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14 pages, 1216 KiB

Open AccessArticle

Living Together, Singing Together: Revealing Similar Patterns of Vocal Activity in Two Tropical Songbirds Applying BirdNET

by David Amorós-Ausina, Karl-L. Schuchmann, Marinez I. Marques and Cristian Pérez-Granados

Sensors 2024, 24(17), 5780; https://doi.org/10.3390/s24175780 - 5 Sep 2024

Cited by 3 | Viewed by 2212

Abstract

In recent years, several automated and noninvasive methods for wildlife monitoring, such as passive acoustic monitoring (PAM), have emerged. PAM consists of the use of acoustic sensors followed by sound interpretation to obtain ecological information about certain species. One challenge associated with PAM is the generation of a significant amount of data, which often requires the use of machine learning tools for automated recognition. Here, we couple PAM with BirdNET, a free-to-use sound algorithm to assess, for the first time, the precision of BirdNET in predicting three tropical songbirds and to describe their patterns of vocal activity over a year in the Brazilian Pantanal. The precision of the BirdNET method was high for all three species (ranging from 72 to 84%). We were able to describe the vocal activity patterns of two of the species, the Buff-breasted Wren (Cantorchilus leucotis) and Thrush-like Wren (Campylorhynchus turdinus). Both species presented very similar vocal activity patterns during the day, with a maximum around sunrise, and throughout the year, with peak vocal activity occurring between April and June, when food availability for insectivorous species may be high. Further research should improve our knowledge regarding the ability of coupling PAM with BirdNET for monitoring a wider range of tropical species. Full article

(This article belongs to the Special Issue Advanced Acoustic Sensing Technology)

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14 pages, 3738 KiB

Open AccessEditor’s ChoiceArticle

Description of the Three Complete Mitochondrial Genomes of Sitta (S. himalayensis, S. nagaensis, and S. yunnanensis) and Phylogenetic Relationship (Aves: Sittidae)

by Qingmiao Yuan, Qiang Guo, Jing Cao, Xu Luo and Yubao Duan

Genes 2023, 14(3), 589; https://doi.org/10.3390/genes14030589 - 26 Feb 2023

Cited by 7 | Viewed by 1943

Abstract

Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis, S. nagaensis, and S. yunnanensis), which were 16,822–16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister group of Troglodytidae, and the genus Sitta can be divided into three major clades. We demonstrated the phylogenetic relationships within the genus Sitta (S. carolinensis + ((S. villosa + S. yunnanensis) + (S. himalayensis + (S. europaea + S. nagaensis)))). Full article

(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)

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16 pages, 2980 KiB

Open AccessArticle

Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications

by Hengwu Ding, De Bi, Shiyun Han, Ran Yi, Sijia Zhang, Yuanxin Ye, Jinming Gao, Jianke Yang and Xianzhao Kan

Animals 2023, 13(1), 96; https://doi.org/10.3390/ani13010096 - 27 Dec 2022

Cited by 11 | Viewed by 2554

Abstract

The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea. Full article

(This article belongs to the Special Issue Integrative Omics Technologies and Machine Learning Approaches in Animal Production)

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8 pages, 1383 KiB

Open AccessBrief Report

Direct Chromosome Preparation Method in Avian Embryos for Cytogenetic Studies: Quick, Easy and Cheap

by Suziane Alves Barcellos, Marcelo Santos de Souza, Victoria Tura, Larissa Rodrigues Pereira, Rafael Kretschmer, Ricardo José Gunski and Analía Del Valle Garnero

DNA 2022, 2(1), 22-29; https://doi.org/10.3390/dna2010002 - 26 Jan 2022

Cited by 4 | Viewed by 6530

Abstract

Avian cell culture is widely applied for cytogenetic studies, the improvement of which increasingly allows for the production of high-quality chromosomes, essential to perform both classical and molecular cytogenetic studies. Among these approaches, there are two main types: fibroblast and bone marrow culture. Despite its high cost and complexity, fibroblast culture is considered the superior approach due to the quality of the metaphases produced. Short-term bone marrow cultivation provides more condensed chromosomes but nonetheless is quicker and easier. In the search for a quicker, cheaper way to prepare metaphases without losing quality, the present work developed a novel, widely applicable protocol for avian chromosome preparation. Twenty-one bird embryos from distinct families were sampled: Icteridae, Columbidae, Furnariidae, Estrildidae, Thraupidae, Troglodytidae and Ardeidae. The protocol was based on a combination of modified fibroblast culture and bone marrow cultivation, taking the advantages of both. The results show that all species consistently presented good mitotic indexes and high-quality chromosomes. Overall, the application of this protocol for bird cytogenetics can optimize the time, considering that most fibroblast cultures take at least 3 days and often much longer. However, our protocol can be performed in 3 h with a much-reduced cost of reagents and equipment. Full article

(This article belongs to the Special Issue Selected Papers from the Joint Meeting of the 23rd International Chromosome Conference (ICC) and the 24th International Colloquium in Animal Cytogenetics and Genomics (ICACG))

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