Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas

Chiou, Kenneth L; Janiak, Mareike C.; Schneider‐Crease, India; Sen, Sharmi; Ayele, Ferehiwot; Chuma, Idrissa S.; Knauf, Sascha; Lemma, Alemayehu; Signore, Anthony V.; D’Ippolito, Anthony; Abebe, Belayneh; Haile, Abebaw Azanaw; Kebede, Fanuel; Fashing, Peter J.; Nguyen, Nga; McCann, Colleen; Houck, Marlys L.; Wall, Jeffrey D.; Burrell, Andrew S.; Bergey, Christina M.; Rogers, Jeffrey; Phillips‐Conroy, Jane E.; Jolly, Clifford J.; Melin, Amanda D.; Storz, Jay F.; Lu, Amy; Beehner, Jacinta C.; Bergman, Thore J.; Snyder‐Mackler, Noah

doi:10.1038/s41559-022-01703-4

Cited by 25 publications

(13 citation statements)

References 160 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Likewise, we found that signatures under positive selection in the coding regions were more related to energy metabolism and development, consistent with the results of previous studies of highland humans, mammals, birds, amphibians and reptiles(Qu et al, 2013;Sun et al, 2018;Witt & Huerta-Sánchez, 2019). By contrast, the accelerated evolution of noncoding regions may contribute to the regulation of nervous system development in giving rise to high-altitude adaptation, in agreement with findings documented in high-altitude geladas(Chiou et al, 2022). The strong contrast between coding and noncoding changes observed in both humans and birds may suggest a potentially universal pattern in adaptive evolution.…”

supporting

confidence: 92%

Divergent contributions of coding and noncoding sequences to initial high‐altitude adaptation in passerine birds endemic to the Qinghai–Tibet Plateau

et al. 2023

View full text Add to dashboard Cite

Early events in the evolution of an ancestral lineage can shape the adaptive patterns of descendant species, but the evolutionary mechanisms driving initial adaptation from an ancestor remain largely unexplored. High‐altitude adaptations have been extensively explored from the viewpoint of protein‐coding genes; however, the contribution of noncoding regions remains relatively neglected. Here, we integrate genomic and transcriptomic data to investigate adaptive evolution in the ancestor of three high‐altitude snowfinch species endemic to the Qinghai–Tibet Plateau. Our genome‐wide scan for adaptation in the snowfinch ancestor identifies strong adaptation signals in functions of development and metabolism for the coding genes, but in functions of the nervous system development for noncoding regions. This pattern is exclusive to the snowfinch ancestor compared to a control ancestral lineage subject to weak selection. Changes in noncoding regions in the snowfinch ancestor, especially those nearest to coding genes, may be disproportionately associated with the differential expression of genes in the brain tissue compared to other tissues. Extensive gene expression in the brain tissue can be further altered via genetic regulatory networks of transcription factors harbouring potential accelerated regulatory regions (e.g., the development‐related transcription factor YEATS4). Altogether, our study provides new evidence concerning how coding and noncoding sequences work through decoupled pathways in initial adaptation to the selective pressure of high‐altitude environments. The analysis highlights the idea that noncoding sequences may be promising elements in facilitating the rapid evolution and adaptation to high altitudes.

show abstract

supporting

confidence: 92%

Divergent contributions of coding and noncoding sequences to initial high‐altitude adaptation in passerine birds endemic to the Qinghai–Tibet Plateau

et al. 2023

View full text Add to dashboard Cite

show abstract

“…We used the 49 markers to build a phylogenetic tree, as done for the Papio screening dataset. T. gelada Y-STRs haplotypes clustered in two groups, corresponding to two demes of origin (Northern and Central), zoo samples clustered with the Central population, as per their genome 32 (Fig. 4 A).…”

Section: Resultsmentioning

confidence: 92%

“…We also analyzed the Theropithecus gelada genome dataset released by Ref. 32 which comprised a total of 68 genomes (35 males and 33 females), ranging in coverage between 1.3X and 47.5X (mean = 14.4X ± 10.7X, Tab. S1 ).…”

Section: Methodsmentioning

confidence: 99%

Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Mutti,

Oteo-Garcia,

Caldon

et al. 2023

Sci Rep

View full text Add to dashboard Cite

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.

show abstract

“…This feature allows them to live and reproduce themselves in high-altitude areas, soil and other environments with a low oxygen concentration. Species with known resistance to hypoxia include Ailurus fulgens HR [ 32 ], Bos mutus grunniens HR [ 33 ], Canis lupus chanco HR [ 34 ], Capra caucasica caucasica HR , Capra nubiana HR [ 35 ], Cavia porcellus HR [ 36 ], Chinchilla lanigera HR [ 37 ], Colobus guereza HR [ 38 ], Ctenomys rionegrensis HR [ 39 , 40 ], Heterocephalus glaber HR [ 6 ], Lama guanicoe HR [ 41 ], Marmota flaviventris HR [ 42 ], Ochotona curzoniae HR [ 43 ], Pantholops hodgsonii HR [ 35 ], Peromyscus maniculatus HR [ 44 ], Procavia capensis habessinica HR [ 45 ], Rhinopithecus roxellana HR [ 46 ], Spalacopus cyanus HR [ 39 , 40 ], Spalax ehrenbergi HR [ 8 ], Talpa europaea HR [ 47 ], Tamias umbrinus HR [ 48 ], Theropithecus gelada HR [ 49 ], Ursus thibetanus HR [ 50 ] and Vicugna pacos HR [ 51 ]. We selected all hemoglobin sequences of these species from the Uniprot database ( , accessed on 20 August 2023).…”

Section: Methodsmentioning

confidence: 99%

Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species

Anashkina,

Simonenko,

Orlov

et al. 2023

IJMS

View full text Add to dashboard Cite

Intracellular tripeptide glutathione is an important agent of cell survival under hypoxia. Glutathione covalently binds to SH groups of hemoglobin cysteine residues, protecting them from irreversible oxidation, and changes its affinity to oxygen. Reduced glutathione (GSH) can also form a noncovalent complex with hemoglobin. Previously, we showed that hemoglobin tetramer has four noncovalent binding sites of glutathione GSH molecules inside, two of which are released during hemoglobin transition to deoxy form. In this study, we characterized the conserved cysteine residues and residues of noncovalent glutathione binding sites in the sequences of a number of hypoxia-tolerant and hypoxia-sensitive mammals. The solvent accessibility of all HbA and HbB residues in oxy and deoxy forms was analyzed. The alpha subunit of all species considered was shown to have no conserved cysteines, whereas the beta subunit contains Cys93 residue, which is conserved across species and whose glutathionylation changes the affinity of hemoglobin for oxygen 5–6-fold. It was found that the key residues of noncovalent glutathione binding sites in both alpha and beta subunits are absolutely conserved in all species considered, suggesting a common mechanism of hemoglobin redox regulation for both hypoxia-sensitive and hypoxia-tolerant mammals.

show abstract

Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas

Cited by 25 publications

References 160 publications

Divergent contributions of coding and noncoding sequences to initial high‐altitude adaptation in passerine birds endemic to the Qinghai–Tibet Plateau

Divergent contributions of coding and noncoding sequences to initial high‐altitude adaptation in passerine birds endemic to the Qinghai–Tibet Plateau

Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Glutathione Non-Covalent Binding Sites on Hemoglobin and Major Glutathionylation Target betaCys93 Are Conservative among Both Hypoxia-Sensitive and Hypoxia-Tolerant Mammal Species

Contact Info

Product

Resources

About