This document summarizes research on social evolution in ants. It discusses various ant species like leaf-cutter ants, weaver ants, and Forelius pusillus ants. It also discusses fire ants and their single and multiple queen social forms which are associated with their Gp-9 gene. Genome sequencing of the fire ant revealed expansion of odor receptor genes and other findings. The document covers topics like kin selection, evolution of eusociality, and using modern technologies to study insect societies.
The document appears to be about the genome of the red fire ant Solenopsis invicta. It summarizes some key findings from sequencing and analyzing the fire ant genome. These include an expansion of gene families related to lipid processing and cuticular hydrocarbons. It also found over 420 putative olfactory receptor genes, more than any other insect genome sequenced. Additionally, the genome appears to have a functional DNA methylation system.
The document discusses the genetic basis of social organization in fire ant populations. Researchers used RAD sequencing of haploid males to discover SNPs and genotype individuals at over 2,400 loci. Principal component analysis separated individuals into two clusters corresponding to their social form (single or multiple queen), with the first principal component explaining over 12% of the variance. A region on chromosome 13 containing the Gp-9 gene was completely associated with social form. This research identified a major gene influencing an important social trait using next-generation sequencing techniques.
50% social chromosomes in ants, 50% bioinformatics for genomics in emerging model organisms. Given at #CTBio http://pathogenomics.bham.ac.uk/blog/2013/07/cream-teas-and-bioinformatics-balti-and-bioinformatics-goes-on-its-holidays/
Apologies - videos and transitions are largely missing as part of the PDF conversion.
The work referenced here includes:
http://dx.doi.org/10.1038/nature11832
http://dx.doi.org/10.1073/pnas.1009690108
http://sequenceserver.com
https://github.com/yeban/afra & http://afra.sbcs.qmul.ac.uk
https://github.com/monicadragan/GeneValidator
Big Data and Outlier Loci: A Cautionary Tale with Genome-Scale Phylogenetic Datajembrown
This document discusses how outlier loci can influence phylogenetic analyses using genome-scale data. The authors analyze several datasets and find that a small percentage of outlier genes strongly support alternative tree topologies compared to the consensus. Removing these outlier genes changes the overall inferred tree. Possible causes of outlier loci include paralogy and systematic errors. The authors recommend using Bayes factors to identify outlier loci and caution that small analytical choices can significantly affect phylogenetic results when using large genomic datasets.
This playlist features songs about love and peace from the 1960s and 1970s. It includes hits from The Black Eyed Peas, The Beatles, Dionne Warwick, Paul Metsa, John Lennon, and others. The songs convey messages of finding love, coming together, and giving peace a chance.
O documento discute a origem biológica do altruísmo entre parentes. Explica que o altruísmo parece paradoxal na teoria da evolução, mas que a visão centrada nos genes, desenvolvida por Hamilton, Williams e Dawkins, mostra como genes egoístas podem programar comportamentos altruístas entre parentes, aumentando a disseminação dos genes compartilhados na população. A teoria da seleção de parentesco de Hamilton fornece uma equação matemática para quando o altruísmo é benéfico aos genes.
Behavioral ecology studies how behavior is controlled, develops, evolves, and contributes to survival. Behaviors can be studied from proximate and ultimate perspectives, with proximate questions focusing on environmental triggers and ultimate questions on evolutionary significance. Fixed action patterns are innate behavioral sequences triggered by stimuli, while imprinting involves both learning and innate components during a limited developmental phase. Both genes and environment influence behavior, with innate behaviors being developmentally fixed regardless of environment.
The document summarizes two theories that explain altruism: kin selection theory and empathy-altruism theory. Kin selection theory proposes that altruism evolved through kin-directed behavior that benefits genetic relatives, increasing their chances of survival. Empathy-altruism theory suggests altruism stems from empathy, the ability to understand another's perspective and experience, which leads to helping behaviors intended to benefit others rather than oneself. Both theories have strengths in explaining certain aspects of altruism but also limitations, such as kin selection not accounting for helping non-relatives and empathy not always predicting altruistic actions.
The document appears to be about the genome of the red fire ant Solenopsis invicta. It summarizes some key findings from sequencing and analyzing the fire ant genome. These include an expansion of gene families related to lipid processing and cuticular hydrocarbons. It also found over 420 putative olfactory receptor genes, more than any other insect genome sequenced. Additionally, the genome appears to have a functional DNA methylation system.
The document discusses the genetic basis of social organization in fire ant populations. Researchers used RAD sequencing of haploid males to discover SNPs and genotype individuals at over 2,400 loci. Principal component analysis separated individuals into two clusters corresponding to their social form (single or multiple queen), with the first principal component explaining over 12% of the variance. A region on chromosome 13 containing the Gp-9 gene was completely associated with social form. This research identified a major gene influencing an important social trait using next-generation sequencing techniques.
50% social chromosomes in ants, 50% bioinformatics for genomics in emerging model organisms. Given at #CTBio http://pathogenomics.bham.ac.uk/blog/2013/07/cream-teas-and-bioinformatics-balti-and-bioinformatics-goes-on-its-holidays/
Apologies - videos and transitions are largely missing as part of the PDF conversion.
The work referenced here includes:
http://dx.doi.org/10.1038/nature11832
http://dx.doi.org/10.1073/pnas.1009690108
http://sequenceserver.com
https://github.com/yeban/afra & http://afra.sbcs.qmul.ac.uk
https://github.com/monicadragan/GeneValidator
Big Data and Outlier Loci: A Cautionary Tale with Genome-Scale Phylogenetic Datajembrown
This document discusses how outlier loci can influence phylogenetic analyses using genome-scale data. The authors analyze several datasets and find that a small percentage of outlier genes strongly support alternative tree topologies compared to the consensus. Removing these outlier genes changes the overall inferred tree. Possible causes of outlier loci include paralogy and systematic errors. The authors recommend using Bayes factors to identify outlier loci and caution that small analytical choices can significantly affect phylogenetic results when using large genomic datasets.
This playlist features songs about love and peace from the 1960s and 1970s. It includes hits from The Black Eyed Peas, The Beatles, Dionne Warwick, Paul Metsa, John Lennon, and others. The songs convey messages of finding love, coming together, and giving peace a chance.
O documento discute a origem biológica do altruísmo entre parentes. Explica que o altruísmo parece paradoxal na teoria da evolução, mas que a visão centrada nos genes, desenvolvida por Hamilton, Williams e Dawkins, mostra como genes egoístas podem programar comportamentos altruístas entre parentes, aumentando a disseminação dos genes compartilhados na população. A teoria da seleção de parentesco de Hamilton fornece uma equação matemática para quando o altruísmo é benéfico aos genes.
Behavioral ecology studies how behavior is controlled, develops, evolves, and contributes to survival. Behaviors can be studied from proximate and ultimate perspectives, with proximate questions focusing on environmental triggers and ultimate questions on evolutionary significance. Fixed action patterns are innate behavioral sequences triggered by stimuli, while imprinting involves both learning and innate components during a limited developmental phase. Both genes and environment influence behavior, with innate behaviors being developmentally fixed regardless of environment.
The document summarizes two theories that explain altruism: kin selection theory and empathy-altruism theory. Kin selection theory proposes that altruism evolved through kin-directed behavior that benefits genetic relatives, increasing their chances of survival. Empathy-altruism theory suggests altruism stems from empathy, the ability to understand another's perspective and experience, which leads to helping behaviors intended to benefit others rather than oneself. Both theories have strengths in explaining certain aspects of altruism but also limitations, such as kin selection not accounting for helping non-relatives and empathy not always predicting altruistic actions.
This document discusses altruism and factors that can hinder it or promote it. It defines altruism as unselfish concern for others simply to help them and not because of obligation. It identifies three factors that can hinder altruism: diffusion of responsibility, pluralistic ignorance, and procrastination. It also discusses reasons people help others, including biological tendencies, neurological rewards, and cognitive benefits like maintaining a positive self-view. Helping others can provide psychological, physical, and social well-being through reduced stress, illness, and increased empathy. The document encourages specific altruistic actions like random acts of kindness and volunteering.
Este documento discute o comportamento reprodutivo e sistemas de acasalamento de asininos. Ele descreve os padrões reprodutivos típicos de machos e fêmeas, incluindo vocalizações, cheiros e montas durante o acasalamento. A observação de campo de um asinino esterilizado não revelou comportamentos sexuais ou de acasalamento.
1) The document discusses whether true altruism exists or if human helping behavior is ultimately motivated by self-interest. It explores different theories on altruism including empathy-altruism theory and socio biological theory.
2) Empirical evidence is presented showing that people with high empathy will help others even at a cost to themselves, supporting the existence of true altruism, while those with low empathy only help to reduce their own distress.
3) Neuroscientific research found increased activity in brain regions associated with perspective taking in highly altruistic individuals, providing a potential biological basis for altruistic motivation.
This document summarizes key concepts around the evolution of behavior through natural selection and genetic inheritance. It discusses how behaviors are co-adapted through evolution to maximize survival and reproduction. Behaviors can be culturally transmitted between individuals without genetic changes. Kin selection theory explains how behaviors that help reproduce relatives' genes can also be selected for, if the degree of relatedness and benefits are high enough. Examples of genetic studies of behaviors in insects and vertebrates are provided to show the interaction between genes, development and environment in determining behaviors.
The document discusses several studies that examine cultural differences in prosocial behavior:
- Whiting (1975) found that children in Kenya were the most prosocial, while those in Japan and India were the least, and that household responsibilities predicted higher prosocial behavior.
- Levine et al (2003) observed helping behaviors across 23 countries and found that places like Brazil and Denmark ranked higher than the US, suggesting cultures emphasizing social responsibility over achievement help more.
- Korte & Ayvalioglu (1981) found that small communities and squatter settlements in Turkey helped strangers more than large cities or suburbs, indicating community size impacts prosocial norms.
This document discusses altruism and how it develops in children. It defines altruism as actions that benefit others without expecting a reward. Children learn altruism through conditioning, observational learning from altruistic models, and as their cognitive and social skills develop. The development of prosocial behaviors like altruism is encouraged through parenting strategies like explaining how one child's actions impact another's feelings.
The document discusses the concept of altruism, defined as concern for the welfare of others, and effective altruism, which applies evidence and reason to improve the world effectively. It also provides a case study on the annual Burning Man Festival, where over 50,000 people form a temporary city based on principles of gift-giving, sharing, and community without monetary exchange or expectations of reciprocity.
Kin selection theory explains the evolution of altruism. While altruism seems to go against individual survival and fitness, kin selection demonstrates that altruistic behavior can persist if the altruistic individual helps genetically similar relatives to survive and pass on shared genes. Key examples discussed are sterile worker ants helping their queen sister reproduce since they share three-quarters of their genes, and ground squirrels whose alarm calls risk individual safety but benefit genetically related neighbors. The theory was developed by W.D. Hamilton and others to explain how natural selection can favor altruism between kin.
What causes people to jeopardize their own health and well-being to help other people?
What is it that inspires individuals to give their time, energy, and money to aid in the betterment of others, even when they receive nothing tangible in return?
Altruism involves the unselfish concern for other people.
It involves doing things simply out of a desire to help, not because you feel obligated to out of duty, loyalty, or religious reasons.
Everyday life is filled with small acts of altruism, from the person who offers his own seats in a Bus OLD/LADIES to the person who gives money to a Beggar or offering blanket to the shivering person on the street.
Psychological explantion for the same has been discussed
1) The bystander effect occurs when the presence of others decreases the likelihood that an individual will help a victim. As the number of bystanders increases, any single person is less likely to notice the emergency, interpret it as such, or take responsibility to help.
2) People are more likely to help those they perceive as similar to themselves in attributes like age, nationality, appearance, or values. Similarity promotes liking and empathy.
3) Having less time available, as in a hurry, reduces the likelihood someone will help in an emergency situation.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against developing mental illness and improve symptoms for those who already suffer from conditions like anxiety and depression.
This document contrasts two theories that explain altruism: the kin selection theory and the empathy-altruism theory. The kin selection theory proposes that altruism evolved through natural selection to benefit an individual's genes, while the empathy-altruism theory argues that feeling empathy for others leads to true altruistic behavior intended to help others rather than oneself. Both theories have strengths in explaining certain aspects of altruism but also have limitations, such as the kin selection theory not accounting for helping non-relatives and the empathy-altruism theory having questionable real-world applicability outside experimental settings.
The document discusses genomic research on fire ants. It summarizes that the genome of a fire ant was sequenced, which revealed an expansion of lipid-processing and olfactory receptor genes. Over 400 putative olfactory receptors were identified, more than any other insect sequenced so far. The genome also contains a functional DNA methylation system. Previous research on fire ants linked their social structure to a single gene (Gp-9), but sequencing of the entire genome allowed further investigation into other genes that may be linked.
The document discusses genomic analysis of the fire ant Solenopsis invicta. It notes that the genome sequencing of a Gp-9 B male fire ant revealed an expansion of lipid-processing gene families and over 420 putative olfactory receptors, more than any other insect. It also identified a functional DNA methylation system. Previous research had linked the fire ant's social structure to its Gp-9 locus, but genome sequencing provided more genomic context around this gene and others related to social behavior and chemical signaling.
Keynote talk given at Fairdom User meeting http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/ .
I begin by summarising how we apply molecular approaches to understand social behaviour in ants. Subsequently, I give an overview of the data-handling challenges the genomic bioinformatics community faces. Finally, I give an overview of some of the tools and approaches my lab have developed to help us get things done better, faster, more reliably and more reproducibly.
Evolution of North American MicruracarusRachel Shoop
My research focuses on the evolution of North American water mites in the genus Arrenurus, Subgenus Micruracarus. In this presentation, I discuss why I chose to study these little known critters, and present some preliminary findings. Please contact me for more info.
"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February...Jonathan Eisen
The document discusses the author's quest to create a field guide to microbes. It describes the challenges in doing so given microbes' small size and high diversity. The author discusses using DNA sequencing and phylogenetic trees to identify microbes and determine their functions and relationships. Examples are given of using DNA to study human microbiomes, forensic analysis, and microbial communities. The need for a comprehensive field guide is argued to better understand the roles and identification of microbes.
Lamarck's theory of evolution proposed that acquired characteristics could be inherited, such as giraffes developing longer necks due to stretching to reach leaves. Darwin later established the theory of evolution by natural selection, whereby favorable variations or adaptations are preserved and passed on during reproduction, while unfavorable traits are selected against. Evidence for evolution includes fossils that show gradual changes in organisms over time, as well as anatomical, embryological, and molecular similarities between different species.
This document discusses using the nematode C. elegans as a model organism to uncover the genetic basis of natural variation in behavior and development. Key points:
1) C. elegans exhibits diverse behaviors and phenotypes in the wild that can be quantified using high-throughput tracking of locomotion features in response to stimuli like CO2.
2) Machine learning techniques like Iterative Denoising Trees are used to reduce the dimensionality of time-series behavior data from many wild C. elegans strains into distinct behavioral profiles.
3) Genome sequencing of wild strains reveals genetic variation that can be tested for association with behavioral profiles using methods like MURAT to identify candidate genes underlying natural phenotypic differences.
This document provides an overview of genome sequencing. It discusses the history of genome sequencing, from early sequencing of small viruses in the 1970s to larger genomes like yeast and the human genome. The document outlines different sequencing technologies over time, from Sanger sequencing to newer single-molecule approaches. It also summarizes key genome projects like ENCODE and 1000 Genomes that have provided insights into non-coding regulatory elements and human genetic variation.
Prokaryotes like bacteria and archaea thrive in nearly all environments on Earth due to their small size and genetic diversity. They have a variety of shapes and structural adaptations, like cell walls, flagella, and capsules, that allow them to live in diverse habitats. Prokaryotes reproduce rapidly through binary fission and exchange genes through transformation, transduction, and conjugation, resulting in high genetic variation. Their simple structures and metabolic diversity allow prokaryotes to fill many ecological roles as decomposers, symbionts, and pathogens.
This document discusses altruism and factors that can hinder it or promote it. It defines altruism as unselfish concern for others simply to help them and not because of obligation. It identifies three factors that can hinder altruism: diffusion of responsibility, pluralistic ignorance, and procrastination. It also discusses reasons people help others, including biological tendencies, neurological rewards, and cognitive benefits like maintaining a positive self-view. Helping others can provide psychological, physical, and social well-being through reduced stress, illness, and increased empathy. The document encourages specific altruistic actions like random acts of kindness and volunteering.
Este documento discute o comportamento reprodutivo e sistemas de acasalamento de asininos. Ele descreve os padrões reprodutivos típicos de machos e fêmeas, incluindo vocalizações, cheiros e montas durante o acasalamento. A observação de campo de um asinino esterilizado não revelou comportamentos sexuais ou de acasalamento.
1) The document discusses whether true altruism exists or if human helping behavior is ultimately motivated by self-interest. It explores different theories on altruism including empathy-altruism theory and socio biological theory.
2) Empirical evidence is presented showing that people with high empathy will help others even at a cost to themselves, supporting the existence of true altruism, while those with low empathy only help to reduce their own distress.
3) Neuroscientific research found increased activity in brain regions associated with perspective taking in highly altruistic individuals, providing a potential biological basis for altruistic motivation.
This document summarizes key concepts around the evolution of behavior through natural selection and genetic inheritance. It discusses how behaviors are co-adapted through evolution to maximize survival and reproduction. Behaviors can be culturally transmitted between individuals without genetic changes. Kin selection theory explains how behaviors that help reproduce relatives' genes can also be selected for, if the degree of relatedness and benefits are high enough. Examples of genetic studies of behaviors in insects and vertebrates are provided to show the interaction between genes, development and environment in determining behaviors.
The document discusses several studies that examine cultural differences in prosocial behavior:
- Whiting (1975) found that children in Kenya were the most prosocial, while those in Japan and India were the least, and that household responsibilities predicted higher prosocial behavior.
- Levine et al (2003) observed helping behaviors across 23 countries and found that places like Brazil and Denmark ranked higher than the US, suggesting cultures emphasizing social responsibility over achievement help more.
- Korte & Ayvalioglu (1981) found that small communities and squatter settlements in Turkey helped strangers more than large cities or suburbs, indicating community size impacts prosocial norms.
This document discusses altruism and how it develops in children. It defines altruism as actions that benefit others without expecting a reward. Children learn altruism through conditioning, observational learning from altruistic models, and as their cognitive and social skills develop. The development of prosocial behaviors like altruism is encouraged through parenting strategies like explaining how one child's actions impact another's feelings.
The document discusses the concept of altruism, defined as concern for the welfare of others, and effective altruism, which applies evidence and reason to improve the world effectively. It also provides a case study on the annual Burning Man Festival, where over 50,000 people form a temporary city based on principles of gift-giving, sharing, and community without monetary exchange or expectations of reciprocity.
Kin selection theory explains the evolution of altruism. While altruism seems to go against individual survival and fitness, kin selection demonstrates that altruistic behavior can persist if the altruistic individual helps genetically similar relatives to survive and pass on shared genes. Key examples discussed are sterile worker ants helping their queen sister reproduce since they share three-quarters of their genes, and ground squirrels whose alarm calls risk individual safety but benefit genetically related neighbors. The theory was developed by W.D. Hamilton and others to explain how natural selection can favor altruism between kin.
What causes people to jeopardize their own health and well-being to help other people?
What is it that inspires individuals to give their time, energy, and money to aid in the betterment of others, even when they receive nothing tangible in return?
Altruism involves the unselfish concern for other people.
It involves doing things simply out of a desire to help, not because you feel obligated to out of duty, loyalty, or religious reasons.
Everyday life is filled with small acts of altruism, from the person who offers his own seats in a Bus OLD/LADIES to the person who gives money to a Beggar or offering blanket to the shivering person on the street.
Psychological explantion for the same has been discussed
1) The bystander effect occurs when the presence of others decreases the likelihood that an individual will help a victim. As the number of bystanders increases, any single person is less likely to notice the emergency, interpret it as such, or take responsibility to help.
2) People are more likely to help those they perceive as similar to themselves in attributes like age, nationality, appearance, or values. Similarity promotes liking and empathy.
3) Having less time available, as in a hurry, reduces the likelihood someone will help in an emergency situation.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against developing mental illness and improve symptoms for those who already suffer from conditions like anxiety and depression.
This document contrasts two theories that explain altruism: the kin selection theory and the empathy-altruism theory. The kin selection theory proposes that altruism evolved through natural selection to benefit an individual's genes, while the empathy-altruism theory argues that feeling empathy for others leads to true altruistic behavior intended to help others rather than oneself. Both theories have strengths in explaining certain aspects of altruism but also have limitations, such as the kin selection theory not accounting for helping non-relatives and the empathy-altruism theory having questionable real-world applicability outside experimental settings.
The document discusses genomic research on fire ants. It summarizes that the genome of a fire ant was sequenced, which revealed an expansion of lipid-processing and olfactory receptor genes. Over 400 putative olfactory receptors were identified, more than any other insect sequenced so far. The genome also contains a functional DNA methylation system. Previous research on fire ants linked their social structure to a single gene (Gp-9), but sequencing of the entire genome allowed further investigation into other genes that may be linked.
The document discusses genomic analysis of the fire ant Solenopsis invicta. It notes that the genome sequencing of a Gp-9 B male fire ant revealed an expansion of lipid-processing gene families and over 420 putative olfactory receptors, more than any other insect. It also identified a functional DNA methylation system. Previous research had linked the fire ant's social structure to its Gp-9 locus, but genome sequencing provided more genomic context around this gene and others related to social behavior and chemical signaling.
Keynote talk given at Fairdom User meeting http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/ .
I begin by summarising how we apply molecular approaches to understand social behaviour in ants. Subsequently, I give an overview of the data-handling challenges the genomic bioinformatics community faces. Finally, I give an overview of some of the tools and approaches my lab have developed to help us get things done better, faster, more reliably and more reproducibly.
Evolution of North American MicruracarusRachel Shoop
My research focuses on the evolution of North American water mites in the genus Arrenurus, Subgenus Micruracarus. In this presentation, I discuss why I chose to study these little known critters, and present some preliminary findings. Please contact me for more info.
"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February...Jonathan Eisen
The document discusses the author's quest to create a field guide to microbes. It describes the challenges in doing so given microbes' small size and high diversity. The author discusses using DNA sequencing and phylogenetic trees to identify microbes and determine their functions and relationships. Examples are given of using DNA to study human microbiomes, forensic analysis, and microbial communities. The need for a comprehensive field guide is argued to better understand the roles and identification of microbes.
Lamarck's theory of evolution proposed that acquired characteristics could be inherited, such as giraffes developing longer necks due to stretching to reach leaves. Darwin later established the theory of evolution by natural selection, whereby favorable variations or adaptations are preserved and passed on during reproduction, while unfavorable traits are selected against. Evidence for evolution includes fossils that show gradual changes in organisms over time, as well as anatomical, embryological, and molecular similarities between different species.
This document discusses using the nematode C. elegans as a model organism to uncover the genetic basis of natural variation in behavior and development. Key points:
1) C. elegans exhibits diverse behaviors and phenotypes in the wild that can be quantified using high-throughput tracking of locomotion features in response to stimuli like CO2.
2) Machine learning techniques like Iterative Denoising Trees are used to reduce the dimensionality of time-series behavior data from many wild C. elegans strains into distinct behavioral profiles.
3) Genome sequencing of wild strains reveals genetic variation that can be tested for association with behavioral profiles using methods like MURAT to identify candidate genes underlying natural phenotypic differences.
This document provides an overview of genome sequencing. It discusses the history of genome sequencing, from early sequencing of small viruses in the 1970s to larger genomes like yeast and the human genome. The document outlines different sequencing technologies over time, from Sanger sequencing to newer single-molecule approaches. It also summarizes key genome projects like ENCODE and 1000 Genomes that have provided insights into non-coding regulatory elements and human genetic variation.
Prokaryotes like bacteria and archaea thrive in nearly all environments on Earth due to their small size and genetic diversity. They have a variety of shapes and structural adaptations, like cell walls, flagella, and capsules, that allow them to live in diverse habitats. Prokaryotes reproduce rapidly through binary fission and exchange genes through transformation, transduction, and conjugation, resulting in high genetic variation. Their simple structures and metabolic diversity allow prokaryotes to fill many ecological roles as decomposers, symbionts, and pathogens.
Prokaryotes like bacteria and archaea thrive in nearly all environments on Earth due to their small size and genetic diversity. They have a variety of shapes and structural adaptations, like cell walls, flagella, and capsules, that allow them to live in diverse habitats. Prokaryotes reproduce rapidly through binary fission and exchange genes through transformation, transduction, and conjugation, resulting in high genetic variation. Their simple structures and metabolic diversity allow prokaryotes to fill many ecological roles as decomposers, symbionts, and pathogens.
This PowerPoint was one very small part of my DNA and Genetics from the website http://sciencepowerpoint.com/index.html . Teaching Duration = 4+ Weeks
A five part, 3,000+ Slide PowerPoint roadmap delivers daily lessons full of meaningful hands-on activities, important red slide notes, built-in quizzes, video links, projects, 3 PowerPoint Review Games with Answers, discussion questions and much more. A homework package and detailed lesson notes chronologically follow the PowerPoint slideshow
The DNA and Genetics Unit covers science topics associated with the DNA molecule, discovery of DNA, DNA's structure, cellular division, cancer, dangers of smoking, meiosis, and genetics. This unit includes a five part interactive and engaging PowerPoint Presentation of 2000+ slides with built-in class notes (Red Slides), lab activities, project ideas, discussion questions, assessments (Quiz Wiz), challenge questions with answers, video links, and much more. Text is in large print (32 font) and is placed at the top of each slide so it can read from all angles of a classroom. A shade technique and color coded text helps to increase student focus and allows the teacher to control the pace of the lesson. The entire unit except for the videos can be edited to fit any curriculum or time requirement. Also included is a 14 page assessment that chronologically goes with the slideshow for nightly homework, as well as an 8 page modified assessment. 12 pages of class notes with images are also included for students who require modifications, as well as answer keys to both of the assessments for support professionals, teachers, and homeschool parents. 13 video links (.flv files) are provided and a slide within the slideshow cues teacher / parent when the videos are most relevant to play. Video shorts usually range from 2-7 minutes (internet connection needed). One PowerPoint review game is included (125+ slides). Answers to the PowerPoint review game are provided in PowerPoint form so students can self-assess. Lastly, several class games such as guess the hidden picture beneath the boxes, and the find the hidden owl somewhere within the slideshow are provided. Difficulty rating 9/10.
Areas of Focus within The DNA and Genetics Unit:
DNA, DNA Extraction, Structure of DNA, Transcription and Translation, Protein Synthesis, Discovery of the Double Helix, Rosalind Franklin, Nucleotides, RNA, Cell Division, Mitosis, Phases of Mitosis, Chromosomes, Cancer, Ways to Avoid Cancer, What's Inside a Cigarette?, Statistics about Smoking, Anti-Smoking Ads, Meiosis, Phases in Meiosis, Mendelian Genetics, Gregor Mendel, Punnett Squares, Probability, Dihybrid Cross, Codominance, Bio-Ethics, Stem Cell Debate, Cloning Debate.
Sincerely,
Ryan Murphy M.Ed
www.sciencepowerpoint@gmail.com
BIO 240 Exceptional Education - snaptutorial.comDavisMurphyB28
The document contains information about various biology worksheets and assignments for the course BIO 240. It includes summaries and questions about topics like crime scene forensics, disruption of a marine food web, DNA and protein synthesis, evolution, human evolution, inheritance of color blindness, invasive species, photosynthesis and cellular respiration, and systematics. The document provides learning objectives, instructions, and questions for students to complete various worksheets and assignments to demonstrate their understanding of key course concepts.
A presentation to the Bedfordshire Natural History Society in November 2016 for their "neglected insects" conference - provides an introduction to the Soldierflies and Allies Recording Scheme.
Inference and informatics in a 'sequenced' worldJoe Parker
Short lecture relating my recent work on real-time phylogenomics, implications for bioinformatics research and future directions of genomic/phylogenetic modelling to explicitly account for phylogeny, synteny and identity through coloured graphs.
University of Reading, 2nd August 2017
Bio 240 Enhance teaching / snaptutorial.comHarrisGeorg46
This document contains summaries of multiple biology worksheets and assignments for the course BIO 240. It includes summaries of worksheets on topics like crime scene forensics, disruption of a marine food web, DNA and protein synthesis, and the inheritance of color blindness. It also summarizes assignments on subjects like comparing cell structures, photosynthesis and respiration, natural selection, speciation, and human evolution. The document provides learning materials and prompts for students taking the BIO 240 course.
Validating and improving the D. melanogaster reference genome sequence using ...Casey Bergman
1) The document discusses using PacBio long read sequencing to improve the Drosophila melanogaster reference genome assembly.
2) PacBio sequencing generated over 15 billion bases of long read data, which was used to assemble the genome into contigs over 15 Mb in length with fewest errors compared to the reference.
3) The PacBio assemblies helped close gaps in the reference genome and generated large contigs from heterochromatic regions that were previously unassembled.
This document discusses the experience of a researcher in genomics with applying FAIR and open approaches. It notes that making data and analysis methods FAIR and open can increase visibility, drive citations, and facilitate collaboration. However, it also enables competition to more easily access and utilize resources without contributing. Striking the right balance between openness and protecting competitive advantages is challenging. Overall, the researcher finds FAIR and open principles have greatly increased the impact and robustness of their work, but there are also costs to consider.
This Presentation is especially for the grade 10 as it is informaive and can be used for the CBSE syllabus of india ( of course ). hope this helps you alot and if any problems please let me know from the comments section below.................peace out......... and message me at bavitharavi@hotmail.com. this is also the chpter 9 of the cbse gr 10 science book biology.
BIO 240 Education Organization -- snaptutorial.comDavisMurphyB94
For more classes visit
www.snaptutorial.com
• how forensic scientists take advantage of genomic variations in noncoding regions of DNA
• the techniques of polymerase chain reaction (PCR) and gel electrophoresis
Similar to 2014 11-24-sbsm028-yannicksocialevolution (20)
2018 08-reduce risks of genomics researchYannick Wurm
Geoffrey Chang, a protein crystallographer at The Scripps Research Institute, had his career trajectory disrupted when several of his high-profile papers describing protein structures had to be retracted. An in-house software program Chang's lab used to process diffraction data from protein crystals introduced a sign error that inverted the structures, invalidating biological interpretations. This included a 2001 Science paper describing the structure of the MsbA protein. A 2006 Nature paper by Swiss researchers casting doubt on Chang's MsbA structure led him to discover the software error. Chang and his co-authors sincerely regretted the confusion and unproductive research caused by the need to retract their influential papers.
Geoffrey Chang was a prominent structural biologist who received prestigious early career awards. However, his work came under scrutiny when other researchers discovered errors in his published protein structures due to a problem with his in-house data analysis software. This led Chang to retract 5 of his papers describing protein structures. The retractions were costly for Chang's career and reputation as well as for other researchers who had performed follow-up work based on the incorrect structures. The incident highlights the importance of using well-tested, reproducible analysis methods in scientific research.
This document provides an agenda for a spring school on bioinformatics and population genomics, including practical sessions on analyzing genomic data from reads to reference genomes and gene predictions in 6 steps: inspecting and cleaning reads, genome assembly, assessing assembly quality, predicting protein-coding genes, assessing gene prediction quality, and assessing the overall process quality using biological measures. It also addresses wifi issues that could reduce bandwidth and lists the VM password.
This document provides information about a spring school on bioinformatics and population genomics that includes practical sessions. The sessions will cover topics like short read cleaning, genome assembly, gene prediction, quality control, mapping reads to call variants, visualizing variants, analyzing variants through PCA and measuring diversity and differentiation, inferring population sizes and gene flow, and analyzing gene expression from raw sequencing data to expression levels. The document lists the team of practitioners leading the sessions and encourages participants to share their favorite software packages.
2015 12-18- Avoid having to retract your genomics analysis - Popgroup Reprodu...Yannick Wurm
Brief (15min) talk I gave at #PopGroup49 in Edinburgh providing a few simple methods to reduce risk in genomics analyses.
Please cite: Avoid having to retract your genomics analysis (2015) Y Wurm. The Winnower 2, e143696.68941 https://thewinnower.com/papers/avoid-having-to-retract-your-genomics-analysis
This document contains information about programming in R, including practical examples. It discusses accessing and subsetting data, using regular expressions for text search, creating functions, and using loops. Examples are provided to demonstrate creating vectors, accessing subsets of vectors, using regular expressions to find patterns in text, creating functions to convert between units or estimate values, and using for loops to repeat operations over multiple elements. The document suggests R is useful for working with big data in biology and other fields due to its ability to automate tasks, integrate with other tools, and handle large datasets through programming.
This document describes oSwitch, a tool that allows easy access to other operating systems via one-line commands. It works by wrapping Docker containers, allowing commands to be run in different OS environments without disrupting the user's current environment. The document provides an example usage where a user is able to run an "abyss-pe" command in a Biolinux container after it is not found in their native OS. It notes how oSwitch aims to preserve the user's current working directory, login shell, home directory and file permissions during usage.
This document provides an outline for a lecture on the genetic basis of evolution. It begins with introducing key terms like gene, locus, allele, genotype, and phenotype. It then discusses genetic drift and how drift is influenced by population size. Selection is also introduced and defined as a process where individuals with different genotypes have different fitnesses. The document emphasizes that both genetic drift and selection influence evolution, and neither process should be overemphasized. It aims to move people away from only considering selection (pan-selectionism) and highlights the importance of genetic drift.
This document discusses human evolution and recent insights from genomics. It summarizes that Neanderthals were the closest evolutionary relatives to modern humans and lived in Europe and Western Asia until disappearing 30,000 years ago. A draft sequence of the Neanderthal genome from three individuals was presented, composed of over 4 billion nucleotides. Comparisons with five modern human genomes identified regions potentially affected by selection in ancestral modern humans, involving genes related to metabolism, cognition, and skeletal development. Analysis suggests Neanderthals shared more genetic variants with non-Africans, indicating gene flow from Neanderthals into their ancestors occurred before Eurasian groups diverged.
The document discusses analyzing ancient plant and insect DNA extracted from ice core samples in Greenland. Key points:
- Plant and insect DNA was recovered from silty ice samples taken between 2-3 km deep in the Dye 3 and JEG ice cores in Greenland, dating back to before the last glacial period.
- The DNA was identified as coming from tree species like pine and alder, indicating a boreal forest environment in southern Greenland at the time, rather than today's Arctic conditions.
- Other plant species identified include those from orders like Asterales, Poales, Rosales and Malpighiales. Insect DNA from Lepidoptera was also recovered.
1. The document discusses best practices for scientific software development, including writing code for people rather than computers, automating repetitive tasks, using version control, and conducting code reviews.
2. Specific approaches and tools recommended are planning for mistakes, automated testing, continuous integration, and using a coding style guide. R and Ruby style guides are provided as examples.
3. The benefits of following such practices are improving productivity, reducing errors, making code easier to read and maintain, and allowing scientists to focus on scientific questions rather than software issues. Reproducible and sustainable software is the overall goal.
This document provides an introduction to regular expressions (regex) for text search and pattern matching. It explains that regex allows for powerful text searches beyond simple keywords. Various special symbols and constructs are demonstrated that allow matching complex patterns and variants in text. Examples show matching names, sequences, microsatellite repeats and more with regex. Functions, loops and logical operators in R programming are also briefly covered.
The document discusses major geological drivers of evolution including tectonic plate movement, vulcanism, climate change, and meteorite impacts. Tectonic plate movement has caused continental drift and formation of supercontinents like Pangaea, affecting species distributions. Vulcanism causes both local and global climate changes through emission of gases and particles and formation of new land barriers and islands. Climate changes over geological timescales have also impacted evolution. Meteorite impacts have precipitated mass extinctions. These geological forces alter Earth's conditions and drive evolution through large-scale migrations, speciation events, mass extinctions, and adaptive radiations.
This document provides an overview and schedule for the course "SBC 361 Research Methods & Comms". The course is a mixture of advanced analytical skills taught in computer labs using the programming language R, and theoretical content covered in lectures and workshops. It includes two workshops on careers in science and popular science writing. Students will complete assignments involving the computer practicals and tutorials, and a mock exam. The schedule details the topics to be covered each week by different professors and teaching staff. It emphasizes the importance of attending classes, completing required work, and doing additional outside reading to succeed in the course.
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
This document outlines the course SBC322 Ecological and Evolutionary Genomics. It discusses how new genomic technologies have changed ecology and evolution research by merging molecular and ecological approaches. It aims to critically evaluate research questions, methods, experimental designs and applications in ecological and evolutionary genomics. The course will improve students' skills in critically reading literature, understanding interdisciplinary science, and oral and written scientific communication through interactive small group work, informal and formal presentations, blog posts, and peer review.
The document provides an overview of topics covered in a bioinformatics course, including using Unix, bioinformatics algorithms, biological databases, sequencing technologies, and genome assembly and variant identification. It lists challenges for students in each topic area and provides examples of concepts that will be covered, such as using HPC systems, dynamic programming for sequence alignment, accessing databases like NCBI, processing sequencing data, and identifying variants from assembly. Images are included of different organisms like ants and sequencing technologies. The document aims to outline the scope and challenges of the bioinformatics course.
Sustainable software institute Collaboration workshopYannick Wurm
The document discusses tools for analyzing biological data. It summarizes four tools:
1. SequenceServer - A simple web interface for BLAST that handles formatting and installing BLAST locally.
2. oSwitch - Allows rapidly switching between operating systems and container environments to access specific bioinformatics software without installation.
3. GeneValidator - Helps curate gene predictions by identifying problematic predictions, choosing best alternative models, and aiding manual curation of individual genes.
4. Afra - A crowdsourcing platform that aims to crowdsource the visual inspection and correction of gene models by recruiting and training students, ensuring quality through tutorials, redundancy and senior review, and creating small, simple initial tasks.
This document provides an overview of genomic tools and best practices for scientific computing. It discusses SequenceServer, a tool for BLAST searches, and Bionode, a collection of Node.js modules for bioinformatics. It also discusses challenges with gene prediction and introduces GeneValidator, a tool for visual inspection and manual correction of gene predictions. Key points include automating repetitive tasks, writing code for people through style guides, and using version control and modularization to improve code quality and reproducibility.
This document discusses the importance of experimental design for ecological and evolutionary genomics experiments. It notes that poor experimental design can lead to insufficient or misleading data due to issues like pseudoreplication, confounding factors, or inappropriate analysis. The document advises considering factors like calibration of measurement tools, reducing subjective decision making, ensuring subjects are in natural conditions, and avoiding easy mistakes to create a robust experimental design. It also cautions that many types of experiments in ecological and evolutionary genomics, such as reference genome work, gene expression studies, field collections, population surveys, and identifying trait genes, have specific risks of going wrong if the experimental design is inadequate.
Falcon stands out as a top-tier P2P Invoice Discounting platform in India, bridging esteemed blue-chip companies and eager investors. Our goal is to transform the investment landscape in India by establishing a comprehensive destination for borrowers and investors with diverse profiles and needs, all while minimizing risk. What sets Falcon apart is the elimination of intermediaries such as commercial banks and depository institutions, allowing investors to enjoy higher yields.
Vicinity Jobs’ data includes more than three million 2023 OJPs and thousands of skills. Most skills appear in less than 0.02% of job postings, so most postings rely on a small subset of commonly used terms, like teamwork.
Laura Adkins-Hackett, Economist, LMIC, and Sukriti Trehan, Data Scientist, LMIC, presented their research exploring trends in the skills listed in OJPs to develop a deeper understanding of in-demand skills. This research project uses pointwise mutual information and other methods to extract more information about common skills from the relationships between skills, occupations and regions.
A toxic combination of 15 years of low growth, and four decades of high inequality, has left Britain poorer and falling behind its peers. Productivity growth is weak and public investment is low, while wages today are no higher than they were before the financial crisis. Britain needs a new economic strategy to lift itself out of stagnation.
Scotland is in many ways a microcosm of this challenge. It has become a hub for creative industries, is home to several world-class universities and a thriving community of businesses – strengths that need to be harness and leveraged. But it also has high levels of deprivation, with homelessness reaching a record high and nearly half a million people living in very deep poverty last year. Scotland won’t be truly thriving unless it finds ways to ensure that all its inhabitants benefit from growth and investment. This is the central challenge facing policy makers both in Holyrood and Westminster.
What should a new national economic strategy for Scotland include? What would the pursuit of stronger economic growth mean for local, national and UK-wide policy makers? How will economic change affect the jobs we do, the places we live and the businesses we work for? And what are the prospects for cities like Glasgow, and nations like Scotland, in rising to these challenges?
[4:55 p.m.] Bryan Oates
OJPs are becoming a critical resource for policy-makers and researchers who study the labour market. LMIC continues to work with Vicinity Jobs’ data on OJPs, which can be explored in our Canadian Job Trends Dashboard. Valuable insights have been gained through our analysis of OJP data, including LMIC research lead
Suzanne Spiteri’s recent report on improving the quality and accessibility of job postings to reduce employment barriers for neurodivergent people.
Decoding job postings: Improving accessibility for neurodivergent job seekers
Improving the quality and accessibility of job postings is one way to reduce employment barriers for neurodivergent people.
KYC Compliance: A Cornerstone of Global Crypto Regulatory FrameworksAny kyc Account
This presentation explores the pivotal role of KYC compliance in shaping and enforcing global regulations within the dynamic landscape of cryptocurrencies. Dive into the intricate connection between KYC practices and the evolving legal frameworks governing the crypto industry.
Dr. Alyce Su Cover Story - China's Investment Leadermsthrill
In World Expo 2010 Shanghai – the most visited Expo in the World History
https://www.britannica.com/event/Expo-Shanghai-2010
China’s official organizer of the Expo, CCPIT (China Council for the Promotion of International Trade https://en.ccpit.org/) has chosen Dr. Alyce Su as the Cover Person with Cover Story, in the Expo’s official magazine distributed throughout the Expo, showcasing China’s New Generation of Leaders to the World.
Discover the Future of Dogecoin with Our Comprehensive Guidance36 Crypto
Learn in-depth about Dogecoin's trajectory and stay informed with 36crypto's essential and up-to-date information about the crypto space.
Our presentation delves into Dogecoin's potential future, exploring whether it's destined to skyrocket to the moon or face a downward spiral. In addition, it highlights invaluable insights. Don't miss out on this opportunity to enhance your crypto understanding!
https://36crypto.com/the-future-of-dogecoin-how-high-can-this-cryptocurrency-reach/
OJP data from firms like Vicinity Jobs have emerged as a complement to traditional sources of labour demand data, such as the Job Vacancy and Wages Survey (JVWS). Ibrahim Abuallail, PhD Candidate, University of Ottawa, presented research relating to bias in OJPs and a proposed approach to effectively adjust OJP data to complement existing official data (such as from the JVWS) and improve the measurement of labour demand.
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19. Animal biomass (Brazilian rainforest)
Mammals
Birds
Reptiles
Other insects Amphibians
from Fittkau & Klinge 1973
!
Earthworms
!
!
Spiders
Soil fauna excluding
earthworms,
ants & termites
Ants & termites
20. We use modern technologies to
understand insect societies.
• evolution of social behaviour
• molecules involved in social behaviour
• consequences of environmental change
21. Major transitions:
eusociality
• Solitary lifestyle --> Eusociality
1. Reproductive division of labor
2. Overlapping generations (older
offspring help younger offspring)
3. Cooperative care of young
Eg: ants, bees, wasps, termites. But also:
naked mole rats, a beetle, a shrimp...
26. Major transitions: eusociality !
Hamilton’s rule: genes for altruistic behavior increase in frequency when:
r ₒ > C
indirect fitness benefits to the receiver (B) ,
reduced by the coefficient of relatedness (r)
Hamilton, 1964
B
between altruist & receiver,
exceeds costs to the altruist (C).
General framework: Kin selection: can favor the reproductive success of
an organism's relatives (ie. indirect fitness), even at a cost to the
organism's own survival and reproduction.
27.
28.
29. Downloaded from www.sciencemag.org on March 12, 2013 Solenopsis invicta fire ants are
REPORTS
a big problem!
very well studied!
Ascunce et al 2011
30. Solenopsis invicta fire ant:
two social forms
Single-queen form: Multiple-queen form:
!
•1 large queen
•Independent founding
•Highly territorial
•Many sizes of workers
!
•2-100 smaller queens
•Dependent founding
•No inter-colony
aggression
•All workers similar size
32. Allozyme screen Social form associated to Gp-9 locus
Frequency of
the most
common allele!
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!
Ken Ross and colleagues
Laurent Keller and colleagues
33. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues
34. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb bb
Ken Ross and colleagues
Laurent Keller and colleagues
35. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
x
BB BB Bb bb
Gp-9 bb females rare
Ken Ross and colleagues
Laurent Keller and colleagues
36. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
Ken Ross and colleagues
Laurent Keller and colleagues
37. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
x
Ken Ross and colleagues
Laurent Keller and colleagues
38. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
BB BB Bb
x x
Ken Ross and colleagues
Laurent Keller and colleagues
39. Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
(< 5% ) (>15% )
BB BB Bb
x x x
Ken Ross and colleagues
Laurent Keller and colleagues
41. Social form completely associated to Gp-9 locus
•Is this gene the single überregulator?
•Only 14 allozyme markers were used
maybe 1/14th of the genome?
Ddh-1!
Pro-5!
Locus!
1.0!
0.9!
0.8!
0.7!
0.6!
0.5!
0.4!
0.3!
Single queen!
Multiple queen!
Est-4!
G3pdh-1! Ca-4!
Est-6!
Pgm-4!
Acy-1!
Pgm-1!
acoh-1!
Pgm-3!
Acoh-5!
Aat-2!
Gp-9!
42. This changes
454 everything.
Illumina
Solid...
Any lab can
sequence anything!
43.
44. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
45. The genome of a Gp-9 B ♂ fire ant
Sequencing from haploid males (for easier assembly):
Single ♂:
His brothers:
45× (330bp-insert paired reads) + (normal single-end reads)
B 20x
11×
4×
(8,000 & 20,000bp-insert paired reads)
46.
47. The genome of a Gp-9 B ♂ fire ant
Sequencing from haploid males (for easier assembly):
Single ♂:
His brothers:
45× (330bp-insert paired reads) + (normal single-end reads)
B 20x
11×
4×
(8,000 & 20,000bp-insert paired reads)
Assembly approach:
1. Assemble short Illumina reads with SOAPdenovo→N50: 3600 bp
2. Chop assembly into “fake 454 reads” (300bp)
3. Assemble fake + real 454 reads with Newbler→N50: 720,000 bp
→ Total: 350,000,000 bp assembled. The rest: repeats
10,000 scaffolds (100 biggest scaffolds: 50% of genome)
Wurm et al 2011
50. Lepidoptera 29
The genome of the fire ant
Some findings:
Diptera 404
Paraneoptera 577
Arachnida 50
Deuterostomia 173
Cnidaria 100
Not assigned 274
★ Expansion of lipid-processing gene families (for Cuticular Hydrocarbons)
3
SiOR03038
SiOR04609+SiOR06843+420 putative olfactory receptors 1 1
SiOR06723+12
★ SiOR04648+(more than any other insect!)
SiOR00899+6 ★ Functional DNA-methylation system
SiOR02694+4
★Ant-specific duplication and subfunctionalization
of vitellogenin (in bees: involved in reproduction & division of labor)
SiOR00899+8 SiOR04648+7
SiOR04648+6
SiOR04171+17
SiOR04171+29
SiOR04171+14
SiOR00330+14SiOR02694+38 SiOR04609+8
SiOR04609+5
SiOR01321
SiOR04609+19
SiOR00899+12 SiOR05901+1
SiOR04171+3
12 SiOR01224+SiOR04510+SiOR04510+16 13
SiOR04171+25 SiOR06577
SiOR04171+24
SiOR01629+3 SiOR01968+26
SiOR04171+21 SiOR06792+6
SiOR02883+2
SiOR05431+SiOR01858+1 1
SiOR05431+4
SiOR04510+7 SiOR01968+21
SiOR05431+3 SiOR04510+6
SiOR01629+1
SiOR01968+7 SiOR01629+6
SiOR05285+2
SiOR03663
SiOR00899+13
Wurm et al 2011
significance of these duplication events in vitellogenins, odor
perception genes, and a family of lipid-processing genes. We also
discuss additional features of interest in the fire ant genome rel-evant
to the complex social biology of this species, including sex
determination genes, DNA methylation genes, telomerase, and
the insulin and juvenile hormone pathways.
Vitellogenins. In contrast to other insects that mainly have only one
or two vitellogenins, the fire ant genome harbors four adjacent
regulation of life span (27, 28) and division of labor (29). Quanti-tative
RT-PCRshows that Vg1 and Vg4 are preferentially expressed
in workers and Vg2 and Vg3 in queens (Fig. 3C, SI Materials and
Methods, and Table S1G). Vitellogenin expression in S. invicta
workers is surprising because they lack ovaries. Given the super-organism
properties of ant societies, the expression patterns sug-gest
that vitellogenins underwent neo- or subfunctionalization
after duplication to acquire caste-specific functions.
Odor Perception. Consistent with studies in other insects, we find
a single S. invicta ortholog to DmOr83b, a broadly expressed ol-factory
receptor (OR) required to interact with other ORs for
Drosophila and Tribolium castaneum olfaction (30–32). Beyond
OR83b, OR number varies greatly between insect species. Blast
searches and GeneWise searches using an HMM profile con-structed
with aligned ORs from N. vitripennis (33) and Pogono-myrmex
barbatus identified more than 400 loci in the S. invicta
genome with significant sequence similarity to ORs. Preliminary
work on gene model reconstruction identified 297 intact full-length
proteins. Many S. invicta ORs are in tandem arrays (Fig.
S2A) and derive from recent expansions. S. invicta may thus har-bor
the largest identified insect OR repertoire because there are
10 ORs in Pediculus humanus (34), 60 in Drosophila, 165 in
A. mellifera, 225 in N. vitripennis (33), and 259 in T. castaneum
(32). The large numbers of N. vitripennis and T. castaneum ORs
are thought to be due to current or past difficulties in host and
food finding. As has been suggested for A. mellifera (35), the large
number of S. invicta ORs may result from the importance of
chemical communication in ants. The odorant-binding proteins
(OBPs) are another family of genes also known to play roles in
chemosensation in Drosophila (36). Intriguingly, the social orga-nization
of S. invicta colonies is completely associated with se-
Eumetazoa
No hits 3424
Coelomata
Bilateria
Nematoda 25
Fig. 2. Taxonomic distribution of best blastp hits of S. invicta proteins to the
nonredundant (nr) protein database (E < 10−5). Results were first plotted
using MEGAN software (22) and then branches with fewer than 20 hits were
removed, branch lengths were reduced for compactness, and tree topology
was adjusted to reflect consensus phylogenies (23, 24).
2,330,000 bp 2,360,000 bp A
Vg4 Vg1 Vg3 Vg2
B Solenopsis Vg1 C
Solenopsis Vg4
Solenopsis Vg2
Solenopsis Vg3
Apis Vg
Bombus Vg
Nasonia Vg1
Pteromalus Vg
Nasonia Vg2
Encarsia Vg
Pimpla Vg
Athalia Vg
Apocrita
Tenthedinoidea
Vespoidea
Apoidea
Aculeata
Chalcidoidea
25000 Vg2 Vg3
20000
15000
10000
5000
Vg1 Vg4
* ***
600
500
400
300
200
100
Ichneumonoidea 0
*** ***
Q W Q W Q W Q W
142 389 1 40 17820 1.4 9269 0.6
0
EVOLUTION
0.05
SiOR04648+10
SiOR01968+4
SiOR00899+7
SiOR02814+3
SiOR04171+6
SiOR04609+4
SiOR00330+28
SiOR02694+25
SiOR04609+20
SiOR05285+6
25
SiOR04510+15
SiOR00330+18 SiOR04609+23
SiOR01968+23
SiOR03952+4
SiOR04648+16
SiOR05901+2
SiOR02944+4
SiOR01968+5
SiOR04171+19SiOR04648+5
SiOR10535+3
SiOR06723+2
SiOR01968+9
SiOR02883+1
SiOR00899+3
SiOR04171+1
SiOR01629+11
SiOR04171+10
SiOR04171+13
SiOR02694+3
SiOR04171+20
SiOR02694+35
SiOR04171+15
SiOR04609+7
SiOR05118+2
SiOR07837+2
SiOR02694+27
SiOR01968+10
SiOR04648+17
SiOR01968+19
SiOR02694+17
13
SiOR01968+6
SiOR00330+20
SiOR02648+2
SiOR02659+2
SiOR01968+16
SiOR00899+11
SiOR02974
SiOR04171+2
SiOR03952+2
SiOR06792+2
SiOR04510+4
SiOR04171+28
SiOR05285+5
SiOR05285+9 SiOR00899+15 SiOR04648+3
SiOR02694+36
SiOR10535+1
SiOR02694+19
SiOR02694+23
SiOR02694+1
SiOR04609+14
SiOR01122
9
SiOR02694+34
SiOR01629+8
SiOR04648+8
SiOR04510+8
SiOR06573
SiOR02944+1
26
SiOR00330+1
SiOR02694+15
SiOR05285+7
SiOR00899+5
SiOR04609+10
SiOR04609+3 SiOR04339
SiOR08068
SiOR04510+2
SiOR05285+8
SiOR01573+4
SiOR04171+8
SiOR01858+2 SiOR01968+2
SiOR01968+1
SiOR02694+5
SiOR01968+3
SiOR06723+3
SiOR01968+15
SiOR05285+1
SiOR00899+4
SiOR04609+22
SiOR04171+9
SiOR02694+9 SiOR02648+1
SiOR06792+3
SiOR01573+2
SiOR02694+20
SiOR10542
SiOR04609+15
SiOR02694+8
SiOR00330+16
SiOR00899+2
SiOR02694+10
SiOR04510+9
SiOR05285+3
SiOR04609+2
SiOR05285+11 SiOR02694+14
SiOR01573+1
SiOR00613
SiOR01968+22
SiOR00899+9
SiOR06843+2
SiOR02694+37
SiOR00899+1
SiOR04609+9
SiOR05431+2 SiOR10535+2
SiOR00330+15
SiOR02694+18
SiOR01224+2
SiOR04510+11
SiOR00330+23
SiOR02694+29
SiOR05416
SiOR05285+10 SiOR02694+2
SiOR01629+9
SiOR08341 SiOR02694+22
SiOR01224+1
SiOR01968+12
SiOR02694+7
SiOR02944+2
SiOR03952+3
SiOR01968+8
SiOR04609+24
SiOR02694+30
SiOR01629+10
SiOR04510+14
SiOR00565 SiOR05118+3
SiOR04171+16
SiOR10455
SiOR04609+16
SiOR04609+21
SiOR02694+28 SiOR02659+1
SiOR04171+5 SiOR00330+29
SiOR01968+14
SiOR03983
SiOR00330+27
SiOR05285+4
SiOR04510+1
SiOR04609+17 SiOR00330+5
SiOR02694+21
SiOR02814+4
SiOR00330+7
SiOR02694+31
SiOR04648+2
SiOR02694+39
SiOR01968+25
SiOR04609+11
SiOR02694+11
SiOR06792+1
SiOR04171+4
SiOR01629+5
SiOR00330+21
SiOR04648+15
SiOR00330+6
SiOR02694+16
11
SiOR04648+4
SiOR00330+3
SiOR06535
SiOR04171+7
SiOR10493
SiOR02694+32
SiOR06792+4
SiOR04510+3
SiOR06890
SiOR01968+20
SiOR04609+12
SiOR04171+3
SiOR01968+18
SiOR01968+11
SiOR04609+13
SiOR01629+12
SiOR00330+22
SiOR02694+33
SiOR00330+13
SiOR01573+3
SiOR05118+1
SiOR02944+3
SiOR04171+26
SiOR00899+14
SiOR02694+13
SiOR00330+24
SiOR00330+19
SiOR04171+27
SiOR02694+24
SiOR04510+5
SiOR07090
SiOR03952+1
SiOR04510+10
SiOR00330+17
SiOR02694+26
SiOR02814+2
SiOR00330+11
SiOR04171+18
SiOR01968+17
SiOR00330+10
SiOR00330+9
SiOR01629+2
SiOR04171+11
SiOR04510+12
SiOR00330+8
SiOR02694+6
SiOR01968+13
SiOR00330+4 SiOR04609+18
SiOR00899+10
SiOR00330+12
SiOR00330+31
SiOR06843+1
SiOR07837+1
SiOR00330+2
SiOR01629+4
SiOR04648+1
SiOR01968+24
SiOR04171+23
SiOR01629+7 SiOR04648+14
SiOR06792+5
SiOR02883+3
SiOR02694+12
SiOR05118+4
SiOR04171+22
SiOR01080 SiOR04609+6
SiOR02814+1
SiOR00330+30
SiOR05285+12
51. Are other genes linked to Gp-9?
Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
(< 5% ) (>15% )
BB BB Bb
x x x
52. Are other genes linked to Gp-9?
Sequenced:
•a Gp-9 B ♂ genome
!
!
•a Gp-9 b ♂ genome
RAD sequencing
“Next Generation Genotyping.”
53. RAD sequencing
“Next Generation Genotyping.”
Bb
unfertilised eggs
haploid ♂
Gp-9 B Gp-9 b Gp-9 B Gp-9 b Gp-9 b Gp-9 B
38 B♂ & 38 b♂
55. RAD sequencing discovery o&f gheanpolotiydp i♂ng for SNP
EcoR1 EcoR1 EcoR1
Gp-9 B
AACTG
AACTG
AACTG
AACTG
Gp-9 B
56. RAD sequencing discovery o&f gheanpolotiydp i♂ng for SNP
Gp-9 B
AACTG
Gp-9 B
Gp-9 B
GGCCT
Gp-9 B
Gp-9 B
AAGGT
Gp-9 B
Gp-9 b
CCAGT
Gp-9 b
Gp-9 b
TAAAT
Gp-9 b
Gp-9 b
GGAAT
Gp-9 b
38 Gp-9 B
males
38 Gp-9 b
males
57. RADseq: sequencing the same 0.01% of the
genome in many individuals
Identify polymorphism
individual x locus
genotype table
A B C D E F
L1 A C A A C C
L2 G G T - T G
L3 - A G A - G
L4 C - - G G C
L5 T T C T C -
L6 G A A - - G
2419 loci
38 B♂ & 38 b♂
PCA: Principal Component Analysis
Amount of variance explained per principal component
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
% Variance Explained
0 5 10 15 20 25 30
12.7%
6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%
30.2%
58. Principal Components: PC2 vs PC3
pc: 2 % variance: 6.073
pc: 3 % variance: 5.441
0.2
0.1
0.0
-0.1
-0.2
-0.2 -0.1 0.0 0.1 0.2
Gp-9 B ♂
Gp-9 b ♂
59. Principal Components: PC1 vs PC2
pc: 1 % variance: 12.666
pc: 2 % variance: 6.073
0.2
0.1
0.0
-0.1
-0.2
-0.10 -0.05 0.00 0.05 0.10 0.15
Gp-9 B ♂
Gp-9 b ♂
63. Why non-recombining? Structural differences
using Flourescence in situ Hybridization
Gp-9B
genetic map
SB Sb
a Gp-9 B male A22
A22
Gp-9 b male
9 B male Gp-9 b male
E17
E3
Gp-9 B male SB Sb
Gp-9B
genetic map
A22
A22
E17
E17
E3
SB Sb
Gp-9B
genetic map
E3
b SB Sb
Gp-9B
genetic map
E17
E3
Gp-9 b male
John Wang @ Taipei
64. X
ʁ
ʂ
X X Y
Single queen colony Multiple queen colony
SB SB SB Sb
Maybe several
rearrangements
Predictions:
•genes in S are responsible for phenotype?
65. Most BB vs Bb gene expression
differences map to S
Non-recombing region of S contains 800 genes
Gene Expression Patterns for a Social Trait
Gene expression: Gp-9 Bb vs BB workers in multiple queen colonies
29 sign i f i c a n t genes
are in the SB/Sb region
(p<10-10)
20 of
Similar for BB vs Bb queens; &
for B vs b males. Wang et al 2008
66. ʂ
Single queen colony Multiple queen colony
SB SB SB Sb
Predictions:
•genes in S are responsible for phenotype?
•Sb is degenerating?
probably!
⟹ directional (antagonistic?) selection?
X
ʁ
X X Y
Maybe several
rearrangements
67. Is Sb degenerating?
Actually quite similar to SB:
(Almost) no SB or Sb-specific sequence
99.8% of non-gap sequences are identical
genes seem to be intact in Sb
But clearly: relaxation of purifying selection
Sb contains more small repeats
SB
Sb
Introns bigger in Sb than SB
68. Sb is degenerating:
repeats cause bad assembly
[a] vs. [c]: p < 10-7
[b] vs. [c]: p < 10-4
Gp-9B male Gp-9b male
6,000,000
5,000,000
4,000,000
3,000,000
2,000,000
1,000,000
Region:
Genome assembly:
Normally recombining
regions from all 16
linkage groups
Normally recombining
regions from all 16
linkage groups
Sb region without
recombination
in Gp-9 Bb queens
SB region without
recombination
in Gp-9 Bb queens
Scaffold length (bp)
0
[a] [a], [b] [a] [c]
SB Sb
69. Is Sb degenerating?
(Almost) no SB or Sb-specific sequence
99.8% of non-gap sequences are identical
genes seem to be intact in Sb
Sb contains more big repeats ⟹ bad assembly
dN/dS bigger in S than rest of the genome
Probably ♂ haploidy = strong purifying selection
⟹ slower degeneration
Actually quite similar to SB:
But clearly: relaxation of purifying selection
Sb contains more small repeats
Introns bigger in Sb than SB
70. Age of the region based on dS
250
250
200
200
150
150
100
100
50
50
0
0
leafcutterdS
0.00 0.05 0.10 0.15 0.20 leafcutterDndsSubset$dS
count
leafcutterdS
0.00 0.05 0.10 0.15 0.20 leafcutterDndsSubset$dS
Leafcutter common ancestor: 8,000,000-10,000,000 years ago
150
150
100
count
gp9linkedSolenopsisdS
count
100
0.00 0.05 0.10 0.15 0.20 subset(dndsdata, gp9linked == TRUE)$dS count
50
50
0
0.00 0.05 0.10 0.15 0.20 subset(dndsdata, gp9linked == TRUE)$dS gp9linkedSolenopsisdS
0
Maximum Likelihood Estimation of SB/Sb age:280,000-425,000
⟹ little time for degeneration
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## Min. 1st Qu. Median Mean 3rd Qu. Max.
71. Summary
Ants are cool.
Solenopsis invicta queen number determined by Gp-9 genotypes:
•only BB workers ➔ single BB queen
•with Bb workers ➔ multiple Bb queens
Genome sequencing + RAD Genotyping
•Gp-9 marks ~4% of genome
•social like sex chromosomes: SB is like X; Sb is like Y
Structural differences between SB and Sb ➔ no recombination
SB and Sb stopped recombining ~400,000 years ago.
some relaxation of purifying selection
but haploid males ➔ strong purifying selection
72. Formica selysi
Alpine silver ant
Single vs Multiple-queen colonies
Convergent social chromosome architecture
Purcell et al 2014
J Meunier
73. ≠ social chromosomes
Purcell et al 2014
Solenopsis
invicta social
chromosome
Formica selysi
social
chromosome
75. QMUL lab (Rodrigo, Brunoet al)
Lausanne lab (L KELLER, J
WANG, D SHOEMAKER
ORIBA-GROGNUZ
MINGKWAN NIPITWATTANAPHON
!
Ecology & Evolution & Vital-IT
@ Lausanne
Evolve & Psych @ Queen Mary
y.wurm@qmul.ac.uk
M Corona, S Nygaard, BG Hunt, KK Ingram, L
Falquet, M Nipitwattanaphon, D Gotzek, MB Dijkstra,
J Oettler, F Comtesse, CJ Shih, WJ Wu, CC Yang, J
Thomas, E Beaudoing, S Pradervand, V Flegel, ED
Cook, R Fabbretti, H Stockinger, L Long, WG
Farmerie, J Oakey, JJ Boomsma, P Pamilo, SV Yi, J
Heinze, MAD Goodisman, L Farinelli, K Harshman, N
Hulo, L Cerutti, Ioannis Xenarios
76. Research themes
Social evolution
Pollinator health
• Biomedical approaches
• International population genomics surveys
• Monitoring via sequencing
• Responses to environmental challenges
Modern Bioinformatics for Genomics
• Reproducibility
• Accuracy
• Sustainability
• Versioning
• Agile & efficient
data handling
• Major social transitions
» social chromosomes
» convergence
» eusociality, queen number, parasitism...
• 100-fold intra-specific variation in lifespan
• Strengths of selection
• Candidate genes/pathway
77.
78. Gp-9 is an odorant binding protein
Hypothesis: influences queen odor & how workers « smell » queens
Krieger & Ross