Lecture 13 Leks, Adaptation, Phylogenetic Tests
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Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
Natural Selection and Adaptation, Part I
Natural Selection and Adaptation, Part I 36-149 The Tree of Life Christopher R. Genovese Department of Statistics 132H Baker Hall x8-7836 http://www.stat.cmu.edu/~genovese/ . Plan • Review of Natural Selection • Detecting Natural Selection (discussion) • Examples of Observed Natural Selection ............................... Next Time: • Adaptive Traits • Methods for Reasoning about and studying adaptations • Explaining Complex Adaptations (discussion) 36-149 The Tree of Life Class #10 -1- Overview The theories of common descent and natural selection play different roles within the theory of evolution. Common Descent explains the unity of life. Natural Selection explains the diversity of life. An adaptation (or adaptive trait) is a feature of an organism that enhances reproductive success, relative to other possible variants, in a given environment. Adaptations become prevalent and are maintained in a population through natural selection. Indeed, natural selection is the only mechanism of evolutionary change that can satisfactorily explain adaptations. 36-149 The Tree of Life Class #10 -2- Darwin's Argument Darwin put forward two main arguments in support of natural selection: An analogical argument: Artificial selection A logical argument: The struggle for existence (As we will see later, we now have more than just argument in support of the theory.) 36-149 The Tree of Life Class #10 -3- The Analogical Argument: Artificial Selection 36-149 The Tree of Life Class #10 -4- The Analogical Argument: Artificial Selection 36-149 The Tree of Life Class #10 -5- The Analogical Argument: Artificial Selection Teosinte to Corn 36-149 The Tree of Life Class #10 -6- The Analogical Argument: Artificial Selection • Darwin was intimately familiar with the efforts of breeders in his day to produce novel varieties. -
1. Adaptation and the Evolution of Physiological Characters
Bennett, A. F. 1997. Adaptation and the evolution of physiological characters, pp. 3-16. In: Handbook of Physiology, Sect. 13: Comparative Physiology. W. H. Dantzler, ed. Oxford Univ. Press, New York. 1. Adaptation and the evolution of physiological characters Department of Ecology and Evolutionary Biology, University of California, ALBERT F. BENNETT 1 Irvine, California among the biological sciences (for example, behavioral CHAPTER CONTENTS science [I241). The Many meanings of "Adaptationn In general, comparative physiologists have been Criticisms of Adaptive Interpretations much more successful in, and have devoted much more Alternatives to Adaptive Explanations energy to, pursuing the former rather than the latter Historical inheritance goal (37). Most of this Handbook is devoted to an Developmentai pattern and constraint Physical and biomechanical correlation examination of mechanism-how various physiologi- Phenotypic size correlation cal systems function in various animals. Such compara- Genetic correlations tive studies are usually interpreted within a specific Chance fixation evolutionary context, that of adaptation. That is, or- Studying the Evolution of Physiological Characters ganisms are asserted to be designed in the ways they Macroevolutionary studies Microevolutionary studies are and to function in the ways they do because of Incorporating an Evolutionary Perspective into Physiological Studies natural selection which results in evolutionary change. The principal textbooks in the field (for example, refs. 33, 52, 102, 115) make explicit reference in their titles to the importance of adaptation to comparative COMPARATIVE PHYSIOLOGISTS HAVE TWO GOALS. The physiology, as did the last comparative section of this first is to explain mechanism, the study of how organ- Handbook (32). Adaptive evolutionary explanations isms are built functionally, "how animals work" (113). -
In Defence of the Three-Domains of Life Paradigm P.T.S
van der Gulik et al. BMC Evolutionary Biology (2017) 17:218 DOI 10.1186/s12862-017-1059-z REVIEW Open Access In defence of the three-domains of life paradigm P.T.S. van der Gulik1*, W.D. Hoff2 and D. Speijer3* Abstract Background: Recently, important discoveries regarding the archaeon that functioned as the “host” in the merger with a bacterium that led to the eukaryotes, its “complex” nature, and its phylogenetic relationship to eukaryotes, have been reported. Based on these new insights proposals have been put forward to get rid of the three-domain Model of life, and replace it with a two-domain model. Results: We present arguments (both regarding timing, complexity, and chemical nature of specific evolutionary processes, as well as regarding genetic structure) to resist such proposals. The three-domain Model represents an accurate description of the differences at the most fundamental level of living organisms, as the eukaryotic lineage that arose from this unique merging event is distinct from both Archaea and Bacteria in a myriad of crucial ways. Conclusions: We maintain that “a natural system of organisms”, as proposed when the three-domain Model of life was introduced, should not be revised when considering the recent discoveries, however exciting they may be. Keywords: Eucarya, LECA, Phylogenetics, Eukaryogenesis, Three-domain model Background (English: domain) as a higher taxonomic level than The discovery that methanogenic microbes differ funda- regnum: introducing the three domains of cellular life, Ar- mentally from Bacteria such as Escherichia coli or Bacillus chaea, Bacteria and Eucarya. This paradigm was proposed subtilis constitutes one of the most important biological by Woese, Kandler and Wheelis in PNAS in 1990 [2]. -
Phylogenetics Topic 2: Phylogenetic and Genealogical Homology
Phylogenetics Topic 2: Phylogenetic and genealogical homology Phylogenies distinguish homology from similarity Previously, we examined how rooted phylogenies provide a framework for distinguishing similarity due to common ancestry (HOMOLOGY) from non-phylogenetic similarity (ANALOGY). Here we extend the concept of phylogenetic homology by making a further distinction between a HOMOLOGOUS CHARACTER and a HOMOLOGOUS CHARACTER STATE. This distinction is important to molecular evolution, as we often deal with data comprised of homologous characters with non-homologous character states. The figure below shows three hypothetical protein-coding nucleotide sequences (for simplicity, only three codons long) that are related to each other according to a phylogenetic tree. In the figure the nucleotide sequences are aligned to each other; in so doing we are making the implicit assumption that the characters aligned vertically are homologous characters. In the specific case of nucleotide and amino acid alignments this assumption is called POSITIONAL HOMOLOGY. Under positional homology it is implicit that a given position, say the first position in the gene sequence, was the same in the gene sequence of the common ancestor. In the figure below it is clear that some positions do not have identical character states (see red characters in figure below). In such a case the involved position is considered to be a homologous character, while the state of that character will be non-homologous where there are differences. Phylogenetic perspective on homologous characters and homologous character states ACG TAC TAA SYNAPOMORPHY: a shared derived character state in C two or more lineages. ACG TAT TAA These must be homologous in state. -
Phylogenetics of Buchnera Aphidicola Munson Et Al., 1991
Türk. entomol. derg., 2019, 43 (2): 227-237 ISSN 1010-6960 DOI: http://dx.doi.org/10.16970/entoted.527118 E-ISSN 2536-491X Original article (Orijinal araştırma) Phylogenetics of Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) based on 16S rRNA amplified from seven aphid species1 Farklı yaprak biti türlerinden izole edilen Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae)’nın 16S rRNA’ya göre filogenetiği Gül SATAR2* Abstract The obligate symbiont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae) is important for the physiological processes of aphids. Buchnera aphidicola genes detected in seven aphid species, collected in 2017 from different plants and altitudes in Adana Province, Turkey were analyzed to reveal phylogenetic interactions between Buchnera and aphids. The 16S rRNA gene was amplified and sequenced for this purpose and a phylogenetic tree built up by the neighbor-joining method. A significant correlation between B. aphidicola genes and the aphid species was revealed by this phylogenetic tree and the haplotype network. Specimens collected in Feke from Solanum melongena L. was distinguished from the other B. aphidicola genes on Aphis gossypii Glover, 1877 (Hemiptera: Aphididae) with a high bootstrap value of 99. Buchnera aphidicola in Myzus spp. was differentiated from others, and the difference between Myzus cerasi (Fabricius, 1775) and Myzus persicae (Sulzer, 1776) was clear. Although, B. aphidicola is specific to its host aphid, certain nucleotide differences obtained within the species could enable specification to geographic region or host plant in the future. Keywords: Aphid, genetic similarity, phylogenetics, symbiotic bacterium Öz Obligat simbiyont, Buchnera aphidicola Munson et al., 1991 (Enterobacteriales: Enterobacteriaceae), yaprak bitlerinin fizyolojik olaylarının sürdürülmesinde önemli bir rol oynar. -
REVIEW Physiological Dependence on Copulation in Parthenogenetic Females Can Reduce the Cost of Sex
ANIMAL BEHAVIOUR, 2004, 67, 811e822 doi:10.1016/j.anbehav.2003.05.014 REVIEW Physiological dependence on copulation in parthenogenetic females can reduce the cost of sex M. NEIMAN Department of Biology, Indiana University, Bloomington (Received 6 December 2002; initial acceptance 10 April 2003; final acceptance 27 May 2003; MS. number: ARV-25) Despite the two-fold reproductive advantage of asexual over sexual reproduction, the majority of eukaryotic species are sexual. Why sex is so widespread is still unknown and remains one of the most important unanswered questions in evolutionary biology. Although there are several hypothesized mechanisms for the maintenance of sex, all require assumptions that may limit their applicability. I suggest that the maintenance of sex may be aided by the detrimental retention of ancestral traits related to sexual reproduction in the asexual descendants of sexual taxa. This reasoning is based on the fact that successful reproduction in many obligately sexual species is dependent upon the behavioural, physical and physiological cues that accompany sperm delivery. More specifically, I suggest that although parthenogenetic (asexual) females have no need for sperm per se, parthenogens descended from sexual ancestors may not be able to reach their full reproductive potential in the absence of the various stimuli provided by copulatory behaviour. This mechanism is novel in assuming no intrinsic advantage to producing genetically variable offspring; rather, sex is maintained simply through phylogenetic constraint. I review and synthesize relevant literature and data showing that access to males and copulation increases reproductive output in both sexual and parthenogenetic females. These findings suggest that the current predominance of sexual reproduction, despite its well-documented drawbacks, could in part be due to the retention of physiological dependence on copulatory stimuli in parthenogenetic females. -
Evolutionary and Historical Biogeography of Animal Diversity Learning Objectives
Evolutionary and historical biogeography of animal diversity Learning objectives • The students can explain the common ancestor of animal kingdom. • The students can explain the historical biogeography of animal. • The students can explain the invasion of animal from aquatic to terrestrial habitat. • The students can explain the basic mechanism of speciation, allopatric and non-allopatric. The Common Ancestor of Animal Kingdom Characteristics of Animals • Animals or “metazoans” are typically heterotrophic, multicellular organisms with diploid, eukaryotic cells. • Trichoplax adhaerens is defined as an animal by the presence of different somatic (i.e., non-reproductive) cell types and by impermeable cell–cell connections. Trichoplax adhaerens Blackstone, 2009 Two Hypotheses for the Branching Order of Groups at the Root of the Metazoan Tree 1 2 The choanoflagellates serve as an outgroup in the Bilaterians are the sister group to the placozoan + analysis, and sponges are the sister group to the sponge + ctenophore + cnidarian clade, while placozoans placozoan + cnidarian + ctenophore + bilaterian are the sister group to the sponge + ctenophore + clade. cnidarian clade. Blackstone, 2009 Ancestry and evolution of animal–bacterial interactions • Choanoflagellates as the last common ancestor of animal kingdom. • Urmetazoan is the group of animal with multicellular and produce differentiated cell types (ex. Egg & sperm) R.A. Alegado & N. King, 2014 Conserved morphology and ultrastructure of Choanoflagellates and Sponge choanocytes The collar complex is conserved in choanoflagellates (A. S. rosetta) and sponge collar cells (B. Sycon coactum) flagellum (fL), microvilli (mv), a nucleus (nu), and a food vacuole (fv) Brunet & King, 2017 The Historical Biogeography of Animal Zoogeographic regions Old New Cox, 2001 Plate tectonic regulation of global marine animal diversity A. -
Introductory Activities
TEACHER’S GUIDE Introduction Dean Madden Introductory NCBE, University of Reading activities Version 1.0 CaseCase Studies introduction Introductory activities The activities in this section explain the basic principles behind the construction of phylogenetic trees, DNA structure and sequence alignment. Students are also intoduced to the Geneious software. Before carrying out the activities in the DNA to Darwin Case studies, students will need to understand: • the basic principles behind the construction of an evolutionary tree or phylogeny; • the basic structure of DNA and proteins; • the reasons for and the principle of alignment; • use of some features of the Geneious computer software (basic version). The activities in this introduction are designed to achieve this. Some of them will reinforce what students may already know; others involve new concepts. The material includes extension activities for more able students. Evolutionary trees In 1837, 12 years before the publication of On the Origin of Species, Charles Darwin famously drew an evolutionary tree in one of his notebooks. The Origin also included a diagram of an evolutionary tree — the only illustration in the book. Two years before, Darwin had written to his friend Thomas Henry Huxley, saying: ‘The time will come, I believe, though I shall not live to see it, when we shall have fairly true genealogical trees of each great kingdom of Nature.’ Today, scientists are trying to produce the ‘Tree of Life’ Darwin foresaw, using protein, DNA and RNA sequence data. Evolutionary trees are covered on pages 2–7 of the Student’s guide and in the PowerPoint and Keynote slide presentations. -
1 "Principles of Phylogenetics: Ecology
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200 Spring 2016 University of California, Berkeley D.D. Ackerly March 7, 2016. Phylogenetics and Adaptation What is to be explained? • What is the evolutionary history of trait x that we see in a lineage (homology) or multiple lineages (homoplasy) - adaptations as states • Is natural selection the primary evolutionary process leading to the ‘fit’ of organisms to their environment? • Why are some traits more prevalent (occur in more species): number of origins vs. trait- dependent diversification rates (speciation – extinction) Some high points in the history of the adaptation debate: 1950s • Modern Synthesis of Genetics (Dobzhansky), Paleontology (Simpson) and Systematics (Mayr, Grant) 1960s • Rise of evolutionary ecology – synthesis of ecology with strong adaptationism via optimality theory, with little to no history; leads to Sociobiology in the 70s • Appearance of cladistics (Hennig) 1972 • Eldredge and Gould – punctuated equilibrium – argue that Modern Synthesis can’t explain pervasive observation of stasis in fossil record; Gould focuses on development and constraint as explanations, Eldredge more on ecology and importance of migration to minimize selective pressure 1979 • Gould and Lewontin – Spandrels – general critique of adaptationist program and call for rigorous hypothesis testing of alternatives for the ‘fit’ between organism and environment 1980’s • Debate on whether macroevolution can be explained by microevolutionary processes • Comparative methods -
The Caper Package: Comparative Analysis of Phylogenetics and Evolution in R
The caper package: comparative analysis of phylogenetics and evolution in R David Orme April 16, 2018 This vignette documents the use of the caper package for R (R Development Core Team, 2011) in carrying out a range of comparative analysis methods for phylogenetic data. The caper package, and the code in this vignette, requires the ape package (Paradis et al., 2004) along with the packages mvtnorm and MASS. Contents 1 Background 2 2 Comparative datasets 3 2.1 The comparative.data class and objects. .3 2.1.1 na.omit ......................................3 2.1.2 subset ......................................5 2.1.3 [ ..........................................5 2.2 Example datasets . .6 3 Methods and functions provided by caper. 7 3.0.1 Phylogenetic linear models . .7 3.0.2 Fitting phylogenetic GLS models: pgls ....................8 3.1 Optimising branch length transformations: profile.pgls...............9 3.1.1 Criticism and simplification ofpgls models: plot, anova and AIC...... 11 3.2 Phylogenetic independent contrasts . 12 3.2.1 Variable names in contrast functions . 12 3.2.2 Continuous variables: crunch .......................... 13 3.2.3 Categorical variables: brunch .......................... 13 3.2.4 Species richness contrasts: macrocaic ..................... 14 3.2.5 Phylogenetic signal: phylo.d .......................... 15 3.3 Checking and comparing contrast models. 16 3.3.1 Testing evolutionary assumptions: caic.diagnostics............. 16 3.3.2 Robust contrasts: caic.robust ......................... 17 3.3.3 Model criticism: plot .............................. 19 3.3.4 Model comparison: anova & AIC ........................ 20 3.4 Other comparative functions . 21 3.4.1 Tree imbalance: fusco.test .......................... 21 3.5 Phylogenetic diversity: pd.calc, pd.bootstrap and ed.calc............ -
Sex-Specific Spawning Behavior and Its Consequences in an External Fertilizer
vol. 165, no. 6 the american naturalist june 2005 Sex-Specific Spawning Behavior and Its Consequences in an External Fertilizer Don R. Levitan* Department of Biological Science, Florida State University, a very simple way—the timing of gamete release (Levitan Tallahassee, Florida 32306-1100 1998b). This allows for an investigation of how mating behavior can influence mating success without the com- Submitted October 29, 2004; Accepted February 11, 2005; Electronically published April 4, 2005 plications imposed by variation in adult morphological features, interactions within the female reproductive sys- tem, or post-mating (or pollination) investments that can all influence paternal and maternal success (Arnqvist and Rowe 1995; Havens and Delph 1996; Eberhard 1998). It abstract: Identifying the target of sexual selection in externally also provides an avenue for exploring how the evolution fertilizing taxa has been problematic because species in these taxa often lack sexual dimorphism. However, these species often show sex of sexual dimorphism in adult traits may be related to the differences in spawning behavior; males spawn before females. I in- evolutionary transition to internal fertilization. vestigated the consequences of spawning order and time intervals One of the most striking patterns among animals and between male and female spawning in two field experiments. The in particular invertebrate taxa is that, generally, species first involved releasing one female sea urchin’s eggs and one or two that copulate or pseudocopulate exhibit sexual dimor- males’ sperm in discrete puffs from syringes; the second involved phism whereas species that broadcast gametes do not inducing males to spawn at different intervals in situ within a pop- ulation of spawning females.