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June 18, 2015
Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200–4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.
MicroRNAs (miRNAs) are a widespread class of regulatory noncoding RNAs with key roles in physiology and development, conferring robustness to noise in regulatory networks. Consistent with this buffering function, it was recently suggested that human miRNAs coevolve with genes in copy number regions (copy number variation [CNV] genes) to reduce dosage imbalance. Here, I compare miRNA regulation between CNV and non-CNV genes in four model organisms. miRNA regulation of CNV genes is elevated in human and fly but reduced in nematode and zebrafish. By analyzing 31 human CNV data sets, careful analysis of human and chimpanzee orthologs, resampling genes within species and comparing structural variant types, I show that the apparent coevolution between CNV genes and miRNAs is due to the strong dependency between 3'-untranslated region length and miRNA target prediction. Deciphering the interplay between CNVs and miRNAs will likely require a deeper understanding of how miRNAs are embedded in regulatory circuits.
The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data
Rates and timescales of viral evolution can be estimated using phylogenetic analyses of time-structured molecular sequences. This involves the use of molecular-clock methods, calibrated by the sampling times of the viral sequences. However, the spread of these sampling times is not always sufficient to allow the substitution rate to be estimated accurately. We conducted Bayesian phylogenetic analyses of simulated virus data to evaluate the performance of the date-randomization test, which is sometimes used to investigate whether time-structured data sets have temporal signal. An estimate of the substitution rate passes this test if its mean does not fall within the 95% credible intervals of rate estimates obtained using replicate data sets in which the sampling times have been randomized. We find that the test sometimes fails to detect rate estimates from data with no temporal signal. This error can be minimized by using a more conservative criterion, whereby the 95% credible interval of the estimate with correct sampling times should not overlap with those obtained with randomized sampling times. We also investigated the behavior of the test when the sampling times are not uniformly distributed throughout the tree, which sometimes occurs in empirical data sets. The test performs poorly in these circumstances, such that a modification to the randomization scheme is needed. Finally, we illustrate the behavior of the test in analyses of nucleotide sequences of cereal yellow dwarf virus. Our results validate the use of the date-randomization test and allow us to propose guidelines for interpretation of its results.
A Protocol for Diagnosing the Effect of Calibration Priors on Posterior Time Estimates: A Case Study for the Cambrian Explosion of Animal Phyla
We present a procedure to test the effect of calibration priors on estimated times, which applies a recently developed calibration-free approach (RelTime) method that produces relative divergence times for all nodes in the tree. We illustrate this protocol by applying it to a timetree of metazoan diversification (Erwin DH, Laflamme M, Tweedt SM, Sperling EA, Pisani D, Peterson KJ. 2011. The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091–1097.), which placed the divergence of animal phyla close to the time of the Cambrian explosion inferred from the fossil record. These analyses revealed that the two maximum-only calibration priors in the pre-Cambrian are the primary determinants of the young divergence times among animal phyla in this study. In fact, these two maximum-only calibrations produce divergence times that severely violate minimum boundaries of almost all of the other 22 calibration constraints. The use of these 22 calibrations produces dates for metazoan divergences that are hundreds of millions of years earlier in the Proterozoic. Our results encourage the use of calibration-free approaches to identify most influential calibration constraints and to evaluate their impact in order to achieve biologically robust interpretations.
June 16, 2015
The standard references for the conceptual history of phylogenetic trees and networks are:
Over the past 20 years, a number of books have appeared that expand upon this topic, which it is worthwhile to list here.
Barsanti, Giulio (1992) La Scala, la Mappa, l'Albero: Immagini e Classificazioni Della Natura Fra Sei e Ottocento. Firenze: Sansoni Editore.
In Italian. A conceptual history of classification up to the time of Haeckel, and the beginning of phylogenetics. Covers the development of ideas and images equally. Networks are treated as "maps".
Stevens, Peter F. (1994) The Development of Biological Systematics: Antoine-Laurent de Jussieu, Nature, and the Natural System. New York: Columbia University Press.
A conceptual history of classification and phylogenetics, mainly as related to plants. Focuses on the early development of ideas within biosystematics, with accompanying illustrations. Networks are effectively treated as variants of trees.
Pietsch, Theodore W. (2012) Trees of Life: a Visual History of Evolution. Baltimore: Johns Hopkins University Press.
A richly illustrated history of trees, with a few networks. Focuses on the illustrations, with some accompanying text. The best source to see what people have drawn in the way of trees, but weaker on networks.
Minaka, Nobuhiro, and Sugiyama, Kunihiko (2012) Phylogeny Mandala: Chain, Tree, and Network. Tokyo: NTT Publishing.
In Japanese. Covers the development of the tree metaphor (with a few networks), as related to pedigrees, phylogenies, and knowledge representation in general. The breadth of the topic is indicated in the "mandala" of the title, which is "a generic term for any diagram, chart or geometric pattern that represents the cosmos metaphysically or symbolically".
Archibald, J. David (2014) Aristotle's Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. New York: Columbia University Press.
A conceptual history of trees, with a few networks. Focuses on the development of the ideas, with accompanying illustrations. Starts with pedigrees, and proceeds from there to phylogenies. The best coverage of phylogeny concepts, but explicitly treats networks as "trees with reticulations".
A 3 year post-doctoral position, including a 25% teaching component, is available at the University of Turku, Finland to work in Prof. Craig Primmer’s research group (http://bit.ly/1GJxNWk). The research component of the position is a part of a research consortium that aims at integrating evolutionary genetics, ecological modelling and environmental sociology to understand the external drivers of life history changes in a heavily fished Atlantic salmon population complex and to advance sustainable use of these aquatic natural resources. This project has been recently funded as a part of the Finnish Academy Arctic Research program (http://bit.ly/1cXXPXY) The post-doc will be responsible for conducting and co-supervising research investigating the genetic basis of life-history traits such as age at maturity (e.g. Johnston et al. 2014) and repeat spawning, as well as conducting genome scans for identifying genes involved in adaptation to local environmental conditions. Teaching will involve giving lectures and computer classes on topics related to the position. Suitable candidates will have a strong background in evolutionary genetics/genomics and/or quantitative genetics research (in any species). Experience with the methodologies for analysis of large-scale SNP and high-throughput sequencing data is an advantage, as is an interest in conservation genetics and fisheries management. Undergraduate teaching experience is also advantageous. Informal inquiries should be directed to Prof. Craig Primmer (firstname.lastname@example.org). Formal applications should include a CV (with names and contact details of at least two referees), a publication list, an academic portfolio and a max. 2 page letter of motivation and can be submitted at http://bit.ly/1GJxNWm. The deadline for applications is August 3, with the preferred starting date being January 2016 or earlier. The position is available until the end of 2018. The starting salary is approx. 3140 - 3500 EUR per month, depending on the previous relevant research and teaching experience of the candidate. Turku, Finland’s 5th largest city (176 000 people), is located in the southwestern Finland. It has a rich cultural history and is the gateway to a beautiful archipelago. The University of Turku is one of the major multidisciplinary universities in Finland and is ranked in the top 5% of universities in the world. Johnston et al. (2014) Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar). Molecular Ecology 23: 3452-3468 via Gmail
ANNOUNCEMENT / REMINDER Dear EVOLdir subscriber Applications are open for PGDH15 Population Genetics and Demographic History: model-based approaches with Mark Beaumont, Lounes Chikhi, Willy Rodriguez and Barbara Parreira IMPORTANT DATES for this Course Deadline for applications: June 28th 2015 Latest notification of acceptance: July 1st 2015 Course date: July 6th - July 9th 2015 Details are available at: http://bit.ly/1BjCdko Course description Genetic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this four-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation, as they are connected to what makes landscape genetics today on the basis of multilocus data. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to detect population structure as implemented in the program STRUCTURE and discuss related programs such as FastSTRUCTURE. We will learn how to perform coalescent simulations of genetic data (using SPAms and ms). Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Thanks for your interest, Pedro via Gmail
**LAST CALL - LIMITED SPACES AVAILABLE** THIRD INTERNATIONAL ENVIRONMENTAL ‘OMICS SYNTHESIS CONFERENCE - IEOS2015 University of St Andrews 6-8 July 2015 http://bit.ly/1HHj0eI DEADLINE for registration and abstract submission (posters only): EXTENDED to 19 June 2015 DEADLINE for application for postgraduate student bursaries: EXTENDED to 19 June 2015 STUDENT BURSARIES: Postgraduate students who submit abstracts are eligible for a bursary, covering 100% of the registration fee. When submitting an abstract, students should indicate they wish to be considered for a bursary. Successful applicants will receive a code for FREE registration. KEYNOTE SPEAKERS: Professor ELIZABETH THOMPSON, University of Washington http://bit.ly/1GJFnOS Professor MARK BLAXTER, University of Edinburgh http://bit.ly/1AG0jpq Professor BARBARA METHE, J Craig Venter Institute http://bit.ly/1R3mPud INVITED SPEAKERS: Dr LOGAN KISTLER, University of Warwick http://bit.ly/1GJFkm9 Dr UMER ZEESHAN IJAZ, University of Glasgow http://bit.ly/1R3mPuf Professor JIANQUAN LIU, Lanzhou University http://bit.ly/1R3mPuh Dr NATHAN BAILEY, University of St Andrews http://bit.ly/1GJFkmd Professor C-H CHRISTINA CHENG, University of Illinois at Urbana-Champaign http://bit.ly/1R3mPuj Dr DAVID MARSHALL, James Hutton Institute http://bit.ly/1GJFnOW Professor DAVID WALLOM, Oxford University http://bit.ly/1R3mPup Professor DANNIE DURAND, Carnegie Mellon University http://bit.ly/1GJFnP1 IEOS2015: The aim of this conference is to bring together researchers and organisations from a range of disciplines with shared interests in the development of new approaches for data handling, generation and analysis in environmental omics. Science areas of interest include bioinformatics, DNA-barcoding, genomics, metagenomics, metabarcoding, transcriptomics, proteomics, metabolomics, epigenetics, evolutionary and ecological omics, phylogenetics, study of ancient DNA and anthropology, new tools, resources and training, and beyond as applied to the study of the natural environmental and environmentally relevant organisms and systems. It is our hope is that the resulting interaction and exchange of ideas will lead to novel approaches, new collaborations and the consolidation of a wider integrated environmental 'omics community. EOS and this conference are supported by Natural Environmental Research Council (NERC) through its Mathematics and Informatics for Environmental 'Omics Data Synthesis programme and the UK Science and Technology Facilities Council (STFC) Global Challenges programme. PRE- and POST- MEETING WORKSHOPS http://bit.ly/1R3mPur 6 July - training workshops provided by the NERC Biomolecular Analysis Facility Gene expression analysis Metabolomics workshop Restriction-site Associated DNA (RAD) Data Analysis eDNA & metabarcoding 9 July Analyzing environmental DNA: Bio-Linux on the EOS Cloud (T. Booth, CEH Wallingford) >From reads to genes, a NGS analysis (Dr M. Pinheiro, University of St Andrews) SUMMER OF V’S IEOS2015 attendees are also welcome at a separate meeting on Data Science, The Summer of V’s, immediately preceding the main registration event for IEOS. Separate registration is required for the Summer of V’s: http://bit.ly/1R3mRT6 IEOS2015: http://bit.ly/1HHj0eI With best wishes, Professor Thomas Meagher, Chair The IEOS Conference Organising Committee http://bit.ly/1R3mPus The University of St Andrews is a charity registered in Scotland : No SC013532 Professor Thomas R. Meagher School of Biology, Sir Harold Mitchell Building University of St Andrews St Andrews KY16 9TH UK +44(0)1334 463364 office +44(0)7793356889 mobile +44(0)1334 463366 fax http://bit.ly/1IUL9NW Thomas Meagher via Gmail
We will welcome and give full support to postdoc applications for a Marie Curie fellowship (deadline 10 september 2015) in the fields of evolutionary ecology, infectious disease ecology and conservation biology. We particularly welcome applications related to evolutionary ecology of host-parasite interactions, ecology of infectious diseases, movement ecology (dispersal, connectivity, invasive species) and landscape genomics. We are a dynamic and internationally oriented research group with three Faculty members (Herwig Leirs, Erik Matthysen, Stefan Van Dongen), several postdocs and 10-15 PhD students. Our main model systems are birds and mammals, including their parasites and infectious diseases, in both temperate and tropical systems. We combine field research with state-of-the-art modelling and molecular approaches. We are core members of two of the nine currently recognized Excellence Consortia in the University of Antwerp (Global Change Ecology and Infectious Diseases). We will be happy to discuss possible projects and assist candidates with applications for Marie Curie funding, as well as other funding options such as FWO postdoctoral fellowships. For more information on our projects and job opportunities, see our website at http://bit.ly/1GJr26P. Erik Prof. Dr. Erik Matthysen Evolutionary Ecology Group University of Antwerp Groenenborgerlaan 171, B-2020 Antwerpen 03 265 3464 Matthysen Erik via Gmail
Multilocus Phylogeny of the Afrotropical Freshwater Crab Fauna Reveals Historical Drainage Connectivity and Transoceanic Dispersal Since the Eocene
Phylogenetic reconstruction, divergence time estimations and ancestral range estimation were undertaken for 66% of the Afrotropical freshwater crab fauna (Potamonautidae) based on four partial DNA loci (12S rRNA, 16S rRNA, cytochrome oxidase one [COI], and histone 3). The present study represents the most comprehensive taxonomic sampling of any freshwater crab family globally, and explores the impact of paleodrainage interconnectivity on cladogenesis among freshwater crabs. Phylogenetic analyses of the total evidence data using maximum-likelihood (ML), maximum parsimony (MP), and Bayesian inference (BI) produced a robust statistically well-supported tree topology that reaffirmed the monophyly of the Afrotropical freshwater crab fauna. The estimated divergence times suggest that the Afrotropical Potamonautidae diverged during the Eocene. Cladogenesis within and among several genera occurred predominantly during the Miocene, which was associated with major tectonic and climatic ameliorations throughout the region. Paleodrainage connectivity was observed with specimens from the Nilo-Sudan and East African coast proving to be sister to specimens from the Upper Guinea Forests in West Africa. In addition, we observed strong sister taxon affinity between specimens from East Africa and the Congo basin, including specimens from Lake Tanganyika, while the southern African fauna was retrieved as sister to the Angolan taxa. Within the East African clade we observed two independent transoceanic dispersal events, one to the Seychelles Archipelago and a second to Madagascar, while we observe a single transoceanic dispersal event from West Africa to São Tomé. The ancestral area estimation suggested a West African/East African ancestral range for the family with multiple dispersal events between southern Africa and East Africa, and between East Africa and Central Africa The taxonomic implications of our results are discussed in light of the widespread paraphyly evident among a number of genera.
Phylogenetic comparative methods offer a suite of tools for studying trait evolution. However, most models inherently assume fixed trait values within species. Although some methods can incorporate error around species means, few are capable of accounting for variation driven by environmental or temporal gradients, such as trait responses to abiotic stress or ontogenetic trajectories. Such traits, often referred to as function-valued or infinite-dimensional, are typically expressed as reaction norms, dose–response curves, or time plots and are described by mathematical functions linking independent predictor variables to the trait of interest. Here, I introduce a method for extending ancestral state reconstruction to incorporate function-valued traits in a phylogenetic generalized least squares (PGLS) framework, as well as extensions of this method for testing phylogenetic signal, performing phylogenetic analysis of variance (ANOVA), and testing for correlated trait evolution using recently proposed multivariate PGLS methods. Statistical power of function-valued comparative methods is compared to univariate approaches using data simulations, and the assumptions and challenges of each are discussed in detail.
Approximate Bayesian Computation Reveals the Crucial Role of Oceanic Islands for the Assembly of Continental Biodiversity
The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology