Abstract:MotivationAccurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.ResultsWe present improvements in the O… Show more
“…Six taxa each had a single peak, with Ks medians of approximately 0.2 ( Tilia ), approximately 0.3 ( Durio , Firmiana , Heritiera ) or approximately 0.4 ( Bombax, Adansonia ), whereas the two members of Malvoideae ( Gossypium and Hibiscus ), each had two peaks at approximately 0.1/0.5 and approximately 0.3/0.6, respectively. We interpret the younger peak in Gossypium as part of the background gene duplication rate, most likely due to tandemly duplicated genes that retain high sequence similarity to one another, via gene conversion (Panchy et al ; Train et al ). The younger peak in Hibiscus, in contrast, is likely the result of a recent WGM unique to this lineage, as previous work suggests this was an independent event with respect to Gossypium (Kim et al ; Teh et al ).…”
Section: Resultsmentioning
confidence: 99%
“…However, there was no agreement among approaches, leaving considerable uncertainty as to the history of genome evolution in the Malvaceae. We discuss some of the better‐supported alternative hypotheses and note some methodological issues that complicate WGM inference, including ILS, asymmetrical gene fractionation, varying rates of evolution, and gene conversion (Panchy et al ; Train et al ).…”
Section: Discussionmentioning
confidence: 99%
“…Numbers in parentheses, next to taxon names, are the mean number of genes/family among the families that were used for analysis. alternative hypotheses and note some methodological issues that complicate WGM inference, including ILS, asymmetrical gene fractionation, varying rates of evolution, and gene conversion (Panchy et al 2016;Train et al 2017).…”
Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.
“…Six taxa each had a single peak, with Ks medians of approximately 0.2 ( Tilia ), approximately 0.3 ( Durio , Firmiana , Heritiera ) or approximately 0.4 ( Bombax, Adansonia ), whereas the two members of Malvoideae ( Gossypium and Hibiscus ), each had two peaks at approximately 0.1/0.5 and approximately 0.3/0.6, respectively. We interpret the younger peak in Gossypium as part of the background gene duplication rate, most likely due to tandemly duplicated genes that retain high sequence similarity to one another, via gene conversion (Panchy et al ; Train et al ). The younger peak in Hibiscus, in contrast, is likely the result of a recent WGM unique to this lineage, as previous work suggests this was an independent event with respect to Gossypium (Kim et al ; Teh et al ).…”
Section: Resultsmentioning
confidence: 99%
“…However, there was no agreement among approaches, leaving considerable uncertainty as to the history of genome evolution in the Malvaceae. We discuss some of the better‐supported alternative hypotheses and note some methodological issues that complicate WGM inference, including ILS, asymmetrical gene fractionation, varying rates of evolution, and gene conversion (Panchy et al ; Train et al ).…”
Section: Discussionmentioning
confidence: 99%
“…Numbers in parentheses, next to taxon names, are the mean number of genes/family among the families that were used for analysis. alternative hypotheses and note some methodological issues that complicate WGM inference, including ILS, asymmetrical gene fractionation, varying rates of evolution, and gene conversion (Panchy et al 2016;Train et al 2017).…”
Previous research suggests that Gossypium has undergone a 5‐ to 6‐fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae‐Bombacoideae and Sterculioideae‐Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae‐Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution.
“…1) 17 . The constructed phylogeny overall agrees with the known relationships among the analysed teleost species and indicates that a comparison with the European sea bass as sister group and three-spined stickle back as outgroup is the most appropriate for the analysis of branch-specific evolutionary rates.Fig.…”
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
“…Resources such as Pfam are suitable for identifying homologs, not orthologs (see Box ). Others, such as Orthologous MAtrix (OMA), focus on identifying pairwise (orthology) relationships between two proteins, while many studies aim for collecting all proteins from an orthologous group (OG) (Box ). Algorithms that infer such groups occasionally split a single group into multiple ones, due to sequence divergence and/or domain dynamics .…”
Comparative genomics has proven a fruitful approach to acquire many functional and evolutionary insights into core cellular processes. Here it is argued that in order to perform accurate and interesting comparative genomics, one first and foremost has to be able to recognize, postulate, and revise different evolutionary scenarios. After all, these studies lack a simple protocol, due to different proteins having different evolutionary dynamics and demanding different approaches. The authors here discuss this challenge from a practical (what are the observations?) and conceptual (how do these indicate a specific evolutionary scenario?) viewpoint, with the aim to guide investigators who want to analyze the evolution of their protein(s) of interest. By sharing how the authors draft, test, and update such a scenario and how it directs their investigations, the authors hope to illuminate how to execute molecular evolution studies and how to interpret them. Also see the video abstract here https://youtu.be/VCt3l2pbdbQ.
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