wild organisms, the maximum reported life span is often considered a key metric. However, the connection between the maximum reported life span for a single individual and the aging rate of that species is far from clear. Our objective was to identify a pragmatic solution to calculate the aging rate from the maximum reported life span of wild birds. We explicitly linked the maximum reported life span to the aging process by employing a Weibull distribution and calculating the shape parameter in this model, which reflects the change in mortality across ages and be used as a surrogate for the aging rate. From simulated data, we demonstrated that the percentile estimator is suitable for calculating the aging rate based on the maximum reported life span. We also calculated the aging rate in 246 bird species based on published information from EURING and tested its relationship with body mass. Our study constitutes a new approach for using maximum reported life span in aging research. The aging rate calculated in the study is based on numerous assumptions/prerequisites and can be improved as more is learned about these assumptions/prerequisites.

The ecological significance of birds feeding from the hand of humans.

Animals keep a safe distance to humans and thus humans rarely physically encounter wild animals. However, birds have been known to feed from the hand of humans. Such behaviour must reflect the trade-off between acquisition of food and the risk of being captured by a potential predator feeding from the hand. Relying on YouTube, an international video-sharing platform, we found 36 European bird species recorded feeding from the hand of humans. We compared ecological traits between these species and all other 490 European bird species, which were not recorded as feeding from a human hand. We found that species with a large number of innovative behaviours, a higher rate of introduction success, larger breeding range, larger population size, and urban tolerance have a higher probability of feeding from the hand of a human. These associations were also supported after control for the similarity among taxa due to common phylogenetic descent. In conclusion, these findings suggest that frequent feeding from the hand of a human results in the transition from natural environments to novel urbanized environments with consequences for population size increasing and range expansion.

Individual identification of birds with complex songs: The case of green-backed flycatchers Ficedula elisae.

Vocal individual identification has been demonstrated in many animals, with discriminant function analysis (DFA) and spectrographic cross-correlation (SPCC) being the two most frequent methods. Successful vocal individual identification requires high among-individual differences and within-individual stability over time for vocal features. Lack of vocal individual identification is common in songbirds with complex songs, and most vocal individual identification studies are made in bird species with simple vocalizations. Here, we applied vocal individual identification with the two methods on a songbird, green-backed flycatcher Ficedula elisae. We based its complex songs by division into first, second, and third phrases. DFA resulted in a correct distinction rate of 94.5 % between one first-phrase type and another. SPCC similarity was significantly higher within than among types for first and second phrases, respectively. For first-phrase types with recordings from different days during a breeding season, the correct DFA rate was 87.1 %. SPCC similarity within type changed significantly among days, but was still significantly higher than that among types. In conclusion, first phrases of the complex songs met the two requirements and could be effectively used for vocal individual identification in this species. This study filled a gap in vocal individual identification in birds with complex songs.

Comparative urbanization of birds in China and Europe based on birds associated with trees.

Urbanization effects on living organisms are spatially heterogeneous. Here we quantified the abundance of birds per tree in forested urban and rural habitats for 85,829 trees mainly in China and Europe. A population model was based on the assumption that: 1) birds have a normally distributed habitat preference; 2) an increase in population size linked to the habitat preference; 3) a population size dependent on the habitat preference; and 4) the removal of a certain fraction of individuals giving rise to extinction. We tested for large-scale differences in the impact of urbanization on the frequency distribution of the difference in abundance between urban and rural habitats in China and parts of Europe. The difference in the frequency distribution of urban population density of birds in trees minus rural population density of birds in trees in China and Europe was statistically significant, suggesting that the abundance of birds differed between trees in urban and rural habitats, but more so in China than in Europe. We hypothesize that more pronounced differences in China than in Europe may have arisen due to the Four Pests Campaign in 1958-1962 that resulted in death of hundreds of millions of birds (mainly tree sparrows Passer montanus, but also numerous other less common species that were starting to become urbanized around 1960). Species that were less common in 1960 could not sustain reductions in population size in urban areas and hence these species are still rare or absent in urban areas today 60 years later.

Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes.

BACKGROUND: Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS: Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS: Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.

From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex.

As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.

Components of variation in female common cuckoo calls.

Investigations on bird vocalizations have largely focused on males. Female vocalizations are widespread in birds but few studies have investigated female vocal characteristics, particularly in non-Passeriformes. In this study, we use new field recordings from China, and calls available from an online sound library to examine temporal patterns, call consistency and geographical variation in vocalizations of female common cuckoos Cuculus canorous. The peak in vocal activity (both male and female) was in the morning, which contrasts to what would be predicted if the sole function of the female call was to distract the attention of hosts after parasitizing a host's nest in the afternoon. Both male and female common cuckoos were more vocally active in sunny weather, than rainy weather. We also found larger intra-individual variation in female rather than in male calls, which may benefit female cuckoos by increasing stimulation to host species. Peak frequency of female calls decreased with increased latitude, while differences in female call features were not associated with geographic distance. In summary, our findings that female calls are used in the morning, rather than at peak egg laying, yet are highly variable and show little geographic patterns suggest that the function of these female calls may be more variable and intricate than previously thought. However, because research on female vocalizations is underrepresented, future studies are still needed.

Song Characteristics of Oriental Cuckoo Cuculus optatus and Himalayan Cuckoo Cuculus saturatus and Implications for Distribution and Taxonomy.

Canwei Xia, Wei Liang, Geoff J. Carey, and Yanyun Zhang (2016) Song features during the breeding season are important in identifying species of cuckoos. Whether Oriental Cuckoo Cuculus optatus and Himalayan Cuckoo C. saturatus inhabiting the Palearctic and Oriental realms respectively can be distinguished according to song characteristics is uncertain. In this study, we performed a thorough investigation of the song characteristics of these taxa by collecting and analyzing recordings of song in their distribution areas. We found that songs could be divided into two groups based on the number of notes per syllable, and significant differences in other frequency and temporal features were also found between these two groups. The group with a song comprising two notes per syllable was shown to breed in Russia, Japan and China including Xinjiang, Inner Mongolia, Heilongjiang and Taiwan, while the group with a song containing more than two notes per syllable was found to breed in the Himalayas and central China, extending northeast through north China as far as northeast Hebei, and south to southwest China. The distribution of these two groups was broadly related to the published distribution of populations of optatus and saturatus, respectively. Our data supported the separation of optatus and saturatus based on their song features, and also suggested refinements to the distribution of these two taxa, as follows: birds in north mainland China are saturatus, and those in Taiwan Island are optatus.

Territory tenure increases with repertoire size in brownish-flanked bush warbler.

Song repertoire size is often cited as a classic example of a secondary sexual trait in birds. Models of sexual selection and empirical tests of their predictions have often related secondary sexual traits to longevity. However, the relationship between repertoire size and longevity is unclear. Using capture-mark-recapture studies in two populations of the brownish-flanked bush warbler Cettia fortipes, we found that males with a repertoire size of three maintained territory tenure for a longer duration than did males with a repertoire size of two. These results provide evidence that even a minimal difference in repertoire size can serve as a potential signal of territory tenure capability.

Are different song types used in different contexts in brownish-flanked bush warblers?

The repertoires of most songbirds consist of two or more different song types. Studies on a growing number of species have indicated that song types are used selectively in different contexts. For example, two bush warblers (Cettia diphone and C. cettia) use song types selectively in spontaneous singing and playback-evoked singing. Most male brownish-flanked bush warblers (C. fortipes) have two distinct song types. In this study, we tested whether these two song types are used selectively in different contexts. Most frequency and temporal variables are significantly different between these two song types, but neither song type is used more frequently during or after playback compared to spontaneous singing. Additionally, males did not respond differently to the two song types during playback experiments. In conclusion, these two song types differ significantly in both frequency and temporal variables, but we did not find any evidence that they are used selectively in different contexts. Comparing two related bush warblers (C. diphone and C. cettia) that selectively use different song types in different contexts, our study offers further evidence that avian vocalization is a plastic characteristic and can vary considerably, even among closely related species.

Acoustic identification of individuals within large avian populations: a case study of the Brownish-flanked Bush Warbler, South-Central China.

Acoustic identification is increasingly being used as a non-invasive method for identifying individuals within avian populations. However, most previous studies have utilized small samples of individuals (<30). The feasibility of using acoustic identification of individuals in larger avian populations has never been seriously tested. In this paper, we assess the feasibility of using distinct acoustic signals to identify individuals in a large avian population (139 colour-banded individuals) of Brownish-flanked Bush Warbler (Cettia fortipes) in the Dongzhai National Nature Reserve, south-central China. Most spectro-temporal variables we measured show greater variation among individuals than within individual. Although there was slight decline in the correct rate of individual identification with increasing sample sizes, the total mean correct rate yielded by discriminant function analysis was satisfactory, with more than 98% of songs correctly recognized to the corresponding individuals. We also found that using a part of randomly selected measured variables was sufficient to obtain a high correct rate of individual identification. We believe that our work will increase confidence in the use of using acoustic recognition techniques for avian population monitoring programs.

[Two distinct parts within the song of Phoenicurus auroreus, and individual identification on the basis of the song].

Bird song has two key functions: attraction and competition. The structures of these songs have been shaped by both intra- and intersexual selection. Accordingly, there are some species that appear to use different parts of song to attract females and repel males. Alongside this functional separation, the structure of song can also have significant divergence. We studied the songs from 32 individuals of Phoenicurus auroreus, recorded in Beijing Xiaolongmen forest Park during the 2011 breeding season. The song of Phoenicurus auroreus consists of two distinct parts, a stereotyped and variable part. Significant differences between these two parts were observed between all the variables we measured. Based on the stereotyped part, the rate of correct individual identification is satisfactory, and most of songs can be correctly classified.