An acoustic detection dataset of birds (Aves) in montane forests using a deep learning approach

Long-term monitoring is needed to understand the statuses and trends of wildlife communities in montane forests, such as those in Yushan National Park (YSNP), Taiwan. Integrating passive acoustic monitoring (PAM) with an automated sound identifier, a long-term biodiversity monitoring project containing six PAM stations, was launched in YSNP in January 2020 and is currently ongoing. SILIC, an automated wildlife sound identification model, was used to extract sounds and species information from the recordings collected. Animal vocal activity can reflect their breeding status, behaviour, population, movement and distribution, which may be affected by factors, such as habitat loss, climate change and human activity. This massive amount of wildlife vocalisation dataset can provide essential information for the National Park's headquarters on resource management and decision-making. It can also be valuable for those studying the effects of climate change on animal distribution and behaviour at a regional or global scale.To our best knowledge, this is the first open-access dataset with species occurrence data extracted from sounds in soundscape recordings by artificial intelligence. We obtained seven bird species for the first release, with more bird species and other taxa, such as mammals and frogs, to be updated annually. Raw recordings containing over 1.7 million one-minute recordings collected between the years 2020 and 2021 were analysed and SILIC identified 6,243,820 vocalisations of seven bird species in 439,275 recordings. The automatic detection had a precision of 0.95 and the recall ranged from 0.48 to 0.80. In terms of the balance between precision and recall, we prioritised increasing precision over recall in order to minimise false positive detections. In this dataset, we summarised the count of vocalisations detected per sound class per recording which resulted in 802,670 occurrence records. Unlike data from traditional human observation methods, the number of observations in the Darwin Core "organismQuantity" column refers to the number of vocalisations detected for a specific bird species and cannot be directly linked to the number of individuals.We expect our dataset will be able to help fill the data gaps of fine-scale avian temporal activity patterns in montane forests and contribute to studies concerning the impacts of climate change on montane forest ecosystems on regional or global scales

Use of Parsimony Analysis to Identify Areas of Endemism of Chinese Birds: Implications for Conservation and Biogeography

Parsimony analysis of endemicity (PAE) was used to identify areas of endemism (AOEs) for Chinese birds at the subregional level. Four AOEs were identified based on a distribution database of 105 endemic species and using 18 avifaunal subregions as the operating geographical units (OGUs). The four AOEs are the Qinghai-Zangnan Subregion, the Southwest Mountainous Subregion, the Hainan Subregion and the Taiwan Subregion. Cladistic analysis of subregions generally supports the division of China’s avifauna into Palaearctic and Oriental realms. Two PAE area trees were produced from two different distribution datasets (year 1976 and 2007). The 1976 topology has four distinct subregional branches; however, the 2007 topology has three distinct branches. Moreover, three Palaearctic subregions in the 1976 tree clustered together with the Oriental subregions in the 2007 tree. Such topological differences may reflect changes in the distribution of bird species through circa three decades

Phylogenomics of Rapid Avian Radiations

I use data from sequence capture of ultraconserved elements to resolve three rapid radiations in the avian tree of life and in the process gain insights on applying analytical strategies with gene tree-based coalescent methods (GCM). In Chapter 1, I explore analytical strategies that can be employed with GCMs to increase phylogenetic resolution and minimize highly supported conflicting results, including subsampling taxa to increase the number of gene trees analyzed, trimming sequences to eliminate sequence length heterogeneity, and filtering loci based on information content. These strategies are used to reconstruct a highly resolved and consistent phylogenetic hypothesis for the relatively young avian family, Zosteropidae. I show how conflicting results from different GCMs can arise from biases introduced by sequence length heterogeneity and uninformative loci that can lead to strongly supported incorrect estimates of phylogeny. In Chapter 2, I examine higher-level relationships in the enigmatic core Corvoidea group of Oscine passerines. A highly resolved phylogeny of core Corvoidea is recovered, with a majority of nodes receiving high support from both ML and coalescent analyses. I show that short sequence lengths do not bias species tree estimates of GCMs if informative sites are present in these sequences. In contrast, some samples that have longer sequence lengths compared to most taxa but shorter sequence lengths compared to taxa in its clade can also bias species tree estimates of GCMs. In Chapter 3, I develop a hypothesis on the origins of the trogons (Trogonidae) based on a robust dated phylogeny estimated from thousands of genome-wide loci. I recover the first well-supported hypothesis of relationships among trogon genera. This topology, combined with the trogon fossil record, geologic, and climatic data, suggests an Old World origin in the Late Oligocene/Early Miocene for the crown group. In this iii chapter, I show that in some datasets in which loci have high information content, exclusion of less informative loci in analysis can lead to lower bootstrap support of species tree estimates of GCMs

Nestling Provisioning in a Joint Nesting Cuckoo: The Smooth-Billed Ani (Crotophaga Ani)

Abstract Not ProvidedThesisMaster of Science (MSc

Type specimens of birds.

132 p. ; 26 cm.Includes bibliographical references (p. 110-127) and index.This sixth part of "Type specimens of birds in the American Museum of Natural History" corresponds to taxa covered in Volume 10 of Peters' Check-list of birds of the world. The original description of each taxon has been consulted unless otherwise noted, coordinates given for type localities when possible, currently accepted names for the taxa included, and comments on taxonomic history provided. Three hundred sixty-four published names are treated. Types of six of these are not in AMNH, and one was discussed in an earlier list

Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests [version 2; peer review: 1 approved, 2 approved with reservations]

Background From passive acoustic monitoring (PAM) recordings, the vocal activity rate (VAR), vocalizations per unit of time, can be calculated and is essential for assessing bird population abundance. However, VAR is subject to influences from a range of factors, including species and environmental conditions. Identifying the optimal sampling design to obtain representative acoustic data for VAR estimation is crucial for research objectives. PAM commonly uses temporal sampling strategies to decrease the volume of recordings and the resources needed for audio data management. Yet, the comprehensive impact of this sampling approach on VAR estimation remains insufficiently explored. Methods In this study, we used vocalizations extracted from recordings of 12 bird species, taken at 14 PAM stations situated in subtropical montane forests over a four-month period, to assess the impact of temporal sampling on VAR across three distinct scales: short-term periodic, diel, and hourly. For short-term periodic sampling analysis, we employed hierarchical clustering analysis (HCA) and the coefficient of variation (CV). Generalized additive models (GAMs) were utilized for diel sampling analysis, and we determined the average difference in VAR values per minute for the hourly sampling analysis. Results We identified significant day and species-specific VAR fluctuations. The survey season was divided into five segments; the earliest two showed high variability and are best avoided for surveys. Data from days with heavy rain and strong winds showed reduced VAR values and should be excluded from analysis. Continuous recordings spanning at least seven days, extending to 14 days is optimal for minimizing sampling variance. Morning chorus recordings effectively capture the majority of bird vocalizations, and hourly sampling with frequent, shorter intervals aligns closely with continuous recording outcomes. Conclusions While our findings are context-specific, they highlight the significance of strategic sampling in avian monitoring, optimizing resource utilization and enhancing the breadth of monitoring efforts

Reproductive Competition and Success in a Joint-Nesting Cuckoo

Joint-nesting species experience complex and diverse social environments which can influence individual reproductive success. When social groups are formed by non- relatives, competition for representation in incubated clutches can be intense and result in substantial reproductive losses. Because conflicts of this nature have direct impli- cations on fitness, resolutions and outcomes of such are of particular interest to evolu- tionary research. For this reason, I explored patterns of reproductive competition and skew in joint-nesting Smooth-billed Anis (Crotophaga ani). In chapter I, I show marked differences in multivariate bill and body size between sexes of Smooth-billed Anis (Cro- tophaga ani) despite reportedly reduced sexual dimorphism in co-operative breeders. I also show that multivariate bill size in males correlates with annual reproductive success and individual contribution to clutches from multiple parents. A similar trend is not observed in females, suggesting potential for sexual selection on male bill size. Together, these data provide evidence for morphological influences on reproductive fitness in joint- nesting species. In chapter II, I show that relative parental effort is positively correlated with reproductive fitness in social groups of Smooth-billed Anis. Nocturnal incubation is risky and is biased toward a single male - akin to Groove-billed (Crotophaga sulcirostris) and Greater Ani (Crotophaga major). I report heightened reproductive contribution by nocturnally incubating males when compared to other males within social groups. In chapter III, I tested whether social group size is correlated with endocrine markers of stress in adult male and female Anis. Using a novel enzyme linked immunosorbent as- say, I show that corticosterone (the primary glucocorticoid in birds) deposited in feathers is highest in birds from atypically large social groups. While the direct consequences of elevated corticosterone on reproductive fitness in Anis is yet unknown, these results suggest that breeding in large social settings is likely to be physiologically expensive.ThesisMaster of Science (MSc

Habitat-specific fitness benefits of sociality in Octodon degus

Recent debate has focused on how ecology shapes the evolution of group-living and cooperation in social vertebrates. Evidence suggests that group-living and cooperation enhance reproductive success under harsh local conditions in some species. Across two years, I studied two populations of Octodon degus, a plurally breeding rodent, to answer three questions: (1) Does living in large groups and having strong social network strength improve access to resources in harsh environments? (2) Does increased access to resources improve the reproductive success of group-living females? (3) Does living in large groups and having strong social network strength improve reproductive success of females in harsh environments? I quantified group sizes and social network strength, ecological conditions at burrow systems, and per capita offspring weaned of social groups to answer these questions. I found site- and year-specific relationships in partial support of predictions, demonstrating habitat-specific costs and benefits of social group-living and cooperation

Group Size and Social Conflict in Complex Societies

Conflicts of interest over resources or reproduction among individuals in a social group have long been considered to result in automatic and universal costs to group living. However, exploring how social conflict varies with group size has produced mixed empirical results. Here we develop a model that generates alternative predictions for how social conflict should vary with group size depending on the type of benefits gained from being in a social group. We show that a positive relationship between social conflict and group size is favored when groups form primarily for the benefits of sociality but not when groups form mainly for accessing group-defended resources. Thus, increased social conflict in animal societies should not be viewed as an automatic cost of larger social groups. Instead, studying the relationship between social conflict and the types of grouping benefits will be crucial for understanding the evolution of complex societies