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Now showing items 1 - 16 of 49

  • The Prevalence and Impact of Model Violations in Phylogenetic Analysis.

    Naser-Khdour, Suha   Minh, Bui Quang   Zhang, Wenqi   Stone, Eric A   Lanfear, Robert  

    In phylogenetic inference, we commonly use models of substitution which assume that sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of such models is often criticized, the extent of SRH violations and their effects on phylogenetic inference of tree topologies and edge lengths are not well understood. Here, we introduce and apply the maximal matched-pairs tests of homogeneity to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic data sets. We show that roughly one-quarter of all the partitions we analyzed (23.5%) reject the SRH assumptions, and that for 25% of data sets, tree topologies inferred from all partitions differ significantly from topologies inferred using the subset of partitions that do not reject the SRH assumptions. This proportion increases when comparing trees inferred using the subset of partitions that rejects the SRH assumptions, to those inferred from partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. Our results also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in, and the new tests we describe are available as a new option in IQ-TREE ( =C2=A9 The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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  • Plant Mating Systems Often Vary Widely Among Populations

    Whitehead, Michael R.   Lanfear, Robert   Mitchell, Randall J.   Karron, Jeffrey D.  

    Most flowering plants are hermaphroditic, yet the proportion of seeds fertilized by self and outcross pollen varies widely among species, ranging from predominant self-fertilization to exclusive outcrossing. A population's rate of outcrossing has important evolutionary outcomes as it influences genetic structure, effective population size, and offspring fitness. Because most mating system studies have quantified outcrossing rates for just one or two populations, past reviews of mating system diversity have not been able to characterize the extent of variation among populations. Here we present a new database of more than 30 years of mating system studies that report outcrossing rates for three or more populations per species. This survey, which includes 741 populations from 105 species, illustrates substantial and prevalent among-population variation in the mating system. Intermediate outcrossing rates (mixed mating) are common; 63% of species had at least one mixed mating population. The variance among populations and within species was not significantly correlated with pollination mode or phylogeny. Our review underscores the need for studies exploring variation in the relative influence of ecological and genetic factors on the mating system, and how this varies among populations. We conclude that estimates of outcrossing rates from single populations are often highly unreliable indicators of the mating system of an entire species.
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  • Estimating Improved Partitioning Schemes for Ultraconserved Elements

    Tagliacollo, Victor A.   Lanfear, Robert  

    Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively simple to collect from distantly-related organisms, and contain sufficient information to infer relationships at almost all taxonomic levels. Most studies of UCEs use partitioning to account for variation in rates and patterns of molecular evolution among sites, for example by estimating an independent model of molecular evolution for each UCE. However, rates and patterns of molecular evolution vary substantially within as well as between UCEs, suggesting that there may be opportunities to improve how UCEs are partitioned for phylogenetic inference. We propose and evaluate new partitioning methods for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC), and UCE Site Position (UCESP). The first method uses site characteristics such as entropy, multinomial likelihood, and GC content to generate partitions that account for heterogeneity in rates and patterns of molecular evolution within each UCE. The second method groups together nucleotides that are found in similar physical locations within the UCEs. We examined the new methods with seven published data sets from a variety of taxa. We demonstrate the UCESP method generates partitions that are worse than other strategies used to partition UCE data sets (e.g., one partition per UCE). The SWSC method, particularly when based on site entropies, generates partitions that account for within-UCE heterogeneity and leads to large increases in the model fit. All of the methods, code, and data used in this study, are available from PartitionUCE. Simplified code for implementing the best method, the SWSC-EN, is available from Tagliacollo/PFinderUCE-SWSC-EN.
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  • The Evolution of Clutch Size in Hosts of Avian Brood Parasites

    Medina, Iliana   Langmore, Naomi E.   Lanfear, Robert   Kokko, Hanna  

    Coevolution with avian brood parasites shapes a range of traits in their hosts, including morphology, behavior, and breeding systems. Here we explore whether brood parasitism is also associated with the evolution of host clutch size. Several studies have proposed that hosts of highly virulent parasites could decrease the costs of parasitism by evolving a smaller clutch size, because hosts with smaller clutches will lose fewer progeny when their clutch is parasitized. We describe a model of the evolution of clutch size, which challenges this logic and shows instead that an increase in clutch size (or no change) should evolve in hosts. We test this prediction using a broad-scale comparative analysis to ask whether there are differences in clutch size within hosts and between hosts and nonhosts. Consistent with our model, this analysis revealed that host species do not have smaller clutches and that hosts that incur larger costs from raising a parasite lay larger clutches. We suggest that brood parasitism might be an influential factor in clutch-size evolution and could potentially select for the evolution of larger clutches in host species.
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  • Do plants have a segregated germline?

    Lanfear, Robert  

    For the last 100 years, it has been uncontroversial to state that the plant germline is set aside late in development, but there is surprisingly little evidence to support this view. In contrast, much evolutionary theory and several recent empirical studies seem to suggest the opposite-that the germlines of some and perhaps most plants may be set aside early in development. But is this really the case? How much does it matter? How can we reconcile the new evidence with existing knowledge of plant development? And is there a way to reliably establish the timing of germline segregation in both model and nonmodel plants? Answering these questions is vital to understanding one of the most fundamental aspects of plant development and evolution.
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  • Body mass-corrected molecular rate for bird mitochondrial DNA

    Nabholz, Benoit   Lanfear, Robert   Fuchs, Jerome  

    Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of similar to 0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species' body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.
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  • The effects of partitioning on phylogenetic inference.

    Kainer, David   Lanfear, Robert  

    Partitioning is a commonly used method in phylogenetics that aims to accommodate variation in substitution patterns among sites. Despite its popularity, there have been few systematic studies of its effects on phylogenetic inference, and there have been no studies that compare the effects of different approaches to partitioning across many empirical data sets. In this study, we applied four commonly used approaches to partitioning to each of 34 empirical data sets, and then compared the resulting tree topologies, branch-lengths, and bootstrap support estimated using each approach. We find that the choice of partitioning scheme often affects tree topology, particularly when partitioning is omitted. Most notably, we find occasional instances where the use of a suboptimal partitioning scheme produces highly supported but incorrect nodes in the tree. Branch-lengths and bootstrap support are also affected by the choice of partitioning scheme, sometimes dramatically so. We discuss the reasons for these effects and make some suggestions for best practice. =C2=A9 The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail:
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  • Population size and the rate of evolution

    Lanfear, Robert   Kokko, Hanna   Eyre-Walker, Adam  

    Does evolution proceed faster in larger or smaller populations? The relationship between effective population size (N-e) and the rate of evolution has consequences for our ability to understand and interpret genomic variation, and is central to many aspects of evolution and ecology. Many factors affect the relationship between Ne and the rate of evolution, and recent theoretical and empirical studies have shown some surprising and sometimes counterintuitive results. Some mechanisms tend to make the relationship positive, others negative, and they can act simultaneously. The relationship also depends on whether one is interested in the rate of neutral, adaptive, or deleterious evolution. Here, we synthesize theoretical and empirical approaches to understanding the relationship and highlight areas that remain poorly understood.
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  • Public Data Archiving in Ecology and Evolution: How Well Are We Doing?

    Roche, Dominique G   Kruuk, Loeske E B   Lanfear, Robert   Binning, Sandra A  

    Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis? We surveyed 100 datasets associated with nonmolecular studies in journals that commonly publish ecological and evolutionary research and have a strong PDA policy. Out of these datasets, 56% were incomplete, and 64% were archived in a way that partially or entirely prevented reuse. We suggest that cultural shifts facilitating clearer benefits to authors are necessary to achieve high-quality PDA and highlight key guidelines to help authors increase their data's reuse potential and compliance with journal data policies. =20
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  • Selecting optimal partitioning schemes for phylogenomic datasets

    Lanfear, Robert   Calcott, Brett   Kainer, David   Mayer, Christoph   Stamatakis, Alexandros  

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  • Phylogenomics resolves the timing and pattern of insect evolution.

    Misof, Bernhard   Liu, Shanlin   Meusemann, Karen   Peters, Ralph S   Donath, Alexander   Mayer, Christoph   Frandsen, Paul B   Ware, Jessica   Flouri, Tomas   Beutel, Rolf G   Niehuis, Oliver   Petersen, Malte   Izquierdo-Carrasco, Fernando   Wappler, Torsten   Rust, Jes   Aberer, Andre J   Aspock, Ulrike   Aspock, Horst   Bartel, Daniela   Blanke, Alexander   Berger, Simon   Bohm, Alexander   Buckley, Thomas R   Calcott, Brett   Chen, Junqing   Friedrich, Frank   Fukui, Makiko   Fujita, Mari   Greve, Carola   Grobe, Peter   Gu, Shengchang   Huang, Ying   Jermiin, Lars S   Kawahara, Akito Y   Krogmann, Lars   Kubiak, Martin   Lanfear, Robert   Letsch, Harald   Li, Yiyuan   Li, Zhenyu   Li, Jiguang   Lu, Haorong   Machida, Ryuichiro   Mashimo, Yuta   Kapli, Pashalia   McKenna, Duane D   Meng, Guanliang   Nakagaki, Yasutaka   Navarrete-Heredia, Jose Luis   Ott, Michael   Ou, Yanxiang   Pass, Gunther   Podsiadlowski, Lars   Pohl, Hans   von Reumont, Bjorn M   Schutte, Kai   Sekiya, Kaoru   Shimizu, Shota   Slipinski, Adam   Stamatakis, Alexandros   Song, Wenhui   Su, Xu   Szucsich, Nikolaus U   Tan, Meihua   Tan, Xuemei   Tang, Min   Tang, Jingbo   Timelthaler, Gerald   Tomizuka, Shigekazu   Trautwein, Michelle   Tong, Xiaoli   Uchifune, Toshiki   Walzl, Manfred G   Wiegmann, Brian M   Wilbrandt, Jeanne   Wipfler, Benjamin   Wong, Thomas K F   Wu, Qiong   Wu, Gengxiong   Xie, Yinlong   Yang, Shenzhou   Yang, Qing   Yeates, David K   Yoshizawa, Kazunori   Zhang, Qing   Zhang, Rui   Zhang, Wenwei   Zhang, Yunhui   Zhao, Jing   Zhou, Chengran   Zhou, Lili   Ziesmann, Tanja   Zou, Shijie   Li, Yingrui   Xu, Xun   Zhang, Yong   Yang, Huanming   Wang, Jian   Wang, Jun   Kjer, Karl M   Zhou, Xin  

    Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects. Copyright =C2=A9 2014, American Association for the Advancement of Science.
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  • Open access is worth considering: a reply to Agrawal

    Lanfear, Robert   Pennell, Matthew W.  

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  • Taller plants have lower rates of molecular evolution

    Lanfear, Robert   Ho, Simon Y. W.   Jonathan Davies, T.   Moles, Angela T.   Aarssen, Lonnie   Swenson, Nathan G.   Warman, Laura   Zanne, Amy E.   Allen, Andrew P.  

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  • Taller plants have lower rates of molecular evolution.

    Lanfear, Robert   Ho, Simon Y W   Jonathan Davies, T   Moles, Angela T   Aarssen, Lonnie   Swenson, Nathan G   Warman, Laura   Zanne, Amy E   Allen, Andrew P  

    Rates of molecular evolution have a central role in our understanding of many aspects of species' biology. However, the causes of variation in rates of molecular evolution remain poorly understood, particularly in plants. Here we show that height accounts for about one-fifth of the among-lineage rate variation in the chloroplast and nuclear genomes of plants. This relationship holds across 138 families of flowering plants, and when accounting for variation in species richness, temperature, ultraviolet radiation, latitude and growth form. Our observations can be explained by a link between height and rates of genome copying in plants, and we propose a mechanistic hypothesis to account for this-the 'rate of mitosis' hypothesis. This hypothesis has the potential to explain many disparate observations about rates of molecular evolution across the tree of life. Our results have implications for understanding the evolutionary history and future of plant lineages in a changing world.
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  • Troubleshooting public data archiving: suggestions to increase participation.

    Roche, Dominique G   Lanfear, Robert   Binning, Sandra A   Haff, Tonya M   Schwanz, Lisa E   Cain, Kristal E   Kokko, Hanna   Jennions, Michael D   Kruuk, Loeske E B  

    An increasing number of publishers and funding agencies require public data archiving (PDA) in open-access databases. PDA has obvious group benefits for the scientific community, but many researchers are reluctant to share their data publicly because of real or perceived individual costs. Improving participation in PDA will require lowering costs and/or increasing benefits for primary data collectors. Small, simple changes can enhance existing measures to ensure that more scientific data are properly archived and made publicly available: (1) facilitate more flexible embargoes on archived data, (2) encourage communication between data generators and re-users, (3) disclose data re-use ethics, and (4) encourage increased recognition of publicly archived data. =20
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  • Calibrating mitochondrial rates in marine invertebrates

    Ho, Simon Y. W.   Lanfear, Robert  

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