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| Open AccessMutation characteristics and molecular evolution of ovarian metastasis from gastric cancer and potential biomarkers for paclitaxel treatment
‘Gastric cancer metastasis to the ovary is difficult to treat and is not fully understood. Here, the authors characterized mutations in a cohort of matched primary and metastatic disease, and found mutations, including in CLDN18, could predict treatment response to paclitaxel.
- Pengfei Yu
- , Can Hu
- & Xiangdong Cheng
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Article
| Open AccessPositive selection in the genomes of two Papua New Guinean populations at distinct altitude levels
This study explores selection signals of Papua New Guinean highlanders and lowlanders using 128 new whole genome sequences. It highlights two genetic variants associated with blood traits that also influence the heart rate of these populations.
- Mathilde André
- , Nicolas Brucato
- & François-Xavier Ricaut
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Article
| Open AccessEmergence of enhancers at late DNA replicating regions
Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.
- Paola Cornejo-Páramo
- , Veronika Petrova
- & Emily S. Wong
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Article
| Open AccessA genomic basis of vocal rhythm in birds
Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.
- Matteo Sebastianelli
- , Sifiso M. Lukhele
- & Alexander N. G. Kirschel
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Matters Arising
| Open AccessReply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Chase W. Nelson
- , Leo L. M. Poon
- & Haogao Gu
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Matters Arising
| Open AccessPopulation genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Vivak Soni
- , John W. Terbot II
- & Jeffrey D. Jensen
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Article
| Open AccessIntrogression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
The evolutionary genetics of a keystone savannah species the blue wildebeest, and the related black wildebeest, remain largely unexplored. This study finds evidence for archaic introgression of black wildebeest to blue wildebeest and detrimental effects of human activities on migratory populations.
- Xiaodong Liu
- , Long Lin
- & Rasmus Heller
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Article
| Open AccessEvolution of T cells in the cancer-resistant naked mole-rat
Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.
- Tzuhua D. Lin
- , Nimrod D. Rubinstein
- & Rochelle Buffenstein
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Article
| Open AccessAdaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events
Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.
- Guangji Chen
- , Dan Yu
- & Shaohong Feng
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Article
| Open AccessA chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.
- Yixue Bao
- , Qing Zhang
- & Muqing Zhang
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Article
| Open AccessNaked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles
The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.
- Chris G. Faulkes
- , Thomas R. Eykyn
- & Dunja Aksentijevic
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Article
| Open AccessMacroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.
- Mirjana Domazet-Lošo
- , Tin Široki
- & Tomislav Domazet-Lošo
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Article
| Open AccessThe Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.
- Leonardo Vallini
- , Carlo Zampieri
- & Luca Pagani
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Article
| Open AccessDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open AccessClearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- , Catherine Riou
- & Alex Sigal
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Article
| Open AccessInter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection closely related to Streptococcus pyogenes. Here the authors investigate the degree of genomic similarity between the two species and assess implications for development of vaccines.
- Ouli Xie
- , Jacqueline M. Morris
- & Mark R. Davies
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Article
| Open AccessDependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos et al show that the virulence of Mycobacterium tuberculosis is dependent on sufficient uptake of exogenous vitamin B12 from host serum and this phenotype is not conserved in environmental, opportunistic and ancestral lineages.
- Elena Campos-Pardos
- , Santiago Uranga
- & Jesús Gonzalo-Asensio
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Article
| Open AccessThe evolutionary impact of childhood cancer on the human gene pool
Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.
- Ulrik Kristoffer Stoltze
- , Jon Foss-Skiftesvik
- & Kjeld Schmiegelow
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Article
| Open AccessDipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests
Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.
- Rong Wang
- , Chao-Nan Liu
- & Xiao-Yong Chen
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Article
| Open AccessEvolution and expression patterns of the neo-sex chromosomes of the crested ibis
The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.
- Lulu Xu
- , Yandong Ren
- & Gang Li
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Article
| Open AccessGenomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.
- Xiao Feng
- , Qipian Chen
- & Ziwen He
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Article
| Open AccessPorous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.
- Lin-Feng Li
- , Tonapha Pusadee
- & Kenneth M. Olsen
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Article
| Open AccessRecurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida
Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.
- Huang Li
- , Soujanya Akella
- & Jeffrey P. Mower
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Article
| Open AccessExperimental evidence for cancer resistance in a bat species
Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.
- Rong Hua
- , Yuan-Shuo Ma
- & Zhen Liu
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Article
| Open AccessDiversity and evolution of the vertebrate chemoreceptor gene repertoire
Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.
- Maxime Policarpo
- , Maude W. Baldwin
- & Walter Salzburger
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Article
| Open AccessThe dynamic genetic determinants of increased transcriptional divergence in spermatids
Here the authors show that genetic changes between species often alter gene expression in a cell type-specific manner. Most of this variability is driven by locally functioning cis-acting variation, and this contributes to the speed at which cell types accumulate expression changes.
- Jasper Panten
- , Tobias Heinen
- & Duncan T. Odom
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Article
| Open AccessHost association and intracellularity evolved multiple times independently in the Rickettsiales
Rickettsiales encompass diverse host-associated bacteria, including pathogens, parasites, and mutualists. This study shows that obligate associations with their hosts likely evolved multiple times independently, thus providing an alternative, generalisable view, on evolution of intracellularity.
- Michele Castelli
- , Tiago Nardi
- & Davide Sassera
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Article
| Open AccessEvolution of chemosensory tissues and cells across ecologically diverse Drosophilids
Chemosensory tissues are remarkably variable between species but the cause of this diversity is unclear. Here, the authors conduct transcriptomic analyses of chemosensory tissues from diverse Drosophila species, revealing evidence of stabilizing selection and recent species- and sex-specific changes.
- Gwénaëlle Bontonou
- , Bastien Saint-Leandre
- & J. Roman Arguello
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Article
| Open AccessUnzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Telomeres protect the extremities of linear chromosomes and are involved in ageing, senescence and genome stability. Here, the authors have identified peculiar and specific telomeric DNA repeats in the genomes of devastating plant-parasitic nematodes, opening new perspectives for their control.
- Ana Paula Zotta Mota
- , Georgios D. Koutsovoulos
- & Etienne G. J. Danchin
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Article
| Open AccessContScout: sensitive detection and removal of contamination from annotated genomes
It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.
- Balázs Bálint
- , Zsolt Merényi
- & László G. Nagy
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Article
| Open AccessConserved chromatin and repetitive patterns reveal slow genome evolution in frogs
Frogs are an ancient and ecologically diverse group of amphibians that include important model systems. This paper reports genome sequences of multiple frog species, revealing remarkable stability of frog chromosomes and centromeres, along with highly recombinogenic extended subtelomeres.
- Jessen V. Bredeson
- , Austin B. Mudd
- & Daniel S. Rokhsar
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Article
| Open AccessIntegrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas
Frugivory evolved multiple times in mammals, including bats. Here, the authors use integrative single-cell sequencing on fruit and insect bat kidneys and pancreases and identify cell population, gene expression and regulatory differences associated with frugivory that also relate to diabetes.
- Wei E. Gordon
- , Seungbyn Baek
- & Nadav Ahituv
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Article
| Open AccessAfrican bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival
The evolutionary history of pigs in Africa is unclear. Here, the authors examine 67 whole genomes, finding incomplete speciation between bushpigs and red river hogs as well as evidence suggesting that humans brought bushpigs to Madagascar 1000-5000 years ago.
- Renzo F. Balboa
- , Laura D. Bertola
- & Rasmus Heller
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Article
| Open AccessGene regulation and speciation in a migratory divide between songbirds
Little is known about the genetic basis of many natural behaviours and how they contribute to speciation. Here the authors address this by identifying genes linked to migration of a songbird, investigating how these gene are regulated, and connecting them to potential barriers between species.
- Matthew I. M. Louder
- , Hannah Justen
- & Kira E. Delmore
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Article
| Open AccessGenomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand
Large log coffins placed on stilts in natural caves characterize the Iron Age of northwestern Thailand. Here, the authors conduct archaeogenetic analyses of 33 individuals, identifying a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual.
- Selina Carlhoff
- , Wibhu Kutanan
- & Johannes Krause
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Article
| Open AccessMultiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family
Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.
- Jiao Yang
- , Ying Wu
- & Jianquan Liu
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Article
| Open AccessDiversity and dissemination of viruses in pathogenic protozoa
Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.
- Senne Heeren
- , Ilse Maes
- & Frederik Van den Broeck
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Article
| Open AccessUbiquitination-mediated Golgi-to-endosome sorting determines the toxin-antidote duality of fission yeast wtf meiotic drivers
Meiotic drivers of the wtf family kill progeny lacking the driver by producing a toxin and an antidote. Here, authors reveal that ubiquitination-mediated sorting of the antidote prevents it from becoming toxic and enables it to neutralize the toxin.
- Jin-Xin Zheng
- , Tong-Yang Du
- & Li-Lin Du
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Article
| Open AccessTopological structures and syntenic conservation in sea anemone genomes
Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.
- Bob Zimmermann
- , Juan D. Montenegro
- & Ulrich Technau
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Article
| Open AccessDispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.
- Youjie Zhao
- , Chengyong Su
- & Jiasheng Hao
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Article
| Open AccessTAD evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function
The authors show that the deletion of ultraconserved TAD boundaries affects gene expression and phenotype, highlighting TAD evolution’s function. Human-specific TAD boundaries reveal a role in brain development and disease.
- Mariam Okhovat
- , Jake VanCampen
- & Lucia Carbone
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Article
| Open AccessEvolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle
Hyaluronic acid is believed to plays a critical role in cancer resistance and longevity of the naked mole rat. Here, Zhao and colleagues show that accumulation of high levels of hyaluronic acid has co-evolved repeatedly in mammalian clades with adaptation to subterranean habitats.
- Yang Zhao
- , Zhizhong Zheng
- & Vera Gorbunova
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Article
| Open AccessDominance in self-compatibility between subgenomes of allopolyploid Arabidopsis kamchatica shown by transgenic restoration of self-incompatibility
Self-incompatibility in diploid Arabidopsis relatives is determined by a dominance relationship that is epigenetically regulated. Using transgenic methods, this study demonstrates that the dominance relationship between subgenomes of the allopolyploid species Arabidopsis kamchatica underlies it’s self-compatibility.
- Chow-Lih Yew
- , Takashi Tsuchimatsu
- & Kentaro K. Shimizu
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Article
| Open AccessGlobal genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle make up half of all cattle populations worldwide. Using a large genomic dataset, this study finds historic migrations and extensive introgression with domestic and wild bovine species has facilitated this species physiological adaptation to extreme environments.
- Ningbo Chen
- , Xiaoting Xia
- & Chuzhao Lei
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Article
| Open AccessAncient diversity in host-parasite interaction genes in a model parasitic nematode
Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.
- Lewis Stevens
- , Isaac Martínez-Ugalde
- & Mark Blaxter
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Article
| Open AccessHorizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes
Bdelloid rotifers can withstand a wide range of genotoxic stresses. Here the authors reveal that a DNA ligase of bacterial origin was acquired by horizontal gene transfer to confer high resistance to ionizing radiation in bdelloid rotifers and other organisms known for their extreme tolerance to stress.
- Emilien Nicolas
- , Paul Simion
- & Karine Van Doninck
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Article
| Open AccessA smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex
The Mycobacterium tuberculosis complex (MTBC) includes several pathogens thought to have originated in East Africa from an ancestor closely related to Mycobacterium canettii. Here, the authors describe a clinical tuberculosis strain isolated in Ethiopia that has typical M. canettii features but is phylogenetically much closer to the MTBC clade, supporting that the emergence of MTBC pathogens is a recent evolutionary event.
- Bazezew Yenew
- , Arash Ghodousi
- & Daniela Maria Cirillo
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Article
| Open AccessCopy number variation of the restorer Rf4 underlies human selection of three-line hybrid rice breeding
Ctyoplasmic male sterility gene WA352 and its fertility restorer Rf4 are widely used for commercial three-line hybrid rice production. Here, the authors investigate the origin, evolution, and variation of Rf4, and show that copy number variation of Rf4 contributes of fertility restoration in a dosage-dependent manner.
- Zhe Zhao
- , Zhi Ding
- & Letian Chen
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Article
| Open AccessEvolution of a ZW sex chromosome system in willows
Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y.
- Nan Hu
- , Brian J. Sanderson
- & Matthew S. Olson