Introduction

• Throughout biology and health science, common ancestry between humans and all other living things is a fundamental principle that explains countless facts.

The Tree of Life, from Darwin to Today

• A phylogenetic tree, Tree of Life”, is a graphic representation of the history of taxa (above species level).

• Common ancestors are a lineage (often designated as a taxon) from which two or more descendant lineages evolved

  • A taxon is a taxonomic group of any rank, such as a species, family, or class.

    • A monophyletic taxon includes all the names of descendants of a particular common ancestor (ex: traditional class Aves, which includes all birds).

    • A paraphyletic taxon includes some, but not all, of the descendants from a particular ancestor (ex: traditional class Reptilia is paraphyletic because it does not include the birds, which share a common ancestor with dinosaurs and crocodiles.

    • A polyphyletic taxon includes species that do not exclusively share a common ancestor.

• Biologists agree that all the organisms we know of have descended from a single ancestral form of life that lived between 4 and 3.7 billion years ago.

Phylogenetic Trees

• Two major processes in the evolution of higher taxa:

  • Anagenesis is the evolutionary change of features within a single lineage (species).

  • Cladogenesis is the branching of a lineage into two or more descendent lineages.

• Divergence (or divergent evolution) is the increasing differences between lineages in one or more characters (traits).

• Phylogeny is the history of the events by which species or other taxa have successively arisen from common ancestors.

  • Each segment, or branch, in a phylogenetic tree is called a lineage.

• A clade is all the descendants from one common ancestor (note, this can also be called a monophyletic group).

• Sister groups are two clades that originate from a common ancestor

• A root is the lineage leading to the most recent common ancestor of all the species in the phylogeny.

• Closeness of a relationship is not the same as similarity. Even though certain aspects of similarity may be used as data to determine the relationships among species, a phylogeny portrays relationship (common ancestry), not similarity.

• Relationships among the taxa are defined by the order of branching, not by the linear order of the tips of the tree

  • The lengths of the branches may or may not have meaning, depending on what information a researcher means to convey.

• A phylogenetic tree may be drawn in several equivalent ways.

Inferring phylogenies: An introduction

• Homologous characters are features among species that have been inherited from common ancestors. They can describe not only morphological and other phenotypic features, but also DNA sequences.

  • Ex: the forelimb bones of tetrapod vertebrates are all homologous with one another

• Fossils can provide important information about the evolutionary history of a group, but many organisms do not leave fossil records, so phylogenies are mostly inferred from living organisms

• A character is a trait of an organism (ex: number of toes on a hindlimb).

  • Character states are one of the variant conditions of a character (ex: yellow vs brown shell, the character would be “color of snail shell”).

• An outgroup is a taxon that diverged from a group of other taxa (the ingroup) before they diverged from one another

  • The outgroup and ingroup form two branches from the common ancestor of all the species

• Parsimony is the principle of accounting for observations by the hypothesis requiring the fewest or simplest assumptions that lack evidence. It is the principle of invoking the minimal number of evolutionary changes to infer phylogenetic relationships and create a tree.

Variations on the Phylogenetic Theme

Branches of a phylogenetic tree sometimes rejoin

• Hybrid speciation is when various phenotypic features and DNA markers throughout the genome reveal two ancestral sources.

• Horizontal gene transfer (HGT) is the movement of genetic material between unicellular or multicellular organisms other than by the “vertical” transmission of DNA from parent to offspring (reproduction).

  • HGT played a major role in the evolution of bacteria in particular.

Not only organisms have “phylogenies”

• Ex: Different copies of a gene, whether within a single species or in more than one species, have a history of divergence from common ancestors.

• A branching tree that portrays the history of DNA sequences of a gene (haplotypes) is often called a gene tree or gene genealogy.

• A species tree is the phylogeny of the species from which the genes are sampled.

  • Gene trees can differ from species trees.

• Gene duplication is the process where new genes arise as copies of preexisting gene sequences. The result can be a gene family. This is an important process by which genomes have increased in size.

  • Paralogous refers to genes that originate from ancestral gene duplication.

  • Orthologous refers to genes that diverge from a common ancestral gene by phylogenetic splitting at the organismal level.

  • A gene family is two or more loci with similar nucleotide sequences that have been derived from a common ancestral sequence.

  • The history of gene duplication and sequence divergence – the relationships among the orthologous and paralogous genes in two or more species – can be determined by standard phylogenetic methods

• Cells give rise to lineages of cells by division, and these lineages can be traced by the somatic mutations that arise and are inherited by descendant cells.

Phylogenetic Insights into Evolutionary History

• Phylogenetic studies, sometimes in concert with information from the fossil record, enable biologists to piece together the evolutionary history of organisms and their characters, ranging from DNA sequences to geographic distributions. They document patterns of evolution- aspects of change that are common to many groups of organisms.

Inferring the history of character evolution

• One of the most important uses of phylogenetic information is to reconstruct the history of evolutionary change in interesting characteristics by “mapping” character states on the phylogeny and inferring the state in each common ancestor, right back to the root of the entire tree.

• In the simplest methods, we assign to ancestors those character states that require us to postulate the fewest evolutionary changes for which we lack independent evidence. This method enables us to infer when changes in characters occurred, and thus trace their history.

Estimating time of divergence

• A molecular clock is the concept of a steady rate of change in DNA sequences over time, providing a basis for dating the time of divergence of lineages if the rate of change can be estimated.

• Rates of evolution differ among the different positions in codons and among different genes in the genome. Rates of sequence evolution also differ among groups of organisms, especially distantly related taxa: there is not a universal molecular clock.

Patterns of evolution

• Most features of organisms have been modified from pre-existing features.

  • This makes it easier to identify patterns of evolution and trace them back to common ancestors.

  • The most common criteria for hypothesizing homology of anatomical characters are correspondence of position relative to other parts of the body and correspondence of structure (the parts of which a complex feature is composed).

  • A character may be homologous among species but a given character state may not be.

• Rates of character evolution differ.

  • Conservative characters are characters that retain little or no change over long periods among the many descendants of an ancestor.

  • Mosaic evolution is the evolution of different characters at different rates within a lineage.

    • A species evolves, not as a whole, but piecemeal, with each feature evolving independently from the others.

    • Every species is a mosaic of plesiomorphic (ancestral, primitive) and apomorphic (derived, advanced) characteristics.

Evolution is often gradual

• Darwin argued that evolution proceeds by small successive changes (gradualism) rather than by large leaps (saltation).

Homoplasy is common

• Homoplasy is the independent evolution of a character or character state in different taxa.

  • It includes:

    • Convergent evolution (convergence) is the evolution of similar features independently in different evolutionary lineages, usually from different antecedent features or by different developmental pathways

      • Ex: The eyes of vertebrates and cephalopod mollusks – both have a lens and a retina, but their many profound differences indicate that they have evolved independently from ancestors without eyes.

    • Parallel evolution (parallelism) is the evolution of similar or identical features independently in related lineages, thought usually to be based on similar modifications of the same developmental pathways.

      • Ex: Mutational changes in a specific gene, Pitx1, is the basis of independent loss of the pelvic girdle and fins in many freshwater populations of a small fish

    • Evolutionary reversal is the evolution of a character from a derived state back toward a condition that resembles an earlier state.

      • Ex: Winged insects evolved from wingless ancestors, but many lineages of insects have lost their wings in the course of subsequent evolution

Phylogenies describe patterns of diversification

• Divergent evolution of numerous related lineages within a relatively short time is called evolutionary radiation.

• Adaptive radiation is the evolutionary divergence of members of a single phylogenetic lineage into a variety of different adaptive forms. Usually, the taxa differ in the use of resources or habitats and have diverged over a relatively short interval of geological time.

Extra “Boxes” of Information

Box 2A: Classification, Taxonomic Practice, and Nomenclature

• Binomial nomenclature is a system of two-part names consisting of a genus name and a specific epithet (ex: Homo sapiens).

  • To make sure every species had its own unique name, standardized rules were developed for naming species.

• Hierarchical classification is a method of categorizing groups of organisms.

  • Kingdom, phylum, class, order, family, genus, species

• Each group of organisms at any one of these levels is a taxon.

Box 2B: Evidence for Evolution

• The hierarchical organization of life.

  • All organisms fall into a hierarchical system, with groups inside of groups, due to divergence and branching throughout history.

• Homology

  • Different organisms share homologous features, both physical and genetic homologies. This supports the idea of evolution from a common ancestor.

• Embryological similarities

  • Many embryos of different species go through the same developmental process, even when some steps may seem unnecessary. Many embryos look physically alike in the womb.

• Vestigial characters

  • Vestigial characters are traits or structures that do not seem to have a purpose but are still there. For example, flightless beetles still have wings. An explanation for this is that these features once had a purpose but are no longer needed due to evolution.

• Convergence

  • Some features in different species have the same function but vary in structure.

• Suboptimal Design

  • The design of characteristics is not optimal. For example, air and food both go down the same pharynx, risking the possibility of choking on food.

• Geographical distribution

  • Some islands that are perfect for many taxa only have a few. Organisms are not evenly spread around the earth.

• Intermediate forms

  • There are graduations in many characteristics, such as beak length.