Phylogeny and historical biogeography of the swallow family (Hirundinidae) inferred from comparisons of thousands of UCE loci

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 197, P. 108111 - 108111

Published: May 25, 2024

Language: Английский

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Philippine herpetology (Amphibia, Reptilia), 20 years on: two decades of progress towards an increasingly collaborative, equitable, and inclusive approach to the study of the archipelago’s amphibians and reptiles

ZooKeys, Journal Year: 2024, Volume and Issue: 1190, P. 213 - 257

Published: Jan. 30, 2024

A first review of the history, status, and prospects for Philippine herpetology conducted more than two decades ago (2002) summarized diverse topics studied highlighted development achievements in research up to year 2000. This study revisits re-assesses what has accomplished, both as a discipline community, during last (2002–2022). total 423 herpetological publications was collated, revealing substantial increase annual publications, rising from approximately four per 2002–2008 around 28 2009–2022. Half published studies focused on squamate reptiles (lizards 30.5%, snakes 21%) 28.4% amphibians, 5.9% turtles, 2.6% crocodiles. The remaining 11.6% simultaneously multiple taxa (i.e., faunal inventories). Diversity distribution (35.2%) ecological (26.5%) remained popular, while taxonomy (14.9%), phylogenetics biogeography (11.8%), conservation (11.6%) all increased. However, geographical gaps persist urging immediate surveys many understudied regions country. Finally, we found balanced representation between Filipino foreign authors (1.0:1.1), yet gender gap exists male female (7.1:1.0). Nonetheless, steep diversity people engaged is remarkable positive finding compared 20 years preceding (1980–2000). Our hope that next will bring increasingly equitable, internationally collaborative, broadly inclusive engagement amphibians Philippines.

Language: Английский

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The Genomics Revolution Drives a New Era in Entomology

Annual Review of Entomology, Journal Year: 2025, Volume and Issue: 70(1), P. 379 - 400

Published: Jan. 28, 2025

Thanks to the fast development of sequencing techniques and bioinformatics tools, genome an insect species for specific research purposes has become increasingly popular practice. Insect genomes not only provide sets gene sequences but also represent a change in focus from reductionism systemic biology field entomology. Using genomes, researchers are able identify study functions all members family, pathway, or network associated with trait interest. Comparative genomics studies new insights into evolution, addressing long-lasting controversies taxonomy. It is now feasible uncover genetic basis important traits by identifying variants using resequencing data individual insects, followed genome-wide association analysis. Here, we review current progress projects application uncovering phylogenetic relationships between insects unraveling mechanisms life-history traits. We summarize challenges sharing possible solutions. Finally, guidance fully deeply mining data.

Language: Английский

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Genome-wide markers test the status of two putative species of North American bumble bees

Conservation Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 13, 2025

Language: Английский

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Phylogenomics of Bivalvia Using Ultraconserved Elements (UCEs) Reveal New Topologies for Pteriomorphia and Imparidentia

Systematic Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 16, 2024

Despite significant advances in phylogenetics over the past decades, deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes phylogeny of Bivalvia. Advances been made recently using transcriptome data, but phylogenetic historically lacked consensus, especially Pteriomorphia and Imparidentia. Here, we inferred lineages matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources 85 newly sequenced specimens 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average 849 UCEs 1085-bp mean length vitro experiments. results introduced novel schemes six major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata Imparidentia), though some inner were poorly resolved, such as paraphyletic Heterodonta topologies potentially due insufficient taxon sampling. The resolution increased when analyzing specific We recovered three different previously published trees, strongest support ((Ostreida + (Arcida Mytilida)) (Pectinida (Limida Pectinida))). Limida nested Pectinida, warranting further studies. For Imparidentia, our strongly supported hypothesis (Galeommatida (Adapedonta Cardiida)), while possible non-monophyly Lucinida was supported. Overall, provide important insights into show that enrichment can be broadly applied study both shallow relationships.

Language: Английский

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Genetic Diversity, Runs of Homozygosity, and Selection Signatures in Native Japanese Chickens: Insights from Single-Nucleotide Polymorphisms

Animals, Journal Year: 2024, Volume and Issue: 14(22), P. 3341 - 3341

Published: Nov. 20, 2024

Understanding genetic diversity, runs of homozygosity (ROH), and selection signatures is critical for the conservation breeding management native Japanese chickens. In this study, ROH, in 11 populations seven breeds three foreign with different behavioral backgrounds were investigated using 11,493 SNPs identified through restriction-site-associated DNA sequencing. The Oh-Shamo (OSM), an aggressive cockfighting breed, exhibited highest diversity. Six breeds, Ingie (IG), Ryujin-Jidori (RYU), Tosa-Jidori (TJI), Tosa-Kukin (TKU), Nagoya (NAG), Ukkokei (UK), showed intermediate levels diversity ROH. Population analyses grouped into four distinct clusters: (1) five comprising (the Fayoumi inbred line, closed-colony G line White Leghorn, commercial T WL, Plymouth Rock) IG breed; (2) OSM two old Jidori (RYU TJI); (3) TKU UK; (4) meat-type breed. ROH Fst on chromosomes 13, 17, 20, 24, 26, which candidate variants fear-related behavior. These findings provide insights conserved genomic segments valuable chicken breeds.

Language: Английский

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Lacewing‐specific Universal Single Copy Orthologs designed towards resolution of backbone phylogeny of Neuropterida

Systematic Entomology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

Abstract Universal Single Copy Orthologs (USCOs), as a set of markers nearly universal single‐copy genes, show superiority in phylogenomic inference. Here, we developed Benchmarking (BUSCOs) dataset, neuropterida_odb10, tailored for Neuropterida, based on high‐quality genome assemblies and transcriptome data, comprising 5438 BUSCOs. A range 1524–5328 complete USCOs could be captured from the transcriptomes 104 species Neuropterida. The reconstruction higher‐level phylogeny Neuropterida comprehensive sampling refined genomic data reference to neuropterida_odb10 validates efficiency this BUSCO dataset We recovered Psychopsidae sister group Ithonidae, corroborated relationship between Sisyridae Nevrorthidae within Osmyloidea Chrysopidae Mantispoidea. Furthermore, our findings highlight that focusing alignments with higher presence parsimony‐informative sites, rather than total number alignments, can diminish errors gene tree estimation, process notably vulnerable error when using multispecies coalescent methods. holds promise phylogenetic studies at various hierarchical levels, well comparative genomics exploration diversity

Language: Английский

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A phylogenomic tree of wood-warblers (Aves: Parulidae): Dealing with good, bad, and ugly samples

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 202, P. 108235 - 108235

Published: Nov. 13, 2024

Language: Английский

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Phylogenomic analysis and molecular identification of true fruit flies

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: June 21, 2024

The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, phylogenetic relationships of remain controversial. Moreover, rapid identification invasive flies is essential for plant quarantine but still challenging. To this end, we sequenced genome 16 fly species at coverage 47-228×. Together with previously reported genomes nine species, reconstructed trees using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. resulting 50% taxon-occupancy dataset each marker type were generally congruent 88% nodes both concatenation coalescent analyses. At subfamily level, Dacinae Trypetinae monophyletic.

Language: Английский

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The Functional Map of Ultraconserved Regions in Humans, Mice and Rats

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 28, 2024

BACKGROUND: Ultraconserved regions (UCRs) encompass 481 DNA segments exceeding 200 base pairs (bp), displaying 100% sequence identity across humans, mice, and rats, indicating profound conservation taxa pivotal functional roles in human health disease. Despite two decades since their discovery, many UCRs remain to be explored owing incomplete annotation, particularly of newly identified long non-coding RNAs (lncRNAs), limited data aggregation large-scale databases. This study offers a comprehensive map UCRs, investigating genomic transcriptomic implications: (i) enriching UCR annotation data, including ancestral genomes; (ii) exploring lncRNAs containing T-UCRs pan-cancers; (iii) elucidating involvement regulatory elements; (iv) analyzing population single-nucleotide variations linked motifs, expression patterns, diseases. RESULTS: Our results indicate that, although high number protein-coding transcripts with (1,945 from 2,303), 1,775 contained outside CDS regions. Focusing on transcripts, 355 are mapped 85 lncRNA genes, 35 them differentially expressed at least one TCGA cancer type, seven strongly associated survival time, 23 according single-cell analysis. Additionally, we elements 373 (77.5%), found 353 SNP-UCRs (with 1% frequency) potential effects, such as motif changes, eQTL potential, associations disease/traits. Finally, 4 novel that had not been previously described. CONCLUSION: report compiles organizes all the above information, providing new insights into mechanisms diagnostic applications.

Language: Английский

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