Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607008
Julien Devilliers, Ben Warren, Ezio Rosato, Charalambos Kyriacou, Roberto Feuda
Blood-feeding (hematophagy) is widespread across Diptera (true flies), yet the underlying molecular mechanisms remain poorly understood. Using phylogenomics, we show that four gene families associated with neuro-modulation, immune responses, embryonic development, and iron metabolism have undergone independent expansions within mosquitoes and sandflies. Our findings illuminate the underlying genetic basis for blood-feeding adaptations in these important disease vectors.
{"title":"Hematophagy generates a convergent genomic signature in mosquitoes and sandflies","authors":"Julien Devilliers, Ben Warren, Ezio Rosato, Charalambos Kyriacou, Roberto Feuda","doi":"10.1101/2024.08.07.607008","DOIUrl":"https://doi.org/10.1101/2024.08.07.607008","url":null,"abstract":"Blood-feeding (hematophagy) is widespread across Diptera (true flies), yet the underlying molecular mechanisms remain poorly understood. Using phylogenomics, we show that four gene families associated with neuro-modulation, immune responses, embryonic development, and iron metabolism have undergone independent expansions within mosquitoes and sandflies. Our findings illuminate the underlying genetic basis for blood-feeding adaptations in these important disease vectors.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.09.607326
BV Aditi, Uma Ramakrishnan
Isolated and inbred populations are at a higher risk to extinction due to the loss of genetic diversity. Carnivores are particularly susceptible to isolation due to their ecological requirements. Studies generally assess genetic vulnerability using neutral loci, but these may not accurately reflect a population's adaptive potential. In contrast, diversity at loci putatively involved in fitness and hence survival, such as immune genes, could be a better proxy for future survival. Research on immune genes has traditionally focused on the MHC loci. We extend this investigation to five families of non-MHC immune genes -Tumor Necrosis Factor, Interleukin, Toll-like Receptor, Leukocyte Immunoglobulin Receptors, and Chemokine - involved in adaptive and innate immunity in tigers which exemplifies an endangered carnivore. We compare immune gene diversity to neutral diversity across the genome using whole genome resequencing data from 107 tigers, representing all extant subspecies and populations of different demographic histories. Our analysis reveals that immune receptor genes (mean nucleotide diversity: 0.0019) show high nucleotide diversity compared to neutral loci (0.0008) and immune signalling genes (0.0004) indicating past positive selection. Heterozygosity at the three classes of loci suggest that most immune genes are evolving neutrally. We confirm that small, isolated populations have lower nucleotide diversity and heterozygosity at both neutral and immune loci compared to large and connected populations. Additionally, genetic differentiation and deleterious mutation load correspond to known signatures from inbreeding and recent bottlenecks. Despite low neutral and immunogenetic diversity in small populations, some loci retain polymorphisms, irrespective of adaptive or innate immune functions. We conclude that drift is the predominant evolutionary force in bottlenecked populations even at adaptive loci.
{"title":"Beyond neutral loci: Examining immune gene variation in tigers (Panthera tigris)","authors":"BV Aditi, Uma Ramakrishnan","doi":"10.1101/2024.08.09.607326","DOIUrl":"https://doi.org/10.1101/2024.08.09.607326","url":null,"abstract":"Isolated and inbred populations are at a higher risk to extinction due to the loss of genetic diversity. Carnivores are particularly susceptible to isolation due to their ecological requirements. Studies generally assess genetic vulnerability using neutral loci, but these may not accurately reflect a population's adaptive potential. In contrast, diversity at loci putatively involved in fitness and hence survival, such as immune genes, could be a better proxy for future survival. Research on immune genes has traditionally focused on the MHC loci. We extend this investigation to five families of non-MHC immune genes -Tumor Necrosis Factor, Interleukin, Toll-like Receptor, Leukocyte Immunoglobulin Receptors, and Chemokine - involved in adaptive and innate immunity in tigers which exemplifies an endangered carnivore. We compare immune gene diversity to neutral diversity across the genome using whole genome resequencing data from 107 tigers, representing all extant subspecies and populations of different demographic histories. Our analysis reveals that immune receptor genes (mean nucleotide diversity: 0.0019) show high nucleotide diversity compared to neutral loci (0.0008) and immune signalling genes (0.0004) indicating past positive selection. Heterozygosity at the three classes of loci suggest that most immune genes are evolving neutrally. We confirm that small, isolated populations have lower nucleotide diversity and heterozygosity at both neutral and immune loci compared to large and connected populations. Additionally, genetic differentiation and deleterious mutation load correspond to known signatures from inbreeding and recent bottlenecks. Despite low neutral and immunogenetic diversity in small populations, some loci retain polymorphisms, irrespective of adaptive or innate immune functions. We conclude that drift is the predominant evolutionary force in bottlenecked populations even at adaptive loci.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"120 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141969036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.07.607048
Madeline Bursell, Manav Rohilla, Lucia Ramirez, Yuhuan Cheng, Enrique J. Schwarzkopf, Rafael F Guerrero, Caiti Smukowski Heil
The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesized to indirectly select for increases in recombination rate. This hypothesis is consistent with theory on the evolution of recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilize population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domestic goats compared to bezoars, but more mixed results in chicken, and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in recombination with domestication.
{"title":"Mixed outcomes in recombination rates after domestication: Revisiting theory and data","authors":"Madeline Bursell, Manav Rohilla, Lucia Ramirez, Yuhuan Cheng, Enrique J. Schwarzkopf, Rafael F Guerrero, Caiti Smukowski Heil","doi":"10.1101/2024.08.07.607048","DOIUrl":"https://doi.org/10.1101/2024.08.07.607048","url":null,"abstract":"The process of domestication has altered many phenotypes. Selection on these phenotypes has long been hypothesized to indirectly select for increases in recombination rate. This hypothesis is consistent with theory on the evolution of recombination rate, but empirical support has been unclear. We review relevant theory, lab-based experiments, and data comparing recombination rates in wild progenitors and their domesticated counterparts. We utilize population sequencing data and a deep learning method to infer genome-wide recombination rates for new comparisons of chicken/red junglefowl, sheep/mouflon, and goat/bezoar. We find evidence of increased recombination in domestic goats compared to bezoars, but more mixed results in chicken, and generally decreased recombination in domesticated sheep compared to mouflon. Our results add to a growing body of literature in plants and animals that finds no consistent evidence of an increase in recombination with domestication.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.09.607325
Suha Naser-Khdour, Fabian Scheuber, Peter D. Fields, Dieter Ebert
Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as homologs. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.
{"title":"The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex in a Planktonic Crustacean","authors":"Suha Naser-Khdour, Fabian Scheuber, Peter D. Fields, Dieter Ebert","doi":"10.1101/2024.08.09.607325","DOIUrl":"https://doi.org/10.1101/2024.08.09.607325","url":null,"abstract":"Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as homologs. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"126 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.08.607158
Jovan Komluski, Sonja Filatova, Frank Schlütz, Benjamin Claassen, Manfred Roesch, Ben Krause-Kyora, Wiebke Kirleis, Eva Stukenbrock
In medieval central Europe, rye was one of the most important agricultural crops. Its properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a secondary domesticate, i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th century from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries.
{"title":"Sequencing of historical plastid genomes reveal exceptional genetic diversity in early domesticated rye plants","authors":"Jovan Komluski, Sonja Filatova, Frank Schlütz, Benjamin Claassen, Manfred Roesch, Ben Krause-Kyora, Wiebke Kirleis, Eva Stukenbrock","doi":"10.1101/2024.08.08.607158","DOIUrl":"https://doi.org/10.1101/2024.08.08.607158","url":null,"abstract":"In medieval central Europe, rye was one of the most important agricultural crops. Its properties of frost resistance, general resilience and resistance to many pathogens made it invaluable for medieval farmers. Rye has a distinct domestication history compared to other cereal crops and was not domesticated directly from its wild ancestors, like barley and wheat. Rye is considered to be a secondary domesticate, i.e. a crop with domestication traits that initially evolved as an arable weed but eventually was intentionally sown and propagated as a crop. To study the history of rye domestication, genetic sequences of present-day plant populations as well as material from historical samples can provide insights into the temporal and spatial signatures of domestication. In this study we combined archaeobotanical methods and ancient DNA sequencing of well-preserved, historical rye material to study patterns of genetic diversity across four centuries. We first applied archaeobotanical methods to characterize rye material acquired from construction material ranging from the 14th to 18th century from different locations in Germany. Next, we extracted DNA to sequence complete chloroplast genomes of six individual samples. We compared the 115,000 bp chloroplast genomes of historical rye samples to chloroplast genomes of other cereal crops and identified 217 single nucleotide variants exclusive to historical samples. By comparing the aDNA chloroplast samples with modern rye chloroplasts, we show that the genetic variation in ancient rye populations was exceptionally high compared to samples from contemporary rye cultivars. This confirms that late domestication and selective breeding have reduced genetic variation in this important crop species only in the last few centuries.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-09DOI: 10.1101/2024.08.09.607286
Xiang Chuanyu, Ivan Jakovlic, Tong Ye, Rui Song, Hong Zou, Guitang Wang, Wenxiang Li, Dong Zhang
Trematodes are obligatory parasites that generally must transmit between hosts to complete their life cycle. They parasitize varying numbers of intermediate hosts (0, 1 or 2), but the evolutionary history of these strategies and the ancestral states remain unknown. We conducted the ancestral state reconstruction of the number of intermediate hosts using mitogenomic (Trematoda) and nuclear-genomic (Neodermata) topologies. Aspidogastrea was identified as the sister-group ("basal") to all other Trematoda using a range of approaches, so it is crucial for studying the evolutionary history of trematodes. However, there is only one transcriptome available for this lineage, and mitochondrial genomes (mitogenomes) remain unavailable. Herein, we sequenced mitogenomes of two aspidogastreans: Aspidogaster ijimai and Aspidogaster conchicola. As the ancestral state reconstruction analysis is topology-sensitive, we tested multiple phylogenetic strategies, comprising the outgroup selection, phylogenetic models, partitioning strategies, and topological constraints. These mitogenomic phylogenies exhibited pronounced topological instability, with Aspidogastrea resolved as the "basal" radiation in most, but not all, topologies. Based on our analyses, Cestoda was the optimal outgroup choice, and the "heterogeneous" CAT-GTR model in PhyloBayes was the optimal model choice. We inferred the time tree and conducted ancestral state reconstruction analyses using this "optimal" topology, as well as constrained mitogenomic and nuclear genomic topologies. Results were ambiguous for some lineages, but scenario that received the strongest support is the direct life cycle (no intermediate hosts) in the ancestors of Trematoda (proto-trematodes) and Aspidogastrea (proto-aspidogastreans), while the ancestor of Digenea (proto-digeneans) had two intermediate hosts. The inferred scenario indicates that host strategies are relatively plastic among trematodes, putatively comprising several independent host gains, and multiple host losses. We propose a timeline for these events and discuss the role that alternating sexual and asexual generations putatively played in the evolution of complex parasitic life histories in digeneans.
{"title":"The Phylogeny and the Evolution of Parasitic Strategies in Trematoda","authors":"Xiang Chuanyu, Ivan Jakovlic, Tong Ye, Rui Song, Hong Zou, Guitang Wang, Wenxiang Li, Dong Zhang","doi":"10.1101/2024.08.09.607286","DOIUrl":"https://doi.org/10.1101/2024.08.09.607286","url":null,"abstract":"Trematodes are obligatory parasites that generally must transmit between hosts to complete their life cycle. They parasitize varying numbers of intermediate hosts (0, 1 or 2), but the evolutionary history of these strategies and the ancestral states remain unknown. We conducted the ancestral state reconstruction of the number of intermediate hosts using mitogenomic (Trematoda) and nuclear-genomic (Neodermata) topologies. Aspidogastrea was identified as the sister-group (\"basal\") to all other Trematoda using a range of approaches, so it is crucial for studying the evolutionary history of trematodes. However, there is only one transcriptome available for this lineage, and mitochondrial genomes (mitogenomes) remain unavailable. Herein, we sequenced mitogenomes of two aspidogastreans: Aspidogaster ijimai and Aspidogaster conchicola. As the ancestral state reconstruction analysis is topology-sensitive, we tested multiple phylogenetic strategies, comprising the outgroup selection, phylogenetic models, partitioning strategies, and topological constraints. These mitogenomic phylogenies exhibited pronounced topological instability, with Aspidogastrea resolved as the \"basal\" radiation in most, but not all, topologies. Based on our analyses, Cestoda was the optimal outgroup choice, and the \"heterogeneous\" CAT-GTR model in PhyloBayes was the optimal model choice. We inferred the time tree and conducted ancestral state reconstruction analyses using this \"optimal\" topology, as well as constrained mitogenomic and nuclear genomic topologies. Results were ambiguous for some lineages, but scenario that received the strongest support is the direct life cycle (no intermediate hosts) in the ancestors of Trematoda (proto-trematodes) and Aspidogastrea (proto-aspidogastreans), while the ancestor of Digenea (proto-digeneans) had two intermediate hosts. The inferred scenario indicates that host strategies are relatively plastic among trematodes, putatively comprising several independent host gains, and multiple host losses. We propose a timeline for these events and discuss the role that alternating sexual and asexual generations putatively played in the evolution of complex parasitic life histories in digeneans.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.06.606717
Michael J. Landis, Ammon Thompson
Many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, a pipeline-based toolkit for performing phylogenetic modeling tasks using likelihood-free deep learning approaches. phyddle coordinates modeling tasks through five analysis steps (Simulate, Format, Train, Estimate, and Plot) that transform raw phylogenetic datasets as input into numerical and visualized model-based output. Benchmarks show that phyddle accurately performs a range of inference tasks, such as estimating macroevolutionary parameters, selecting among continuous trait evolution models, and passing coverage tests for epidemiological models, even for models that lack tractable likelihoods. phyddle has a flexible command-line interface, making it easy to integrate deep learning approaches for phylogenetics into research workflows. Learn more about phyddle at https://phyddle.org.
{"title":"phyddle: software for phylogenetic model exploration with deep learning","authors":"Michael J. Landis, Ammon Thompson","doi":"10.1101/2024.08.06.606717","DOIUrl":"https://doi.org/10.1101/2024.08.06.606717","url":null,"abstract":"Many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, a pipeline-based toolkit for performing phylogenetic modeling tasks using likelihood-free deep learning approaches. <kbd>phyddle</kbd> coordinates modeling tasks through five analysis steps (<em>Simulate, Format, Train, Estimate</em>, and <em>Plot</em>) that transform raw phylogenetic datasets as input into numerical and visualized model-based output. Benchmarks show that <kbd>phyddle</kbd> accurately performs a range of inference tasks, such as estimating macroevolutionary parameters, selecting among continuous trait evolution models, and passing coverage tests for epidemiological models, even for models that lack tractable likelihoods. <kbd>phyddle</kbd> has a flexible command-line interface, making it easy to integrate deep learning approaches for phylogenetics into research workflows. Learn more about <kbd>phyddle</kbd> at https://phyddle.org.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-08DOI: 10.1101/2024.08.08.607143
Yoav Mathov, Naomi Rosen, Chen Leibson, Eran Meshorer, Benjamin Yakir, Liran Carmel
Identifying evolutionary changes in DNA methylation bears a huge potential for unraveling adaptations that have occurred in modern humans. Over the past decade, computational methods to reconstruct DNA methylation patterns from ancient DNA sequences have been developed, allowing for the exploration of DNA methylation changes during the past hundreds of thousands of years of human evolution. Here, we introduce a new version of RoAM (Reconstruction of Ancient Methylation), a flexible tool that allows for the reconstruction of ancient methylomes, as well as the identification of differentially methylated regions between ancient populations. RoAM incorporates a series of filtering and quality control steps, resulting in highly reliable DNA methylation maps that exhibit similar characteristics to modern maps. To showcase RoAM’s capabilities, we used it to compare ancient methylation patterns between pre- and post-Neolithic revolution samples from the Balkans. Differentially methylated regions separating these populations are shown to be associated with genes related to regulation of sugar metabolism. Notably, we provide evidence for overexpression of the gene PTPRN2 in post-Neolithic revolution samples. PTPRN2 is a key regulator of insulin secretion, and our finding is compatible with hypoinsulinism in pre-Neolithic revolution hunter-gatherers. Additionally, we observe methylation changes in the genes EIF2AK4 and SLC2A5, which provide further evidence to metabolic adaptations to a changing diet during the Neolithic transition. RoAM offers powerful algorithms that position it as a key asset for researchers seeking to identify evolutionary regulatory changes through the lens of paleoepigenetics.
识别 DNA 甲基化的进化变化对于揭示现代人类的适应性具有巨大的潜力。在过去的十年中，人们开发出了从古DNA序列重建DNA甲基化模式的计算方法，从而可以探索过去数十万年人类进化过程中DNA甲基化的变化。在这里，我们介绍了新版本的 RoAM（古代甲基化重建），它是一种灵活的工具，可以重建古代甲基组，并识别古代人群之间不同的甲基化区域。RoAM 采用了一系列过滤和质量控制步骤，可绘制出高度可靠的 DNA 甲基化图谱，其特征与现代图谱相似。为了展示 RoAM 的能力，我们用它比较了巴尔干地区新石器时代革命前和革命后样本的古代甲基化模式。结果表明，将这些人群分开的不同甲基化区域与糖代谢调控相关的基因有关。值得注意的是，我们提供了新石器时代革命后样本中 PTPRN2 基因过度表达的证据。PTPRN2 是胰岛素分泌的一个关键调节因子，我们的发现与新石器时代革命前狩猎采集者的胰岛素过低相吻合。此外，我们还观察到了基因 EIF2AK4 和 SLC2A5 的甲基化变化，这进一步证明了新石器时代过渡期间饮食变化对新陈代谢的适应。RoAM 提供了强大的算法，使其成为研究人员通过古表观遗传学的视角识别进化调控变化的关键资产。
{"title":"RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions","authors":"Yoav Mathov, Naomi Rosen, Chen Leibson, Eran Meshorer, Benjamin Yakir, Liran Carmel","doi":"10.1101/2024.08.08.607143","DOIUrl":"https://doi.org/10.1101/2024.08.08.607143","url":null,"abstract":"Identifying evolutionary changes in DNA methylation bears a huge potential for unraveling adaptations that have occurred in modern humans. Over the past decade, computational methods to reconstruct DNA methylation patterns from ancient DNA sequences have been developed, allowing for the exploration of DNA methylation changes during the past hundreds of thousands of years of human evolution. Here, we introduce a new version of RoAM (Reconstruction of Ancient Methylation), a flexible tool that allows for the reconstruction of ancient methylomes, as well as the identification of differentially methylated regions between ancient populations. RoAM incorporates a series of filtering and quality control steps, resulting in highly reliable DNA methylation maps that exhibit similar characteristics to modern maps. To showcase RoAM’s capabilities, we used it to compare ancient methylation patterns between pre- and post-Neolithic revolution samples from the Balkans. Differentially methylated regions separating these populations are shown to be associated with genes related to regulation of sugar metabolism. Notably, we provide evidence for overexpression of the gene PTPRN2 in post-Neolithic revolution samples. PTPRN2 is a key regulator of insulin secretion, and our finding is compatible with hypoinsulinism in pre-Neolithic revolution hunter-gatherers. Additionally, we observe methylation changes in the genes EIF2AK4 and SLC2A5, which provide further evidence to metabolic adaptations to a changing diet during the Neolithic transition. RoAM offers powerful algorithms that position it as a key asset for researchers seeking to identify evolutionary regulatory changes through the lens of paleoepigenetics.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141968996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.05.606707
Yasmin Asar, Hervé Sauquet, Simon Y. W. Ho
Plants carry genetic material in three separate compartments, the nuclear, mitochondrial, and chloroplast genomes. These genomes interact with each other to various degrees and are subject to shared evolutionary drivers exerted by their host organisms. Although animal mitochondrial and nuclear genomes display linked evolutionary rates, a well-documented phenomenon termed “mito-nuclear covariation”, it is not clear whether the three plant genomes display covarying evolutionary signals on a broad scale. We tested for correlated evolutionary rates between nuclear and organellar genomes using extensive data sets from the major clades of land plants (Embryophyta), including mosses, ferns, gymnosperms, and angiosperms. To examine the evolutionary dynamics in parasitic angiosperms, which are under distinctive selective pressures, we also analysed data sets from mistletoes, broomrapes, sandalwoods, and rafflesias. Evolutionary rates of nuclear and organellar genomes were positively linked in each group of land plants tested, except in the parasitic angiosperms. We also found positive correlations between rates of nonsynonymous and synonymous change. Our results reveal extensive evolutionary rate variation across land plant taxa, particularly in mitochondrial genomes in angiosperms. Overall, we find that nuclear, mitochondrial, and chloroplast genomes in land plants share similar drivers of mutation rates, despite considerable variation in life history, morphology, and genome sizes among clades. Our findings lay the foundation for further exploration of the impact of co-evolutionary interactions on shared evolutionary rates between genomes.
{"title":"Evolutionary rates of nuclear and organellar genomes are linked in land plants","authors":"Yasmin Asar, Hervé Sauquet, Simon Y. W. Ho","doi":"10.1101/2024.08.05.606707","DOIUrl":"https://doi.org/10.1101/2024.08.05.606707","url":null,"abstract":"Plants carry genetic material in three separate compartments, the nuclear, mitochondrial, and chloroplast genomes. These genomes interact with each other to various degrees and are subject to shared evolutionary drivers exerted by their host organisms. Although animal mitochondrial and nuclear genomes display linked evolutionary rates, a well-documented phenomenon termed “mito-nuclear covariation”, it is not clear whether the three plant genomes display covarying evolutionary signals on a broad scale. We tested for correlated evolutionary rates between nuclear and organellar genomes using extensive data sets from the major clades of land plants (Embryophyta), including mosses, ferns, gymnosperms, and angiosperms. To examine the evolutionary dynamics in parasitic angiosperms, which are under distinctive selective pressures, we also analysed data sets from mistletoes, broomrapes, sandalwoods, and rafflesias. Evolutionary rates of nuclear and organellar genomes were positively linked in each group of land plants tested, except in the parasitic angiosperms. We also found positive correlations between rates of nonsynonymous and synonymous change. Our results reveal extensive evolutionary rate variation across land plant taxa, particularly in mitochondrial genomes in angiosperms. Overall, we find that nuclear, mitochondrial, and chloroplast genomes in land plants share similar drivers of mutation rates, despite considerable variation in life history, morphology, and genome sizes among clades. Our findings lay the foundation for further exploration of the impact of co-evolutionary interactions on shared evolutionary rates between genomes.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-07DOI: 10.1101/2024.08.06.606840
Ben Krause-Kyora, Nicolas Antonio da Silva, Elif Kaplan, Daniel Kolbe, Archaeological Civilization Disease Consortium (ACDC), Inken Wohlers, Hauke Busch, David Ellinghaus, Amke Caliebe, Efe Sezgin, Almut Nebel, Stefan Schreiber
Background The hypomorphic variant rs11209026-A in the IL23R gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel disease (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe.
{"title":"Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans","authors":"Ben Krause-Kyora, Nicolas Antonio da Silva, Elif Kaplan, Daniel Kolbe, Archaeological Civilization Disease Consortium (ACDC), Inken Wohlers, Hauke Busch, David Ellinghaus, Amke Caliebe, Efe Sezgin, Almut Nebel, Stefan Schreiber","doi":"10.1101/2024.08.06.606840","DOIUrl":"https://doi.org/10.1101/2024.08.06.606840","url":null,"abstract":"<strong>Background</strong> The hypomorphic variant rs11209026-A in the <em>IL23R</em> gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel disease (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141938266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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