Genomic status of yellow-breasted bunting following recent rapid population decline
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ABSTRACT:
SUBMITTER: Wang P
PROVIDER: S-EPMC9207672 | biostudies-literature | 2022 Jun
REPOSITORIES: biostudies-literature
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Project description:The critically endangered Yellow-breasted Bunting has undergone population collapse globally because of illegal hunting and habitat deterioration. It was listed as critically endangered (CR) by the International Union for Conservation of Nature (IUCN) in 2017 and designated a Class I (highest level) national conservation bird species in China in 2021. Birdsong in the breeding season is the main communicative signal under sexual selection, and song variations have long been considered critical evidence of divergence among subspecies or populations. We compared the songs of 89 males from 18 populations to test subspecies taxonomy. We found that songs of the Yellow-breasted Bunting Emberiza aureola are subspecies specific and that three subspecies can be clearly discriminated by song divergences. Moreover, an analysis of multiple vocal traits supports the claim that insulana is distinct from aureola and ornata. Finally, at the geographic population level, populations can be clearly classified in accordance with the three subspecies, although the aureola population in Xinjiang, China is differentiated from other populations of the same subspecies. The results of this study demonstrate that all populations and subspecies are unique and should be protected to maintain intraspecies song diversity. In addition, several specific populations, such as insulana populations in Japan and the Xinjiang, China population of aureola, need to be paid special attention to prevent the extinction of unique or local taxa.
| S-EPMC9454650 | biostudies-literature
Project description:The population of the Yellow-breasted Bunting Emberiza aureola, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before the effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range. We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing, or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs, and grasses. Highest probabilities were found at shrub cover values of 40%-70%. Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.
| S-EPMC8258230 | biostudies-literature
Project description:Migratory animals are threatened by human-induced global change. However, little is known about how stopover habitat, essential for refuelling during migration, affects the population dynamics of migratory species. Using 20 years of continent-wide citizen science data, we assess population trends of ten shorebird taxa that refuel on Yellow Sea tidal mudflats, a threatened ecosystem that has shrunk by >65% in recent decades. Seven of the taxa declined at rates of up to 8% per year. Taxa with the greatest reliance on the Yellow Sea as a stopover site showed the greatest declines, whereas those that stop primarily in other regions had slowly declining or stable populations. Decline rate was unaffected by shared evolutionary history among taxa and was not predicted by migration distance, breeding range size, non-breeding location, generation time or body size. These results suggest that changes in stopover habitat can severely limit migratory populations.
| S-EPMC5399291 | biostudies-literature
Project description:Human populations have experienced dramatic growth since the Neolithic revolution. Recent studies that sequenced a very large number of individuals observed an extreme excess of rare variants and provided clear evidence of recent rapid growth in effective population size, although estimates have varied greatly among studies. All these studies were based on protein-coding genes, in which variants are also impacted by natural selection. In this study, we introduce targeted sequencing data for studying recent human history with minimal confounding by natural selection. We sequenced loci far from genes that meet a wide array of additional criteria such that mutations in these loci are putatively neutral. As population structure also skews allele frequencies, we sequenced 500 individuals of relatively homogeneous ancestry by first analyzing the population structure of 9,716 European Americans. We used very high coverage sequencing to reliably call rare variants and fit an extensive array of models of recent European demographic history to the site frequency spectrum. The best-fit model estimates ∼ 3.4% growth per generation during the last ∼ 140 generations, resulting in a population size increase of two orders of magnitude. This model fits the data very well, largely due to our observation that assumptions of more ancient demography can impact estimates of recent growth. This observation and results also shed light on the discrepancy in demographic estimates among recent studies.
| S-EPMC3896169 | biostudies-literature
Project description:The yellow crazy ant, Anoplolepis gracilipes was first reported in Kenting National Park, Taiwan, in the 2000s, raising the concern of this invasive ant's potential effects on the native land crab populations. We investigated the distribution and abundance of A. gracilipes and its adverse effect on the land crab populations at four land crab hotspots within the park. Our survey results indicated that A. gracilipes was widespread and abundant at three of the study sites (Hsiangchiaowan, Shadao, and Natural Spring), while the distribution was much more confined at the fourth site (Houwan). Land crab populations experienced a notable decline at all the study sites except Houwan, indicating an inverse relationship between the population of land crabs and distribution/abundance of A. gracilipes. Combining the results of visual observations, the decline of land crab populations can be attributed, at least partially, to direct attacks by A. gracilipes on land crabs in their natural habitat and during the breeding migration season. Generalized additive model showed that worker abundance of this ant is associated with human disturbance levels, suggesting that anthropogenic disturbance may have contributed to the decline in land crab populations via promoting the abundance of A. gracilipes.
| S-EPMC8192946 | biostudies-literature
Project description:How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Native Americans diversified into two basal genetic branches around 13 KYA, one in North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians and Australo-Melanesians, the latter possibly through the ancestors of Aleutian Islanders. Putative relict populations in South America, including the historical Pericúes and Fuego-Patagonians, are not directly related to modern Australo-Melanesians.
2015-07-20 | GSE70987 | GEO
Project description:Detailed information spanning the full annual cycle is lacking for most songbird populations. We examined breeding, migration, and non-breeding sites for the Yellow-breasted Chat (Icteria virens, chat). We deployed archival GPS tags and light-level geolocators on breeding chats in British Columbia and light-level geolocators in California from 2013 to 2017 to determine migration routes and non-breeding sites. We examined whether chats overwintered in protected areas and characterized the percent of land cover within 1 km. We used a combination of genetics and stable hydrogen isotopes from feathers collected on non-breeding chats in Nayarit, Mexico (2017-2019) and migrating chats in Chiapas, Mexico (2018) and Veracruz, Mexico (2014-2015) to determine subspecies and infer breeding location. Endangered chats in British Columbia followed the Pacific Flyway and spent the non-breeding period in Sinaloa and Nayarit, Mexico. Two out of five chats spent the non-breeding period in protected areas, and the most common landcover type used was tropical or subtropical broadleaf deciduous forest. We found no mixing of eastern and western chats in our Mexico sites, suggesting strong migratory connectivity at the subspecies level. Western chats likely originating from multiple breeding latitudes spent the non-breeding period in Nayarit. Eastern Yellow-breasted Chats likely breeding across various latitudes migrated through Veracruz and Chiapas. Our results provide precise migration routes and non-breeding locations, and describe habitat cover types for chats, notably an endangered population in British Columbia, which may be valuable for habitat protection and conservation efforts.Supplementary informationThe online version contains supplementary material available at 10.1007/s10336-021-01931-8.
| S-EPMC8761137 | biostudies-literature
Project description:BackgroundBirds have extremely well-developed acoustic communication and have become popular in bioacoustics research. The majority of studies on bird song have been conducted in the temperate zones where usually males of birds sing to attract females and defend territories. In over 360 bird species mostly inhabiting the tropics both males and females sing together in duets. Avian duets are usually formed when a male and female coordinate their songs. We focused on a species with relatively weakly coordinated duets, with male solo as the prevailing vocalisation type.MethodsInstead of analysing a set of recordings spread over a long time, we analysed whole day microphone-array recordings of the Yellow-breasted Boubou (Laniarius atroflavus), a species endemic to West African montane rainforests. We described the structure of the solo and duet vocalisations and temporal characteristics of daily activity based on 5,934 vocal bouts of 18 focal pairs and their neighbours.ResultsBirds had small, sex specific repertoires. All males shared three types of loud whistles functioning as song type repertoires in both solos and duets. Females vocalised with five types of harsh, atonal notes with a more variable and usually lower amplitude. Three of them were produced both as solos and in duets, while two seem to function as alarm and excitement calls given almost exclusively as a solo. Solos were the most common vocalisation mode (75.4%), with males being more vocally active than females. Duets accounted for 24.6% of all vocalisations and in most cases were initiated by males (81%). The majority of duets were simple (85.1%) consisting of a single male and female song type, but altogether 38 unique duet combinations were described. Males usually initiated singing at dawn and for this used one particular song type more often than expected by chance. Male solo and duet activities peaked around dawn, while female solos were produced evenly throughout the day.DiscussionYellow-breasted Boubou is a duetting species in which males are much more vocal than females and duetting is not a dominating type of vocal activity. Duet structure, context and timing of daily production support the joint resource defence hypothesis and mate guarding/prevention hypotheses, however maintaining pair contact also seems to be important. This study provides for the first time the basic quantitative data describing calls, solos and duet songs in the Yellow-breasted Boubou.
| S-EPMC7585374 | biostudies-literature
Project description:Although scientists have warned of possible social perils resulting from climate change, the impacts of long-term climate change on social unrest and population collapse have not been quantitatively investigated. In this study, high-resolution paleo-climatic data have been used to explore at a macroscale the effects of climate change on the outbreak of war and population decline in the preindustrial era. We show that long-term fluctuations of war frequency and population changes followed the cycles of temperature change. Further analyses show that cooling impeded agricultural production, which brought about a series of serious social problems, including price inflation, then successively war outbreak, famine, and population decline successively. The findings suggest that worldwide and synchronistic war-peace, population, and price cycles in recent centuries have been driven mainly by long-term climate change. The findings also imply that social mechanisms that might mitigate the impact of climate change were not significantly effective during the study period. Climate change may thus have played a more important role and imposed a wider ranging effect on human civilization than has so far been suggested. Findings of this research may lend an additional dimension to the classic concepts of Malthusianism and Darwinism.
| S-EPMC2148270 | biostudies-literature
Project description:Obesity and metabolic syndrome are strong risk factors for incident chronic kidney disease (CKD). However, the predictive accuracy of metabolic body composition status (MBCS), which combines the status of obesity and metabolic syndrome, for rapid kidney function decline (RKFD) is unclear. The aim of this study was to investigate the relationship between MBCS and RKFD in a healthy population in a prospective community-based cohort study. In the current study, we followed changes in renal function in 731 people residing in northern Taiwan for 5 years. The participants were divided into four groups according to their MBCS, including metabolically healthy normal weight (MHNW), metabolically healthy overweight (MHOW), metabolically unhealthy normal weight (MUNW), and metabolically unhealthy overweight (MUOW). We evaluated traditional risk factors for CKD and metabolic profiles. The primary outcome was RKFD, which was defined as a 15% decline in estimated glomerular filtration rate (eGFR) within the first 4 years, and a reduction in eGFR which did not improve in the 5th year. During the study period, a total of 731 participants were enrolled. The incidence of RKFD was 17.1% (125/731). Multiple Cox logistic regression hazard analysis revealed that age, cerebrovascular accident, eGFR, urine albumin-to-creatinine ratio, use of painkillers, depressive mood, MUNW and MUOW were independent predictors of RKFD. After adjusting for age, sex, eGFR and total cholesterol, the participants with MUNW and MUOW had higher hazard ratios (HRs) for RKFD [HR: 2.19, 95% confidence interval (CI): 1.22-3.95 for MUNW; HR: 1.86, 95% CI: 1.21-2.87 for MUOW] than those with MHNW. Similar results were also observed in subgroup analysis of those aged above 65 years. On the basis of the results of this study, we conclude that MBCS was independently associated with RKFD, especially in the older adults. On the basis of our results, we suggest that MUNW and MUOW should be considered as risk factors for RKFD.
| S-EPMC9204180 | biostudies-literature