Evolutionary Biology Homework - Specializing in Hardy Weinberg Equilibrium, Allele Frequencies, How Evolution/Development of characters evolve, population size, and overall evolutionary biology.
Name: Score: /100 Name: Question #1 (30 points) Genotype Observed Expected Chi-square AA 210 205.71 AC 60 1.0714 CC 10 Total 280 280 Test for Hardy-Weinberg proportions by filling in the five missing values in the above table (10 points). Is this population at Hardy-Weinberg equilibrium? Explain your reasoning (5 points). Name four different reasons why departures from Hardy-Weinberg proportions might be observed (20 points). Question #2 (5 points) The black line in this plot shows a simulated allele frequency trajectory. Allele A is beneficial, and it increases in frequency over time. Does the above plot show evolution for a small population (100 individuals) or a large population (10000 individuals)? Question #3 (15 points) Explaining how novel characters can evolve. Use this as a chance to demonstrate your understanding of evo-devo (three to five sentences in total). Question #4 (25 points) The neutral theory holds that the amount of genetic diversity found in a species should be proportional to effective population size and mutation rate (i.e., in the shaded gray region of the above figure). However, real-world genetic data paints a different picture. Give two different explanations why the above pattern might arise. Explain your reasoning (four to eight sentences in total). Question #5 (25 points) Many human genomes contain traces of Neanderthal ancestry. However the autosomes of non-Africans contain approximately five times as much Neanderthal DNA per base pair as X chromosomes. Hypothesize why there is a relative lack of introgressed Neanderthal DNA in human X chromosomes, and explain your reasoning. Use this as a chance to demonstrate your comprehensive understanding of evolutionary biology (four to eight sentences in total). 1/4 4/4 µ = 10−8 µ = 10−9 Acyrthosiphon pisum Aedes aegypti Ailuropoda melanoleuca Allolobophora chlorotica Amphimedon queenslandica Anopheles arabiensis Anopheles gambiae Aporrectodea icterica Aquila clanga Bactrocera depressa Balaenoptera bonaerensis Bos taurus Bostrycapulus aculeatus Caenorhabditis elegans Callithrix jacchus Camponotus ligniperdus Ceratitis capitata Chelonoidis nigra Cichla pleiozona Ciona intestinalis Ciona savignyi Crassostrea gigas Culex pipiens Cystodytes dellechiajei Daubentonia madagascariensis Drosophila americana Drosophila ananassae Drosophila arizonae Drosophila bipectinata Drosophila buzzatii Drosophila kikkawai Drosophila malerkotliana Drosophila melanogaster Drosophila miranda Drosophila mojavensis Drosophila novamexicana Drosophila parabipectinata Drosophila persimilis Drosophila pseudoobscura Drosophila sechellia Drosophila simulans Drosophila subobscura Echinocardium cordatum Eschrichtius robustus Eudyptes filholi Eudyptes moseleyi Eulemur mongoz Eunicella verrucosa Gorilla gorilla Gulo gulo Halictus scabiosaeHippocampus kuda Homo sapiens Leptogorgia sarmentosa Lynx lynx Mytilus edulis Mytilus galloprovincialis Mytilus trossulus Nasonia vitripennis Nomascus gabriellae Ostreola stentina Ovis canadensis Pan paniscus Pheidole pallidulaPongo abelii Propithecus coquereli Reticulitermes flavipes Reticulitermes grassei Reticulitermes lucifugus Sistrurus catenatus 104 106 108 1010 1012 1014 1016 1018 10−4 10−3 10−2 10−1 100 pa irw is e di ve rs ity (d iff er en ce s pe r b p) approximate population size Echinodermata Arthropoda Chordata Annelida Porifera Mollusca Nematoda Cnidaria Nemertea Ne Nc log10(π) = log10(θ) − log10 (1 + 4θ/3) θ = 4Ncµ µ = 10−8 µ = 10−9 [0.08, 0.12] 10−3.5 .CC-BY-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted February 3, 2021. ; https://doi.org/10.1101/2021.02.03.429633doi: bioRxiv preprint https://doi.org/10.1101/2021.02.03.429633 http://creativecommons.org/licenses/by-nd/4.0/ m=10 −8 m=10 −9 Acyrthosiphon pisum Aedes aegypti Ailuropoda melanoleuca Allolobophora chlorotica Amphimedon queenslandica Anopheles arabiensis Anopheles gambiae Aporrectodea icterica Aquila clanga Bactrocera depressa Balaenoptera bonaerensis Bos taurus Bostrycapulus aculeatus Caenorhabditis elegans Callithrix jacchus Camponotus ligniperdus Ceratitis capitata Chelonoidis nigra Cichla pleiozona Ciona intestinalis Ciona savignyi Crassostrea gigas Culex pipiens Cystodytes dellechiajei Daubentonia madagascariensis Drosophila americana Drosophila ananassae Drosophila arizonae Drosophila bipectinata Drosophila buzzatii Drosophila kikkawai Drosophila malerkotliana Drosophila melanogaster Drosophila miranda Drosophila mojavensis Drosophila novamexicana Drosophila parabipectinata Drosophila persimilis Drosophila pseudoobscura Drosophila sechellia Drosophila simulans Drosophila subobscura Echinocardium cordatum Eschrichtius robustus Eudyptes filholi Eudyptes moseleyi Eulemur mongoz Eunicella verrucosa Gorilla gorilla Gulo gulo Halictus scabiosae Hippocampus kuda Homo sapiens Leptogorgia sarmentosa Lynx lynx Mytilus edulis Mytilus galloprovincialis Mytilus trossulus Nasonia vitripennis Nomascus gabriellae Ostreola stentina Ovis canadensis Pan paniscus Pheidole pallidula Pongo abelii Propithecus coquereli Reticulitermes flavipes Reticulitermes grassei Reticulitermes lucifugus Sistrurus catenatus 10 4 10 6 10 8 10 10 10 12 10 14 10 16 10 18 10 −4 10 −3 10 −2 10 −1 10 0 p a i r w i s e d i v e r s i t y ( d i f f e r e n c e s p e r b p ) approximate population siz e Echinodermata Arthropoda Chordata Annelida Porifera Mollusca Nematoda Cnidaria Nemertea N e N c log 10 (π)=log 10 (θ)−log 10 (1+ 4θ /3)θ=4N c µ µ=10 −8 µ=10 −9 [0.08,0.12] 10 −3.5 .CC-BY-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted February 3, 2021. ; https://doi.org/10.1101/2021.02.03.429633doi: bioRxiv preprint Name: Score: /100 Name: Question #1 (30 points) Genotype Observed Expected Chi-square AA 210 205.71 AC 60 1.0714 CC 10 Total 280 280 Test for Hardy-Weinberg proportions by filling in the five missing values in the above table (10 points). Is this population at Hardy-Weinberg equilibrium? Explain your reasoning (5 points). Name four different reasons why departures from Hardy-Weinberg proportions might be observed (20 points). Question #2 (5 points) The black line in this plot shows a simulated allele frequency trajectory. Allele A is beneficial, and it increases in frequency over time. Does the above plot show evolution for a small population (100 individuals) or a large population (10000 individuals)? Question #3 (15 points) Explaining how novel characters can evolve. Use this as a chance to demonstrate your understanding of evo-devo (three to five sentences in total). Question #4 (25 points) The neutral theory holds that the amount of genetic diversity found in a species should be proportional to effective population size and mutation rate (i.e., in the shaded gray region of the above figure). However, real-world genetic data paints a different picture. Give two different explanations why the above pattern might arise. Explain your reasoning (four to eight sentences in total). Question #5 (25 points) Many human genomes contain traces of Neanderthal ancestry. However the autosomes of non-Africans contain approximately five times as much Neanderthal DNA per base pair as X chromosomes. Hypothesize why there is a relative lack of introgressed Neanderthal DNA in human X chromosomes, and explain your reasoning. Use this as a chance to demonstrate your comprehensive understanding of evolutionary biology (four to eight sentences in total). 1/4 4/4 µ = 10−8 µ = 10−9 Acyrthosiphon pisum Aedes aegypti Ailuropoda melanoleuca Allolobophora chlorotica Amphimedon queenslandica Anopheles arabiensis Anopheles gambiae Aporrectodea icterica Aquila clanga Bactrocera depressa Balaenoptera bonaerensis Bos taurus Bostrycapulus aculeatus Caenorhabditis elegans Callithrix jacchus Camponotus ligniperdus Ceratitis capitata Chelonoidis nigra Cichla pleiozona Ciona intestinalis Ciona savignyi Crassostrea gigas Culex pipiens Cystodytes dellechiajei Daubentonia madagascariensis Drosophila americana Drosophila ananassae Drosophila arizonae Drosophila bipectinata Drosophila buzzatii Drosophila kikkawai Drosophila malerkotliana Drosophila melanogaster Drosophila miranda Drosophila mojavensis Drosophila novamexicana Drosophila parabipectinata Drosophila persimilis Drosophila pseudoobscura Drosophila sechellia Drosophila simulans Drosophila subobscura Echinocardium cordatum Eschrichtius robustus Eudyptes filholi Eudyptes moseleyi Eulemur mongoz Eunicella verrucosa Gorilla gorilla Gulo gulo Halictus scabiosaeHippocampus kuda Homo sapiens Leptogorgia sarmentosa Lynx lynx Mytilus edulis Mytilus galloprovincialis Mytilus trossulus Nasonia vitripennis Nomascus gabriellae Ostreola stentina Ovis canadensis Pan paniscus Pheidole pallidulaPongo abelii Propithecus coquereli Reticulitermes flavipes Reticulitermes grassei Reticulitermes lucifugus Sistrurus catenatus 104 106 108 1010 1012 1014 1016 1018 10−4 10−3 10−2 10−1 100 pa irw is e di ve rs ity (d iff er en ce s pe r b p) approximate population size Echinodermata Arthropoda Chordata Annelida Porifera Mollusca Nematoda Cnidaria Nemertea Ne Nc log10(π) = log10(θ) − log10 (1 + 4θ/3) θ = 4Ncµ µ = 10−8 µ = 10−9 [0.08, 0.12] 10−3.5 .CC-BY-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted February 3, 2021. ; https://doi.org/10.1101/2021.02.03.429633doi: bioRxiv preprint https://doi.org/10.1101/2021.02.03.429633 http://creativecommons.org/licenses/by-nd/4.0/ m=10 −8 m=10 −9 Acyrthosiphon pisum Aedes aegypti Ailuropoda melanoleuca Allolobophora chlorotica Amphimedon queenslandica Anopheles arabiensis Anopheles gambiae Aporrectodea icterica Aquila clanga Bactrocera depressa Balaenoptera bonaerensis Bos taurus Bostrycapulus aculeatus Caenorhabditis elegans Callithrix jacchus Camponotus ligniperdus Ceratitis capitata Chelonoidis nigra Cichla pleiozona Ciona intestinalis Ciona savignyi Crassostrea gigas Culex pipiens Cystodytes dellechiajei Daubentonia madagascariensis Drosophila americana Drosophila ananassae Drosophila arizonae Drosophila bipectinata Drosophila buzzatii Drosophila kikkawai Drosophila malerkotliana Drosophila melanogaster Drosophila miranda Drosophila mojavensis Drosophila novamexicana Drosophila parabipectinata Drosophila persimilis Drosophila pseudoobscura Drosophila sechellia Drosophila simulans Drosophila subobscura Echinocardium cordatum Eschrichtius robustus Eudyptes filholi Eudyptes moseleyi Eulemur mongoz Eunicella verrucosa Gorilla gorilla Gulo gulo Halictus scabiosae Hippocampus kuda Homo sapiens Leptogorgia sarmentosa Lynx lynx Mytilus edulis Mytilus galloprovincialis Mytilus trossulus Nasonia vitripennis Nomascus gabriellae Ostreola stentina Ovis canadensis Pan paniscus Pheidole pallidula Pongo abelii Propithecus coquereli Reticulitermes flavipes Reticulitermes grassei Reticulitermes lucifugus Sistrurus catenatus 10 4 10 6 10 8 10 10 10 12 10 14 10 16 10 18 10 −4 10 −3 10 −2 10 −1 10 0 p a i r w i s e d i v e r s i t y ( d i f f e r e n c e s p e r b p ) approximate population siz e Echinodermata Arthropoda Chordata Annelida Porifera Mollusca Nematoda Cnidaria Nemertea N e N c log 10 (π)=log 10 (θ)−log 10 (1+ 4θ /3)θ=4N c µ µ=10 −8 µ=10 −9 [0.08,0.12] 10 −3.5 .CC-BY-ND 4.0 International licenseavailable under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprintthis version posted February 3, 2021. ; https://doi.org/10.1101/2021.02.03.429633doi: bioRxiv preprint