1
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Wanders K, Chen G, Feng S, Székely T, Urrutia AO. Role-reversed polyandry is associated with faster fast-Z in shorebirds. Proc Biol Sci 2024; 291:20240397. [PMID: 38864333 DOI: 10.1098/rspb.2024.0397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 05/14/2024] [Indexed: 06/13/2024] Open
Abstract
In birds, males are homogametic and carry two copies of the Z chromosome ('ZZ'), while females are heterogametic and exhibit a 'ZW' genotype. The Z chromosome evolves at a faster rate than similarly sized autosomes, a phenomenon termed 'fast-Z evolution'. This is thought to be caused by two independent processes-greater Z chromosome genetic drift owing to a reduced effective population size, and stronger Z chromosome positive selection owing to the exposure of partially recessive alleles to selection. Here, we investigate the relative contributions of these processes by considering the effect of role-reversed polyandry on fast-Z in shorebirds, a paraphyletic group of wading birds that exhibit unusually diverse mating systems. We find stronger fast-Z effects under role-reversed polyandry, which is consistent with particularly strong selection on polyandrous females driving the fixation of recessive beneficial alleles. This result contrasts with previous research in birds, which has tended to implicate a primary role of genetic drift in driving fast-Z variation. We suggest that this discrepancy can be interpreted in two ways-stronger sexual selection acting on polyandrous females overwhelms an otherwise central role of genetic drift, and/or sexual antagonism is also contributing significantly to fast-Z and is exacerbated in sexually dimorphic species.
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Affiliation(s)
- Kees Wanders
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Department of Evolutionary Zoology and Human Biology, HUN-REN-DE Reproductive strategies Research Group, University of Debrecen , Debrecen, Hungary
- Natural History Museum of Denmark, University of Copenhagen , Copenhagen, Denmark
| | - Guangji Chen
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, People's Republic of China
- BGI Research , Wuhan, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing, People's Republic of China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Liangzhu Laboratory, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, People's Republic of China
| | - Tamás Székely
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Department of Evolutionary Zoology and Human Biology, HUN-REN-DE Reproductive strategies Research Group, University of Debrecen , Debrecen, Hungary
- Debrecen Biodiversity Centre, University of Debrecen , Debrecen, Hungary
| | - Arraxi O Urrutia
- Department of Life Sciences, Milner Centre for Evolution, University of Bath , Bath, UK
- Instituto de Ecologia, UNAM , Mexico City, Mexico
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2
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Chen X, Wang Z, Zhang C, Hu J, Lu Y, Zhou H, Mei Y, Cong Y, Guo F, Wang Y, He K, Liu Y, Li F. Unraveling the complex evolutionary history of lepidopteran chromosomes through ancestral chromosome reconstruction and novel chromosome nomenclature. BMC Biol 2023; 21:265. [PMID: 37981687 PMCID: PMC10658929 DOI: 10.1186/s12915-023-01762-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/06/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Lepidoptera is one of the most species-rich animal groups, with substantial karyotype variations among species due to chromosomal rearrangements. Knowledge of the evolutionary patterns of lepidopteran chromosomes still needs to be improved. RESULTS Here, we used chromosome-level genome assemblies of 185 lepidopteran insects to reconstruct an ancestral reference genome and proposed a new chromosome nomenclature. Thus, we renamed over 5000 extant chromosomes with this system, revealing the historical events of chromosomal rearrangements and their features. Additionally, our findings indicate that, compared with autosomes, the Z chromosome in Lepidoptera underwent a fast loss of conserved genes, rapid acquisition of lineage-specific genes, and a low rate of gene duplication. Moreover, we presented evidence that all available 67 W chromosomes originated from a common ancestor chromosome, with four neo-W chromosomes identified, including one generated by fusion with an autosome and three derived through horizontal gene transfer. We also detected nearly 4000 inter-chromosomal gene movement events. Notably, Geminin is transferred from the autosome to the Z chromosome. When located on the autosome, Geminin shows female-biased expression, but on the Z chromosome, it exhibits male-biased expression. This contributes to the sexual dimorphism of body size in silkworms. CONCLUSIONS Our study sheds light on the complex evolutionary history of lepidopteran chromosomes based on ancestral chromosome reconstruction and novel chromosome nomenclature.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zuoqi Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chaowei Zhang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jingheng Hu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yueqi Lu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hang Zhou
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yuyang Cong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fangyuan Guo
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Ying Liu
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province and Agricultural Environment/ Agriculture Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.
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3
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Mrnjavac A, Khudiakova KA, Barton NH, Vicoso B. Slower-X: reduced efficiency of selection in the early stages of X chromosome evolution. Evol Lett 2023; 7:4-12. [PMID: 37065438 PMCID: PMC10091493 DOI: 10.1093/evlett/qrac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 12/17/2022] [Indexed: 02/04/2023] Open
Abstract
Abstract
Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.
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Affiliation(s)
- Andrea Mrnjavac
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Ksenia A Khudiakova
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria , Am Campus 1, 3400 Klosterneuburg , Austria
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4
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Mongue AJ, Hansen ME, Walters JR. Support for faster and more adaptive Z chromosome evolution in two divergent lepidopteran lineages. Evolution 2021; 76:332-345. [PMID: 34463346 PMCID: PMC9291949 DOI: 10.1111/evo.14341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/21/2021] [Accepted: 08/06/2021] [Indexed: 12/14/2022]
Abstract
The rateof divergence for Z or X chromosomes is usually observed to be greater than autosomes, but the proposed evolutionary causes for this pattern vary, as do empirical results from diverse taxa. Even among moths and butterflies (Lepidoptera), which generally share a single-origin Z chromosome, the handful of available studies give mixed support for faster or more adaptive evolution of the Z chromosome, depending on the species assayed. Here, we examine the molecular evolution of Z chromosomes in two additional lepidopteran species: the Carolina sphinx moth and the monarch butterfly, the latter of which possesses a recent chromosomal fusion yielding a segment of newly Z-linked DNA. We find evidence for both faster and more adaptive Z chromosome evolution in both species, although this effect is strongest in the neo-Z portion of the monarch sex chromosome. The neo-Z is less male-biased than expected of a Z chromosome, and unbiased and female-biased genes drive the signal for adaptive evolution here. Together these results suggest that male-biased gene accumulation and haploid selection have opposing effects on long-term rates of adaptation and may help explain the discrepancies in previous findings as well as the repeated evolution of neo-sex chromosomes in Lepidoptera.
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Affiliation(s)
- Andrew J Mongue
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH93FL, United Kingdom
| | - Megan E Hansen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
| | - James R Walters
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, 66045
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5
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Hayes K, Barton HJ, Zeng K. A Study of Faster-Z Evolution in the Great Tit (Parus major). Genome Biol Evol 2021; 12:210-222. [PMID: 32119100 PMCID: PMC7144363 DOI: 10.1093/gbe/evaa044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus major) genome, aiming to detect signals of faster-Z evolution. We find mixed evidence of faster divergence on the Z chromosome than autosomes, with significantly higher divergence being found in ancestral repeats, but not at 4- or 0-fold degenerate sites. Interestingly, some 4-fold sites appear to be selectively constrained, which may mislead analyses that use these sites as the neutral reference (e.g., dN/dS). Consistent with other studies in birds, the mutation rate is significantly higher in males than females, and the long-term Z-to-autosome effective population size ratio is only 0.5, significantly lower than the expected value of 0.75. These are indicative of male-driven evolution and high variance in male reproductive success, respectively. We find no evidence for an increased efficacy of positive selection on the Z chromosome. In contrast, the Z chromosome in great tits appears to be affected by increased genetic drift, which has led to detectable signals of weakened intensity of purifying selection. These results provide further evidence that the Z chromosome often has a low effective population size, and that this has important consequences for its evolution. They also highlight the importance of considering multiple factors that can affect the rate of evolution and effective population sizes of sex chromosomes.
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Affiliation(s)
- Kai Hayes
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom.,Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
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6
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Saccheri IJ, Whiteford S, Yung CJ, Van't Hof AE. Recessive Z-linked lethals and the retention of haplotype diversity in a captive butterfly population. Heredity (Edinb) 2020; 125:28-39. [PMID: 32404940 DOI: 10.1038/s41437-020-0316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 04/23/2020] [Accepted: 04/23/2020] [Indexed: 11/09/2022] Open
Abstract
Sex chromosomes are predicted to harbour elevated levels of sexually antagonistic variation due to asymmetries in the heritability of recessive traits in the homogametic versus heterogametic sex. This evolutionary dynamic may manifest as high recessive load specifically affecting the homogametic sex, and the retention of haplotype diversity in small populations. We tested the hypothesis that the Z chromosome in the butterfly Bicyclus anynana carries a high inbred load for male fertility and viability. Homozygosity of Z chromosome blocks was produced by daughter-father backcrosses, and inferred from marker loci positioned via a linkage map. Male sterility was, in general, unrelated to homozygosity in any region of the Z, but there was an extreme deficit of homozygous males within a 2 cM interval in all families. In contrast, no corresponding skew in Z genotype was detected in their (hemizygous) sisters. The same pattern was observed in historically inbred lines, indicating a high frequency of recessive lethals in the ancestral population. Allele-frequency changes between 1993 and 2006 (70 generations at Ne ~ 160) show that, despite the loss of many haplotypes, diversity was retained significantly above the neutral expectation. Effective overdominance in the lethal region can account for this effect locally but not in other parts of the chromosome, that are also associated with persistent linkage disequilibrium. These unexpected patterns suggest the operation of other factors, such as epistatic selection, recombination suppression, assortative mating and meiotic drive. Our results highlight the role of balancing selection in maintaining the inbred load and linked genetic diversity.
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Affiliation(s)
- Ilik J Saccheri
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Samuel Whiteford
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Carl J Yung
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Arjen E Van't Hof
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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7
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Rousselle M, Simion P, Tilak MK, Figuet E, Nabholz B, Galtier N. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PLoS Genet 2020; 16:e1008668. [PMID: 32251427 PMCID: PMC7162527 DOI: 10.1371/journal.pgen.1008668] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/16/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with species effective population size (Ne) and genetic diversity. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover no significant correlation between ωa and θ at a larger taxonomic scale, suggesting that the proportion of beneficial mutations scales negatively with species' long-term Ne.
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Affiliation(s)
| | - Paul Simion
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEGE, Department of Biology, University of Namur, Namur, Belgium
| | - Marie-Ka Tilak
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emeric Figuet
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Benoit Nabholz
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Galtier
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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8
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Abstract
The faster-X effect, namely the rapid evolution of protein-coding genes on the X chromosome, has been widely reported in metazoans. However, the prevalence of this phenomenon across diverse systems and its potential causes remain largely unresolved. Analysis of sex-biased genes may elucidate its possible mechanisms: for example, in systems with X/Y males a more pronounced faster-X effect in male-biased genes than in female-biased or unbiased genes may suggest fixation of recessive beneficial mutations rather than genetic drift. Further, theory predicts that the faster-X effect should be promoted by X chromosome dosage compensation. Here, we asked whether we could detect a faster-X effect in genes of the beetle Tribolium castaneum (and T. freemani orthologs), which has X/Y sex-determination and heterogametic males. Our comparison of protein sequence divergence (dN/dS) on the X chromosome vs. autosomes indicated a rarely observed absence of a faster-X effect in this organism. Further, analyses of sex-biased gene expression revealed that the X chromosome was particularly highly enriched for ovary-biased genes, which evolved slowly. In addition, an evaluation of male X chromosome dosage compensation in the gonads and in non-gonadal somatic tissues indicated a striking lack of compensation in the testis. This under-expression in testis may limit fixation of recessive beneficial X-linked mutations in genes transcribed in these male sex organs. Taken together, these beetles provide an example of the absence of a faster-X effect on protein evolution in a metazoan, that may result from two plausible factors, strong constraint on abundant X-linked ovary-biased genes and a lack of gonadal dosage compensation.
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9
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Xu L, Wa Sin SY, Grayson P, Edwards SV, Sackton TB. Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds. Genome Biol Evol 2020; 11:2376-2390. [PMID: 31329234 PMCID: PMC6735826 DOI: 10.1093/gbe/evz154] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/20/2022] Open
Abstract
Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.
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Affiliation(s)
- Luohao Xu
- Department of Molecular Evolution and Development, University of Vienna, Austria
| | - Simon Yung Wa Sin
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
- School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
- Museum of Comparative Zoology, Harvard University
| | - Timothy B Sackton
- Informatics Group, Division of Science, Harvard University
- Corresponding author: E-mail:
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10
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Talla V, Soler L, Kawakami T, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species. Genome Biol Evol 2019; 11:2875-2886. [PMID: 31580421 PMCID: PMC6795238 DOI: 10.1093/gbe/evz212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Biology, Biodiversity Unit, Lund University, Sweden
| | - Christer Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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11
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Bechsgaard J, Schou MF, Vanthournout B, Hendrickx F, Knudsen B, Settepani V, Schierup MH, Bilde T. Evidence for Faster X Chromosome Evolution in Spiders. Mol Biol Evol 2019; 36:1281-1293. [PMID: 30912801 PMCID: PMC6526907 DOI: 10.1093/molbev/msz074] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In species with chromosomal sex determination, X chromosomes are predicted to evolve faster than autosomes because of positive selection on recessive alleles or weak purifying selection. We investigated X chromosome evolution in Stegodyphus spiders that differ in mating system, sex ratio, and population dynamics. We assigned scaffolds to X chromosomes and autosomes using a novel method based on flow cytometry of sperm cells and reduced representation sequencing. We estimated coding substitution patterns (dN/dS) in a subsocial outcrossing species (S. africanus) and its social inbreeding and female-biased sister species (S. mimosarum), and found evidence for faster-X evolution in both species. X chromosome-to-autosome diversity (piX/piA) ratios were estimated in multiple populations. The average piX/piA estimates of S. africanus (0.57 [95% CI: 0.55-0.60]) was lower than the neutral expectation of 0.75, consistent with more hitchhiking events on X-linked loci and/or a lower X chromosome mutation rate, and we provide evidence in support of both. The social species S. mimosarum has a significantly higher piX/piA ratio (0.72 [95% CI: 0.65-0.79]) in agreement with its female-biased sex ratio. Stegodyphus mimosarum also have different piX/piA estimates among populations, which we interpret as evidence for recurrent founder events. Simulations show that recurrent founder events are expected to decrease the piX/piA estimates in S. mimosarum, thus underestimating the true effect of female-biased sex ratios. Finally, we found lower synonymous divergence on X chromosomes in both species, and the male-to-female substitution ratio to be higher than 1, indicating a higher mutation rate in males.
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Affiliation(s)
| | - Mads Fristrup Schou
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Department of Biology, Lund University, SE-223 62 Lund, Sweden
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Evolution and Optics of Nanostructure Group (EON), Biology Department, Ghent University, Ghent, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit (TEREC), Biology Department, Ghent University, Ghent, Belgium
| | | | | | - Mikkel Heide Schierup
- Department of Bioscience, Aarhus University, Aarhus C, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
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12
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Galtier N, Roux C, Rousselle M, Romiguier J, Figuet E, Glémin S, Bierne N, Duret L. Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion. Mol Biol Evol 2019; 35:1092-1103. [PMID: 29390090 DOI: 10.1093/molbev/msy015] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied in a handful of model organisms so far, and can be affected by confounding, nonadaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data, we analyzed the relationship between codon usage, gene expression, allele frequency distribution, and recombination rate in 30 nonmodel species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analyzing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons tend to be preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.
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Affiliation(s)
- Nicolas Galtier
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Camille Roux
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,UMR 8198 - Evo-Eco-Paleo, CNRS, Université de Lille-Sciences et Technologies, Villeneuve d'Ascq, France
| | - Marjolaine Rousselle
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Jonathan Romiguier
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emeric Figuet
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sylvain Glémin
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Nicolas Bierne
- UMR5554, Institut des Sciences de l'Evolution, University Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, Villeurbanne, France
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13
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Pinharanda A, Rousselle M, Martin SH, Hanly JJ, Davey JW, Kumar S, Galtier N, Jiggins CD. Sexually dimorphic gene expression and transcriptome evolution provide mixed evidence for a fast-Z effect in Heliconius. J Evol Biol 2019; 32:194-204. [PMID: 30523653 PMCID: PMC6850379 DOI: 10.1111/jeb.13410] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/06/2018] [Accepted: 11/27/2018] [Indexed: 12/30/2022]
Abstract
Sex chromosomes have different evolutionary properties compared to autosomes due to their hemizygous nature. In particular, recessive mutations are more readily exposed to selection, which can lead to faster rates of molecular evolution. Here, we report patterns of gene expression and molecular evolution for a group of butterflies. First, we improve the completeness of the Heliconius melpomene reference annotation, a neotropical butterfly with a ZW sex determination system. Then, we analyse RNA from male and female whole abdomens and sequence female ovary and gut tissue to identify sex‐ and tissue‐specific gene expression profiles in H. melpomene. Using these expression profiles, we compare (a) sequence divergence and polymorphism; (b) the strength of positive and negative selection; and (c) rates of adaptive evolution, for Z and autosomal genes between two species of Heliconius butterflies, H. melpomene and H. erato. We show that the rate of adaptive substitutions is higher for Z than autosomal genes, but contrary to expectation, it is also higher for male‐biased than female‐biased genes. Additionally, we find no significant increase in the rate of adaptive evolution or purifying selection on genes expressed in ovary tissue, a heterogametic‐specific tissue. Our results contribute to a growing body of literature from other ZW systems that also provide mixed evidence for a fast‐Z effect where hemizygosity influences the rate of adaptive substitutions.
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Affiliation(s)
- Ana Pinharanda
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Marjolaine Rousselle
- UMR 5554 Institut des Sciences de l'Evolution, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Joe J Hanly
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - John W Davey
- Department of Zoology, University of Cambridge, Cambridge, UK.,Department of Biology, University of York, York, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Nicolas Galtier
- Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
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14
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Bolívar P, Guéguen L, Duret L, Ellegren H, Mugal CF. GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes. Genome Biol 2019; 20:5. [PMID: 30616647 PMCID: PMC6322265 DOI: 10.1186/s13059-018-1613-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations. RESULTS We analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location. CONCLUSIONS Our study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.
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Affiliation(s)
- Paulina Bolívar
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Laurent Guéguen
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurent Duret
- Laboratoire de Biologie et Biométrie Évolutive CNRS UMR 5558, Université Claude Bernard Lyon 1, Lyon, France
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Carina F. Mugal
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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15
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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16
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A Comparison of Selective Pressures in Plant X-Linked and Autosomal Genes. Genes (Basel) 2018; 9:genes9050234. [PMID: 29751495 PMCID: PMC5977174 DOI: 10.3390/genes9050234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 01/30/2023] Open
Abstract
Selection is expected to work differently in autosomal and X-linked genes because of their ploidy difference and the exposure of recessive X-linked mutations to haploid selection in males. However, it is not clear whether these expectations apply to recently evolved sex chromosomes, where many genes retain functional X- and Y-linked gametologs. We took advantage of the recently evolved sex chromosomes in the plant Silene latifolia and its closely related species to compare the selective pressures between hemizygous and non-hemizygous X-linked genes as well as between X-linked genes and autosomal genes. Our analysis, based on over 1000 genes, demonstrated that, similar to animals, X-linked genes in Silene evolve significantly faster than autosomal genes—the so-called faster-X effect. Contrary to expectations, faster-X divergence was detectable only for non-hemizygous X-linked genes. Our phylogeny-based analyses of selection revealed no evidence for faster adaptation in X-linked genes compared to autosomal genes. On the other hand, partial relaxation of purifying selection was apparent on the X-chromosome compared to the autosomes, consistent with a smaller genetic diversity in S. latifolia X-linked genes (πx = 0.016; πaut = 0.023). Thus, the faster-X divergence in S. latifolia appears to be a consequence of the smaller effective population size rather than of a faster adaptive evolution on the X-chromosome. We argue that this may be a general feature of “young” sex chromosomes, where the majority of X-linked genes are not hemizygous, preventing haploid selection in heterogametic sex.
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17
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Campos JL, Johnston KJA, Charlesworth B. The Effects of Sex-Biased Gene Expression and X-Linkage on Rates of Sequence Evolution in Drosophila. Mol Biol Evol 2017; 35:655-665. [DOI: 10.1093/molbev/msx317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- José Luis Campos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Keira J A Johnston
- Institute of Health and Wellbeing, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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18
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Huylmans AK, Macon A, Vicoso B. Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome. Mol Biol Evol 2017; 34:2637-2649. [PMID: 28957502 PMCID: PMC5850747 DOI: 10.1093/molbev/msx190] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.
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Affiliation(s)
| | - Ariana Macon
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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19
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Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol 2017; 15:25. [PMID: 28356154 PMCID: PMC5370491 DOI: 10.1186/s12915-017-0366-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 01/06/2023] Open
Abstract
Background Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing. Results Using cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts. Conclusions We report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient FIT, and Tajima’s D, are sensitive to this problem to various extents. Control analyses suggest that our published results are probably robust to the problem of contamination. Recommendations on how to prevent or avoid contamination in large-scale population genomics/molecular ecology are provided based on this analysis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0366-6) contains supplementary material, which is available to authorized users.
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