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in category evolutionary biology

5,382 results found. For more information, click each entry to expand.

141: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria
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Posted to bioRxiv 20 Dec 2016

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria
2,076 downloads evolutionary biology

Thomas D. Otto, Aude Gilabert, Thomas Crellen, Ulrike Böhme, Céline Arnathau, Mandy Sanders, Samuel Oyola, Alain Prince Okouga, Larson Boundenga, Eric Willaume, Barthélémy Ngoubangoye, Nancy Diamella Moukodoum, Christophe Paupy, Patrick Durand, Virginie Rougeron, Benjamin Ollomo, François Renaud, Chris Newbold, Matthew Berriman, Franck Prugnolle

Plasmodium falciparum, the most virulent agent of human malaria, shares a recent common ancestor with the gorilla parasite P. praefalciparum. Little is known about the other gorilla and chimpanzee-infecting species in the same (Laverania) subgenus as P. falciparum but none of them are capable of establishing repeated infection and transmission in humans. To elucidate underlying mechanisms and the evolutionary history of this subgenus, we have generated multiple genomes from all known Laverania species. The completeness of our dataset allows us to conclude that interspecific gene transfers as well as convergent evolution were important in the evolution of these species. Striking copy number and structural variations were observed within gene families and one, stevor shows a host specific sequence pattern. The complete genome sequence of the closest ancestor of P. falciparum enables us to estimate confidently for the first time the timing of the beginning of speciation to be 40,000-60,000 years ago followed by a population bottleneck around 4,000-6,000 years ago. Our data allow us also to search in detail for the features of P. falciparum that made it the only member of the Laverania able to infect and spread in humans.

142: Harsh environments and "fast" human life histories: What does the theory say?
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Posted to bioRxiv 04 Feb 2015

Harsh environments and "fast" human life histories: What does the theory say?
2,064 downloads evolutionary biology

Ryan Baldini

A common belief among human life history researchers is that "harsher" environments - i.e., those with higher mortality rates and resource stress - select for "fast" life histories, i.e. earlier reproduction and faster senescence. I show that these "harsh environments, fast life histories" - or HEFLH - hypotheses are poorly supported by evolutionary theory. First, I use a simple model to show that effects of environmental harshness on life history evolution are incredibly diverse. In particular, small changes in basic but poorly understood variables - e.g., whether and how population density affects vital rates - can cause selection to favor very different life histories. Furthermore, I show that almost all life history theory used to justify HEFLH hypotheses is misapplied in the first place. The reason is that HEFLH hypotheses usually treat plastic responses to heterogeneous environmental conditions within a population, whereas the theory used to justify such hypotheses treat genetic responses to environmental changes across an entire population. Counter-intuitively, the predictions of the former do not generally apply to the latter: the optimal response to a harsh environment within a large heterogeneous environment is not necessarily the optimal strategy of a population uniformly inhabiting the same harsh environment. I discuss these theoretical results in light of the current state of empirical research.

143: Genomic epidemiology of the current wave of artemisinin resistant malaria
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Posted to bioRxiv 22 May 2015

Genomic epidemiology of the current wave of artemisinin resistant malaria
2,040 downloads evolutionary biology

Roberto Amato, Olivo Miotto, Charles Woodrow, Jacob Almagro-Garcia, Ipsita Sinha, Susana Campino, Daniel Mead, Eleanor Drury, Mihir Kekre, Mandy Sanders, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Tim J C Anderson, Voahangy Andrianaranjaka, Tobias Apinjoh, Elizabeth Ashley, Sarah Auburn, Gordon A. Awandare, Vito Baraka, Alyssa Barry, Maciej F Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C Bull, Kesinee Chotivanich, David J Conway, Alister Craig, Nicholas P Day, Abdoulaye Djimdé, Christiane Dolecek, Arjen M Dondorp, Chris Drakeley, Patrick Duffy, Diego F Echeverri-Garcia, Thomas G Egwang, Rick M. Fairhurst, Abul Faiz, Caterina I Fanello, Tran Tinh Hien, Abraham Hodgson, Mallika Imwong, Deus Ishengoma, Pharath Lim, Chanthap Lon, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Victor Mobegi, Olugbenga Mokuolu, Jacqui Montgomery, Ivo Mueller, Myat Phone Kyaw, Paul N Newton, François Nosten, Rintis Noviyanti, Alexis Nzila, Harold Ocholla, Abraham Oduro, Marie Onyamboko, Jean-Bosco Ouedraogo, Aung Pyae Phyo, Christopher V Plowe, Ric N Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Pascal Ringwald, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Shannon Takala-Harrison, Thuy-Nhien Nguyen Thanh, Vandana Thathy, Federica Verra, Nicholas J. White, Ye Htut, Victoria J Cornelius, Rachel Giacomantonio, Dawn Muddyman, Christa Henrichs, Cinzia Malangone, Dushyanth Jyothi, Richard D. Pearson, Julian C. Rayner, Gilean McVean, Kirk Rockett, Alistair Miles, Paul Vauterin, Ben Jeffery, Magnus Manske, Jim Stalker, Bronwyn MacInnis, Dominic Kwiatkowski, MalariaGEN Plasmodium falciparum Community Project

Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non‐synonymous mutations, many of which cause radical amino‐acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.

144: The evolutionary history of Neandertal and Denisovan Y chromosomes
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Posted to bioRxiv 09 Mar 2020

The evolutionary history of Neandertal and Denisovan Y chromosomes
2,038 downloads evolutionary biology

Martin Petr, Mateja Hajdinjak, Qiaomei Fu, Elena Essel, Hélène Rougier, Isabelle Crevecoeur, Patrick Semal, Liubov V. Golovanova, Vladimir B. Doronichev, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Michael V. Shunkov, Maxim B. Kozlikin, Anatoli P. Derevianko, Benjamin Vernot, Matthias Meyer, Janet Kelso

Ancient DNA has allowed the study of various aspects of human history in unprecedented detail. However, because the majority of archaic human specimens preserved well enough for genome sequencing have been female, comprehensive studies of Y chromosomes of Denisovans and Neandertals have not yet been possible. Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.

145: Cycad coralloid roots contain bacterial communities including cyanobacteria and Caulobacter spp that encode niche-specific biosynthetic gene clusters
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Posted to bioRxiv 27 Mar 2017

Cycad coralloid roots contain bacterial communities including cyanobacteria and Caulobacter spp that encode niche-specific biosynthetic gene clusters
2,035 downloads evolutionary biology

Karina Gutiérrez-García, Edder D. Bustos-Díaz, José Antonio Corona-Gómez, Hilda E. Ramos-Aboites, Nelly Sélem-Mojica, Pablo Cruz-Morales, Miguel A. Pérez-Farrera, Francisco Barona-Gómez, Angélica Cibrián-Jaramillo

Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Nostoc, and Rhizobium species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities and used for whole-genome inferences that suggest two Dioon-specific monophyletic groups and a level of specialization characteristic of co-evolved symbiotic relationships. In agreement with this, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with metabolite profiling using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.

146: No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics
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Posted to bioRxiv 22 Feb 2020

No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics
2,033 downloads evolutionary biology

Galaxy and HyPhy developments teams, Anton Nekrutenko, Sergei L. Kosakovsky Pond

The current state of much of the Wuhan pneumonia virus (COVID-19) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies, and requires unimpeded access to data, analysis tools, and computational infrastructure. Here we show that community efforts in developing open analytical software tools over the past ten years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all COVID-19 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and to (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises. All our analyses are fully documented at <https://github.com/galaxyproject/SARS-CoV-2>.

147: Phylogenetic scale in ecology and evolution
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Posted to bioRxiv 12 Jul 2016

Phylogenetic scale in ecology and evolution
2,028 downloads evolutionary biology

Catherine H. Graham, David Storch, Antonin Machac

It has been widely acknowledged that many phenomena in ecology and evolution depend on spatial and temporal scale. However, important patterns and processes may also vary across the phylogeny and depend on phylogenetic scale. Though phylogenetic scale has been implicitly considered in some previous studies, it has never been formally conceptualized and its potential remains unexplored. Here, we develop the concept of phylogenetic scale and, building on previous work in the field, we introduce phylogenetic grain and extent, phylogenetic scaling and the domains of phylogenetic scale. We use examples from published research to demonstrate how phylogenetic scale has been considered so far and illustrate how it can inform, and possibly resolve, some of the longstanding controversies in evolutionary biology, community ecology, biogeography and macroecology. To promote the concept of phylogenetic scale empirically, we propose methodological guidelines for its treatment.

148: A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
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Posted to bioRxiv 11 Apr 2018

A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
2,009 downloads evolutionary biology

Martin Kuhlwilm, Cedric Boeckx

Throughout the past decade, studying ancient genomes provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.

149: Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
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Posted to bioRxiv 09 Feb 2018

Whole-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) in the presence of an empirical anomaly zone
2,008 downloads evolutionary biology

Alison Cloutier, Timothy B. Sackton, Phil Grayson, Michele Clamp, Allan J. Baker, Scott V. Edwards

Palaeognathae represent one of the two basal lineages in modern birds, and comprise the volant (flighted) tinamous and the flightless ratites. Resolving palaeognath phylogenetic relationships has historically proved difficult, and short internal branches separating major palaeognath lineages in previous molecular phylogenies suggest that extensive incomplete lineage sorting (ILS) might have accompanied a rapid ancient divergence. Here, we investigate palaeognath relationships using genome-wide data sets of three types of noncoding nuclear markers, together totalling 20,850 loci and over 41 million base pairs of aligned sequence data. We recover a fully resolved topology placing rheas as the sister to kiwi and emu + cassowary that is congruent across marker types for two species tree methods (MP-EST and ASTRAL-II). This topology is corroborated by patterns of insertions for 4,274 CR1 retroelements identified from multi-species whole genome screening, and is robustly supported by phylogenomic subsampling analyses, with MP-EST demonstrating particularly consistent performance across subsampling replicates as compared to ASTRAL. In contrast, analyses of concatenated data supermatrices recover rheas as the sister to all other non-ostrich palaeognaths, an alternative that lacks retroelement support and shows inconsistent behavior under subsampling approaches. While statistically supporting the species tree topology, conflicting patterns of retroelement insertions also occur and imply high amounts of ILS across short successive internal branches, consistent with observed patterns of gene tree heterogeneity. Coalescent simulations indicate that the majority of observed topological incongruence among gene trees is consistent with coalescent variation rather than arising from gene tree estimation error alone, and estimated branch lengths for short successive internodes in the inferred species tree fall within the theoretical range encompassing the anomaly zone. Distributions of empirical gene trees confirm that the most common gene tree topology for each marker type differs from the species tree, signifying the existence of an empirical anomaly zone in palaeognaths.

150: An epigenetic mechanism for cavefish eye degeneration
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Posted to bioRxiv 05 Oct 2017

An epigenetic mechanism for cavefish eye degeneration
2,008 downloads evolutionary biology

Aniket V. Gore, Kelly A. Tomins, James Iben, Li Ma, Daniel Castranova, Andrew Davis, Amy Parkhurst, William R. Jeffery, Brant M. Weinstein

Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss of eyes phenotype in the Pachon blind cave morph of the Mexican tetra Astyanax mexicanus1-6, no inactivating mutations have been found in any of these genes2,3,7-10. Here we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave Astyanax mexicanus. By performing parallel analyses in Astyanax mexicanus cave and surface morphs and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and down-regulated genes in the cave morph are also linked to human eye disorders, suggesting the function of these genes is conserved across the vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.

151: Active mode of excretion across digestive tissues predates the origin of excretory organs
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Posted to bioRxiv 11 May 2017

Active mode of excretion across digestive tissues predates the origin of excretory organs
1,997 downloads evolutionary biology

Carmen Andrikou, Daniel Thiel, Juan A. Ruiz-Santiesteban, Andreas Hejnol

Most bilaterian animals excrete toxic metabolites through specialized organs, such as nephridia and kidneys, which share morphological and functional correspondences. In contrast, the excretory mechanisms in non-nephrozoans are largely unknown, and therefore the reconstruction of ancestral excretory mechanisms is problematic. Here, we investigated the excretory mode of members of the Xenacoelomorpha, the sister group to Nephrozoa, and Cnidaria, the sister group to Bilateria. By combining gene expression, inhibitor experiments and exposure to varying environmental ammonia conditions we show that both, Xenacoelomorpha and Cnidaria, are able to excrete across digestive-associated tissues. Based on these results we propose that digestive-associated tissues functioned as excretory sites before the evolution of specialized organs in nephrozoans. We conclude that diffusion was likely the ancestral mode of excretion, whilst the emergence of a compact, multiple-layered bilaterian body plan necessitated the evolution of active transport excretory mechanisms that was later recruited into the specialized excretory organs.

152: Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes
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Posted to bioRxiv 09 Aug 2019

Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes
1,993 downloads evolutionary biology

Sriram G. Garg, Nils Kapust, Weili Lin, Fernando D. K. Tria, Shijulal Nelson-Sathi, Sven B. Gould, Lu Fan, Ruixin Zhu, Chuanlun Zhang, William F. Martin

Metagenomic studies have claimed the existence of novel lineages with unprecedented properties never before observed in prokaryotes. Such lineages include Asgard archaea, which are claimed to represent archaea with eukaryotic cell complexity, and the Candidate Phyla Radiation (CPR), a novel domain level taxon erected solely on the basis of metagenomic data. However, it has escaped the attention of most biologists that these metagenomic sequences are not assembled into genomes by sequence overlap, as for cultured archaea and bacteria. Instead, short contigs are sorted into computer files by a process called binning in which they receive taxonomic assignment on the basis of sequence properties like GC content, dinucleotide frequencies, and stoichiometric co-occurrence across samples. Consequently, they are not genome sequences as we know them, reflecting the gene content of real organisms. Rather they are metagenome assembled genomes (MAGs). Debates that Asgard data are contaminated with individual eukaryotic sequences are overshadowed by the more pressing issue that no evidence exists to indicate that any sequences in binned Asgard MAGs actually stem from the same chromosome, as opposed to simply stemming from the same environment. Here we show that Asgard and CPR MAGs fail spectacularly to meet the most basic phylogenetic criterion fulfilled by genome sequences of all cultured prokaryotes investigated to date: the ribosomal proteins of Asgard and CPR MAGs do not share common evolutionary histories. Their phylogenetic behavior is anomalous to a degree never observed with genomes of real organisms. CPR and Asgard MAGs are binning artefacts, assembled from environments where up to 90% of the DNA is from dead cells. Asgard and CPR MAGs are unnatural constructs, genome-like patchworks of genes that have been stitched together into computer files by binning.

153: Non-adaptive evolution of the m. palmaris longus in the Homininae.
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Posted to bioRxiv 17 Feb 2015

Non-adaptive evolution of the m. palmaris longus in the Homininae.
1,987 downloads evolutionary biology

Zach Throckmorton, Nicole Forth, Nathanial Thomas

The palmaris longus muscle is widely recognized for its notable variability in living humans. These variations include not only muscle belly reversal, distinct double muscle bellies, duplication and triplication, but also total uni- or bilateral agenesis (absence). A review of the literature and data novel to this study illustrate that different populations of humans exhibit remarkable variation in the frequency of palmaris longus agenesis, from less than 5% of Chinese to nearly 65% of Indians. Comparative dissection-derived data reveal substantial variation in palmaris longus agenesis (PLA) in populations of extant humans (H. sapiens), chimpanzees (Pan spp.), and gorillas (Gorilla spp.) - but not orangutans (Pongo spp.), which apparently always develop this muscle. From this pattern, we infer that palmaris longus is undergoing non-adaptive, stochastic evolution in the extant African Homininae, while it continues to have adaptive purpose in Pongo, likely due to the orangutans' greater degree of arboreality than the African apes and humans. Clinical evidence supports this conclusion, at least as it applies to humans. This study highlights the utility of comparative soft tissue data collection and interpretation in elucidating the evolution of anatomical structures that do not fossilize.

154: On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al.
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Posted to bioRxiv 18 Nov 2013

On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al.
1,980 downloads evolutionary biology

Claudiu I Bandea

In a recent article entitled “On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE”, Graur et al. dismantle ENCODE’s evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNA’s biological functions to informational roles, sidestepping putative non-informational functions. Here, I bring forward an old hypothesis on the evolution of genome size and on the role of so called ‘junk DNA’ (jDNA), which might explain C-value enigma. According to this hypothesis, the jDNA functions as a defense mechanism against insertion mutagenesis by endogenous and exogenous inserting elements such as retroviruses, thereby protecting informational DNA sequences from inactivation or alteration of their expression. Notably, this model couples the mechanisms and the selective forces responsible for the origin of jDNA with its putative protective biological function, which represents a classic case of ‘fighting fire with fire.’ One of the key tenets of this theory is that in humans and many other species, jDNAs serves as a protective mechanism against insertional oncogenic transformation. As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size.

155: A Multidisciplinary Approach to Explain Biological Aging and Longevity
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Posted to bioRxiv 24 Mar 2016

A Multidisciplinary Approach to Explain Biological Aging and Longevity
1,976 downloads evolutionary biology

Brett N. Augsburger

Scientists have been unable to reach a consensus on why organisms age and why they live as long as they do. Here, a multidisciplinary approach was taken in an attempt to understand the root causes of aging. Nonequilibrium thermodynamics may play a previously unappreciated role in determining longevity by governing the dynamics of degradation and renewal within biomolecular ensembles and dictating the inevitability of fidelity loss. The proposed model offers explanations for species longevity trends that have been previously unexplained and for aging-related observations that are considered paradoxical within current paradigms--for example, the elevated damage levels found even in youth within many long-lived species, such as the naked mole-rat. This framework questions whether declining selective pressure is the primary driver of aging, and challenges major tenets of the disposable soma theory. Unifying pertinent principles from diverse disciplines leads to a theoretical framework of biological aging with fewer anomalies, and may be useful in predicting outcomes of experimental attempts to modulate the aging phenotype.

156: A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering
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Posted to bioRxiv 04 Jul 2018

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering
1,971 downloads evolutionary biology

Matthew G. Johnson, Lisa Pokorny, Steven Dodsworth, Laura R Botigue, Robyn S Cowan, Alison Devault, Wolf L. Eiserhardt, Niroshini Epitawalage, Félix Forest, Jan T Kim, James H Leebens-Mack, Ilia J Leitch, Olivier Maurin, Douglas E Soltis, Pamela S. Soltis, Gane Ka-Shu Wong, William J. Baker, Norman J. Wickett

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm lineage. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order lineages of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order lineages, including all angiosperms.

157: Accurate inference of tree topologies from multiple sequence alignments using deep learning
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Posted to bioRxiv 24 Feb 2019

Accurate inference of tree topologies from multiple sequence alignments using deep learning
1,959 downloads evolutionary biology

Anton Suvorov, Joshua Hochuli, Daniel R. Schrider

Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and empirical studies have identified several “zones” of parameter space where accuracy of some methods can plummet, even for four-taxon trees. Further, some methods can have undesirable statistical properties such as statistical inconsistency and/or the tendency to be positively misleading (i.e. assert strong support for the incorrect tree topology). Recently, deep learning techniques have made inroads on a number of both new and longstanding problems in biological research. Here we designed a deep convolutional neural network (CNN) to infer quartet topologies from multiple sequence alignments. This CNN can readily be trained to make inferences using both gapped and ungapped data. We show that our approach is highly accurate on simulated data, often outperforming traditional methods, and is remarkably robust to bias-inducing regions of parameter space such as the Felsenstein zone and the Farris zone. We also demonstrate that the confidence scores produced by our CNN can more accurately assess support for the chosen topology than bootstrap and posterior probability scores from traditional methods. While numerous practical challenges remain, these findings suggest that deep learning approaches such as ours have the potential to produce more accurate phylogenetic inferences.

158: Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
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Posted to bioRxiv 03 May 2018

Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
1,957 downloads evolutionary biology

Martin Kapun, Maite G. Barrón, Fabian Staubach, Darren J. Obbard, R Axel W Wiberg, Jorge Vieira, Clément Goubert, Omar Rota-Stabelli, Maaria Kankare, María Bogaerts-Márquez, Annabelle Haudry, Lena Waidele, Iryna Kozeretska, Elena G. Pasyukova, Volker Loeschcke, Marta Pascual, Cristina P. Vieira, Svitlana Serga, Catherine Montchamp-Moreau, Jessica K. Abbott, Patricia Gibert, Damiano Porcelli, Nico Posnien, Alejandro Sánchez-Gracia, Sonja Grath, Elio Sucena, Alan O. Bergland, Maria Pilar Garcia Guerreiro, Banu Sebnem Onder, Eliza Argyridou, Lain Guio, Mads Fristrup Schou, Bart Deplancke, Cristina Vieira, Michael G Ritchie, B. J. Zwaan, E. Tauber, Dorcas J. Orengo, Eva Puerma, Montserrat Aguadé, Paul Schmidt, John Parsch, Andrea J. Betancourt, Thomas Flatt, Josefa González

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster . Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

159: Neural Changes Underlying Rapid Fly Song Evolution
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Posted to bioRxiv 21 Dec 2017

Neural Changes Underlying Rapid Fly Song Evolution
1,951 downloads evolutionary biology

Yun Ding, Joshua L Lillvis, Jessica Cande, Gordon J. Berman, Benjamin J Arthur, Min Xu, Barry J. Dickson, David L. Stern

The neural basis for behavioural evolution is poorly understood. Functional comparisons of homologous neurons may reveal how neural circuitry contributes to behavioural evolution, but homologous neurons cannot be identified and manipulated in most taxa. Here, we compare the function of homologous courtship song neurons by exporting neurogenetic reagents that label identified neurons in Drosophila melanogaster to D. yakuba. We found a conserved role for a cluster of brain neurons that establish a persistent courtship state. In contrast, a descending neuron with conserved electrophysiological properties drives different song types in each species. Our results suggest that song evolved, in part, due to changes in the neural circuitry downstream of this descending neuron. This experimental approach can be generalized to other neural circuits and therefore provides an experimental framework for studying how the nervous system has evolved to generate behavioural diversity.

160: The CARD-CC/Bcl10/paracaspase signaling complex is functionally conserved since the last common ancestor of planulozoa.
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Posted to bioRxiv 02 Apr 2016

The CARD-CC/Bcl10/paracaspase signaling complex is functionally conserved since the last common ancestor of planulozoa.
1,951 downloads evolutionary biology

Jens Staal, Yasmine Driege, Alice Borghi, Paco Hulpiau, Laurens Lievens, Ismail Sahin Gul, Srividhya Sundararaman, Amanda Gonçalves, Ineke Dhondt, Bart P. Braeckman, U. Technau, Yvan Saeys, Frans van Roy, Rudi Beyaert

Type 1 paracaspases originated in the Ediacaran geological period before the last common ancestor of bilaterans and cnidarians (planulozoa). Cnidarians have several paralog type 1 paracaspases, type 2 paracaspases, and a homolog of Bcl10. Notably in bilaterans, lineages like nematodes and insects lack Bcl10 whereas other lineages such as vertebrates, hemichordates, annelids and mollusks do contain Bcl10. A survey of invertebrate CARD-coiled-coil (CC) domain homologs of CARMA/CARD9 revealed such homologs only in species with Bcl10, indicating an ancient co-evolution of the entire CARD-CC/Bcl10/MALT1-like paracaspase (CBM) complex. Furthermore, vertebrate-like Syk/Zap70 tyrosine kinase homologs with the ITAM-binding SH2 domain were found in invertebrate organisms with CARD-CC/Bcl10, indicating that this pathway might be the original user of the CBM complex. We also established that the downstream signaling proteins TRAF2 and TRAF6 are functionally conserved in cnidaria. There also seems to be a correlation where invertebrates with CARD-CC and Bcl10 have type 1 paracaspases which are more similar to the paracaspases found in vertebrates. A proposed evolutionary scenario includes at least two ancestral type 1 paracaspase paralogs in the planulozoan last common ancestor, where at least one paralog usually is dependent on CARD-CC/Bcl10 for its function. Functional analyses of invertebrate type 1 paracaspases and Bcl10 homologs support this scenario and indicate an ancient origin of the CARD-CC/Bcl10/paracaspase signaling complex. Results from cnidaria, nematodes and mice also suggest an ancient neuronal role for the type 1 paracaspases.

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