Peter A. Hosner
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View article: Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life
Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life Open
The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data…
View article: The Earth Hologenome Initiative: Data Release 1
The Earth Hologenome Initiative: Data Release 1 Open
Background The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host–microbiota perspective, through the standardized generation and analysis of…
View article: 2024 AOS Early Professional Awards to Sheela P. Turbek, Jessie L. Williamson, and Gavin M. Jones
2024 AOS Early Professional Awards to Sheela P. Turbek, Jessie L. Williamson, and Gavin M. Jones Open
View article: A global initiative for ecological and evolutionary hologenomics
A global initiative for ecological and evolutionary hologenomics Open
View article: Complexity of avian evolution revealed by family-level genomes
Complexity of avian evolution revealed by family-level genomes Open
View article: Specimen collection is essential for modern science
Specimen collection is essential for modern science Open
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying w…
View article: Changes in the functional diversity of modern bird species over the last million years
Changes in the functional diversity of modern bird species over the last million years Open
Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturban…
View article: Draft genome assemblies of four manakins
Draft genome assemblies of four manakins Open
View article: The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU’s zero pollution ambition
The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU’s zero pollution ambition Open
View article: Species-specific traits mediate avian demographic responses under past climate change
Species-specific traits mediate avian demographic responses under past climate change Open
Anticipating species’ responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking and the tra…
View article: AVONET: morphological, ecological and geographical data for all birds
AVONET: morphological, ecological and geographical data for all birds Open
Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models o…
View article: Cover Image: Volume 25 Number 3, March 2022
Cover Image: Volume 25 Number 3, March 2022 Open
The cover image is based on the Letter AVONET: morphological, ecological and geographical data for all birds by Tobias et al., https://doi.org/10.1111/ele.13898. The sword-billed hummingbird (Ensifera ensifera) is exquisitely adapted to it…
View article: Reconciling GenBank names with standardized avian taxonomies to improve linkage between phylogeny and phenotype
Reconciling GenBank names with standardized avian taxonomies to improve linkage between phylogeny and phenotype Open
Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years h…
View article: one-to-one orthologs
one-to-one orthologs Open
The sheet contains 9653 one-to-one orthologs used in phylogeny inferring, with species name in the first row. We used the Taeniopygia guttata gene sets as the reference and performed a reciprocal best hit (RBH) method to get one-t…
View article: Phylogenetic_tree
Phylogenetic_tree Open
The dataset contains a newick format species tree with RAxML branch lengths and a fasta format file, in which we combinded 9653 alignments into one.
View article: Discordance_trees
Discordance_trees Open
The alternative topologies for six branches. Each file contains three topologies with the relative frequency values.
View article: Diploid_genome_assembly
Diploid_genome_assembly Open
The dataset contains four folders corresponding to four manakins and each folder contains two fasta format files. We used the "style=pseudohap2" in Supernova version 2.0.1 to assemble the two ‘parallel’ pseudohaplotypes in separate FASTA f…
View article: Functional_annotation
Functional_annotation Open
The dataset contains the functional annotation sheets of four manakins. The translated gene coding sequences were aligned to the SwissProt database (release-2020_05). Motifs and domains of each gene was annotated with modules PRINTS, SMART…
View article: Repeat_annotation
Repeat_annotation Open
The dataset contains repeat annotation files of four manakins. We used Tandem Repeat Finder (TRF, v4.09.1) to identify Tandem repeats. We used de novo methods with RepeatModeler (v2.0.2a) and LTR_Finder (v1.07), and homolog-based RepeatMas…
View article: Protein-coding_gene_annotation
Protein-coding_gene_annotation Open
The dataset contains protein coding gene annotation files of four manakins. We used the homolog-based approach to annotate the protein-coding genes by using the protein sequences of Gallus gallus, Taeniopygia guttata and …
View article: Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements Open
View article: Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)
Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae) Open
As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps …
View article: IUCN Red List protects avian genetic diversity
IUCN Red List protects avian genetic diversity Open
Low genetic diversity may be associated with an increase in species' extinction risk (Spielman et al. 2004, Frankham 2005). Still, global conservation assessments do not consider relevant genetic-based estimates for evaluating species thre…
View article: Author Correction: Dense sampling of bird diversity increases power of comparative genomics
Author Correction: Dense sampling of bird diversity increases power of comparative genomics Open
A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.
View article: A novel role for natural science collections in European contaminant monitoring
A novel role for natural science collections in European contaminant monitoring Open
View article: Additional file 4 of Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
Additional file 4 of Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements Open
Additional file 4: Table S1. UCE phylogenomic studies of Galliformes and novel UCEs used in this study.
View article: Dense sampling of bird diversity increases power of comparative genomics
Dense sampling of bird diversity increases power of comparative genomics Open
View article: Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness
Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness Open
Data used in phylogenomic analyses of manakin birds. Datasets number 1 to 7 include sequence alignments for each locus analyzed, and datasets 4 to 7 also contain gene trees used as input for ASTRAL.
View article: Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness
Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness Open
Data used in phylogenomic analyses of manakin birds. Datasets number 1 to 7 include sequence alignments for each locus analyzed, and datasets 4 to 7 also contain gene trees used as input for ASTRAL.
View article: Genomic differentiation in an endemic Philippine genus (Aves:<i>Sarcophanops</i>) owing to geographical isolation on recently disassociated islands
Genomic differentiation in an endemic Philippine genus (Aves:<i>Sarcophanops</i>) owing to geographical isolation on recently disassociated islands Open
Phylogeographical studies of Philippine vertebrates have demonstrated that genetic variation is broadly partitioned by Pleistocene island aggregation. Contemporary island discontinuity is expected to influence genetic differentiation but r…