Eighty million years of rapid evolution of the primate Y chromosome

The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary trajectories. Here we generated 19 new primate sex chromosome assemblies, analysed them with 10 existing assemblies and report rapid evolution of the Y chromosome across primates. The pseudoautosomal boundary has shifted at least six times during primate evolution, leading to the formation of a Simiiformes-specific evolutionary stratum and to the independent start of young strata in Catarrhini and Platyrrhini. Different primate lineages experienced different rates of gene loss and structural and chromatin change on their Y chromosomes. Selection on several Y-linked genes has contributed to the evolution of male developmental traits across the primates. Additionally, lineage-specific expansions of ampliconic regions have further increased the diversification of the structure and gene composition of the Y chromosome. Overall, our comprehensive analysis has broadened our knowledge of the evolution of the primate Y chromosome.This study was supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31020000 to G.Z.), International Partnership Program of Chinese Academy of Sciences (no. 152453KYSB20170002 to G.Z.), Villum Investigator Grant (no. 25900 to G.Z.), National Natural Science Foundation of China (31822048 to D.-D.W.), Yunnan Fundamental Research Project (2019FI010 to D.-D.W.) and The Animal Branch of the Germplasm Bank of Wild Species of Chinese Academy of Science (the Large Research Infrastructure Funding to D.-D.W.).N

High-coverage genomes to elucidate the evolution of penguins

Background: Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes. Results: Here we present a novel dataset of 19 high-coverage genomes that, together with 2 previously published genomes, encompass all extant penguin species. We also present a well-supported phylogeny to clarify the relationships among penguins. In contrast to recent studies, our results demonstrate that the genus Aptenodytes is basal and sister to all other extant penguin genera, providing intriguing new insights into the adaptation of penguins to Antarctica. As such, our dataset provides a novel resource for understanding the evolutionary history of penguins as a clade, as well as the fine-scale relationships of individual penguin lineages. Against this background, we introduce a major consortium of international scientists dedicated to studying these genomes. Moreover, we highlight emerging issues regarding ensuring legal and respectful indigenous consultation, particularly for genomic data originating from New Zealand Taonga species. Conclusions: We believe that our dataset and project will be important for understanding evolution, increasing cultural heritage and guiding the conservation of this iconic southern hemisphere species assemblage.Fil: Pan, Hailin. Bgi-shenzhen; ChinaFil: Cole, Theresa L. University Of Otago; CanadáFil: Bi, Xupeng. Bgi-shenzhen; ChinaFil: Fang, Miaoquan. Bgi-shenzhen; ChinaFil: Zhou, Chengran. Bgi-shenzhen; ChinaFil: Yang, Zhengtao. Bgi-shenzhen; ChinaFil: Ksepka, Daniel T. Bruce Museum; Estados UnidosFil: Hart, Tom. University of Oxford; Reino UnidoFil: Bouzat, Juan L.. Bowling Green State University; Estados UnidosFil: Boersma, P. Dee. University of Washington; Estados UnidosFil: Bost, Charles-André. Centre Detudes Biologiques de Chizé; FranciaFil: Cherel, Yves. Centre Detudes Biologiques de Chizé; FranciaFil: Dann, Peter. Phillip Island Nature Parks; AustraliaFil: Mattern, Thomas. University of Otago; Nueva ZelandaFil: Ellenberg, Ursula. Global Penguin Society; Estados Unidos. La Trobe University; AustraliaFil: Garcia Borboroglu, Jorge Pablo. University of Washington; Estados Unidos. Global Penguin Society; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Argilla, Lisa S.. Otago Polytechnic; Nueva ZelandaFil: Bertelsen, Mads F.. Copenhagen Zoo; Dinamarca. University of Copenhagen; DinamarcaFil: Fiddaman, Steven R.. University of Oxford; Reino UnidoFil: Howard, Pauline. Hornby Veterinary Centre; Nueva Zelanda. South Island Wildlife Hospital; Nueva ZelandaFil: Labuschagne, Kim. National Zoological Garden; SudáfricaFil: Miller, Gary. University of Western Australia; Australia. University of Tasmania; AustraliaFil: Parker, Patricia. University of Missouri St. Louis; Estados UnidosFil: Phillips, Richard A.. Natural Environment Research Council; Reino UnidoFil: Quillfeldt, Petra. Justus-Liebig-Universit ̈ at Giessen; AlemaniaFil: Ryan, Peter G.. University of Cape Town; SudáfricaFil: Taylor, Helen. Vet Services Hawkes Bay Ltd; Nueva Zelanda. Wairoa Farm Vets; Nueva ZelandaFil: Zhang, De-Xing. Chinese Academy of Sciences; República de ChinaFil: Zhang, Guojie. BGI-Shenzhen; China. Chinese Academy of Sciences; República de China. University of Copenhagen; DinamarcaFil: McKinlay, Bruce. Department of Conservation; Nueva Zeland

High-coverage genomes to elucidate the evolution of penguins

Penguins (Sphenisciformes) are a remarkable order of flightless wing-propelled diving seabirds distributed widely across the southern hemisphere. They share a volant common ancestor with Procellariiformes close to the Cretaceous-Paleogene boundary (66 million years ago) and subsequently lost the ability to fly but enhanced their diving capabilities. With ∼20 species among 6 genera, penguins range from the tropical Galápagos Islands to the oceanic temperate forests of New Zealand, the rocky coastlines of the sub-Antarctic islands, and the sea ice around Antarctica. To inhabit such diverse and extreme environments, penguins evolved many physiological and morphological adaptations. However, they are also highly sensitive to climate change. Therefore, penguins provide an exciting target system for understanding the evolutionary processes of speciation, adaptation, and demography. Genomic data are an emerging resource for addressing questions about such processes

Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies

For social animals, the genotypes of group members affect the social environment, and thus individual behavior, often indirectly. We used genome-wide association studies (GWAS) to determine the influence of individual vs. group genotypes on aggression in honey bees. Aggression in honey bees arises from the coordinated actions of colony members, primarily nonreproductive "soldier" bees, and thus, experiences evolutionary selection at the colony level. Here, we show that individual behavior is influenced by colony environment, which in turn, is shaped by allele frequency within colonies. Using a population with a range of aggression, we sequenced individual whole genomes and looked for genotype–behavior associations within colonies in a common environment. There were no significant correlations between individual aggression and specific alleles. By contrast, we found strong correlations between colony aggression and the frequencies of specific alleles within colonies, despite a small number of colonies. Associations at the colony level were highly significant and were very similar among both soldiers and foragers, but they covaried with one another. One strongly significant association peak, containing an ortholog of the Drosophila sensory gene dpr4 on linkage group (chromosome) 7, showed strong signals of both selection and admixture during the evolution of gentleness in a honey bee population. We thus found links between colony genetics and group behavior and also, molecular evidence for group-level selection, acting at the colony level. We conclude that group genetics dominates individual genetics in determining the fatal decision of honey bees to sting.Funding provided by: Office of Extramural Research, National Institutes of HealthCrossref Funder Registry ID: http://dx.doi.org/10.13039/100006955Award Number: R01GM11746

Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors

Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations

Data for "Eighty million years of rapid evolution of the primate Y chromosomes"

This folder contains data for "Eighty million years of rapid evolution of the primate Y chromosome" gene_set.zip contains gene annotation (GFF, CDS, PEP, POS.ADD) for the 30 species used in this study XY_location.zip contains the genomic coordinates for PAR, nonPARX and nonPARY (BED format). Species names are in the 4th column.  gametolog_alignment.tar.gz contains gametolog alignment (PHY format) used to calculate pairwise dN/dS.  S5.tree.zip contains alignment (FASTA format) and constructed phylogeny (NWK format) for each S5 gametologs.  Conserved_Segments.100K.inferCARs contains conserved blocks of the X chromosome across species (inferCARs format) XY_SV.zip contains the sequences used in Y reconstruction analysis (FASTA format), and the recontruction results under 30 Kb resolution (30K/) and 50 Kb resolution (50K/) NLGN4XY.sort.prank.best.fas contains alignment of NLGN4X/Y of each primate trait_selection_analysis.zip contains sequence alignment (FASTA format) of each Y-linked genes used for dN/dS calculation in trait selection analysis. </p

Genomic insights into the secondary aquatic transition of penguins.

Penguins lost the ability to fly more than 60 million years ago, subsequently evolving a hyper-specialized marine body plan. Within the framework of a genome-scale, fossil-inclusive phylogeny, we identify key geological events that shaped penguin diversification and genomic signatures consistent with widespread refugia/recolonization during major climate oscillations. We further identify a suite of genes potentially underpinning adaptations related to thermoregulation, oxygenation, diving, vision, diet, immunity and body size, which might have facilitated their remarkable secondary transition to an aquatic ecology. Our analyses indicate that penguins and their sister group (Procellariiformes) have the lowest evolutionary rates yet detected in birds. Together, these findings help improve our understanding of how penguins have transitioned to the marine environment, successfully colonizing some of the most extreme environments on Earth.This article is published as Cole, T.L., Zhou, C., Fang, M. et al. Genomic insights into the secondary aquatic transition of penguins. Nat Commun 13, 3912 (2022). https://doi.org/10.1038/s41467-022-31508-9. Posted with permission. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/