Jim's Discussion Notes - Classification

(Campbell, Ch.25 (subset) and Johnson/Raven, Ch.20)

*See also notes on Evolutionary History of Life on Earth.

Introduction

· Classification and Taxonomy are parts of a process for organizing and understanding the relationships of living things.

· Systematics is the study of biological diversity in an evolutionary context.

· Part of the scope of systematics is the development of phylogeny, the evolutionary history of a species or group of related species.

1. Taxonomy employs a hierarchical system of classification

· The Linnean system, first formally proposed by Linneaus in Systema naturae in the 18th century, has two main characteristics.

· Each species has a two-part name.

· Species are organized hierarchically into broader and broader groups of organisms.

· Under the binomial system, each species is assigned a two-part latinized name, a binomial.

· The first part, the genus, is the closest group to which a species belongs.

· The second part, the specific epithet, refers to one species within each genus.

· The first letter of the genus is capitalized and both names are italicized and latinized.

· For example, Linnaeus assigned to humans the scientific name Homo sapiens, which means “wise man,” perhaps in a show of optimism.

· A hierachical classification groups species into broader taxonomic categories.

· Species that appear to be closely related are grouped into the same genus.

· For example, the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris).

· Biology’s taxonomic scheme formalizes our tendency to group related objects.

· Genera are grouped into progressively broader categories: family, order, class, phylum, kingdom and domain.

· Each taxonomic level is more comprehensive than the previous one.

· As an example, all species of cats are mammals, but not all mammals are cats.

· The named taxonomic unit at any level is called a taxon.

· Example: Pinus is a taxon at the genus level, the generic name for various species of pine trees.

· Mammalia, a taxon at the class level, includes all the many orders of mammals.

· Phylogenetic trees reflect the hierarchical classification of taxonomic groups nested within more inclusive groups.

2. Modern phylogenetic systematics is based on cladistic analysis

· A phylogeny is determined by a variety of evidence including fossils, molecular data, anatomy, and other features.

· Most systematists use cladistic analysis, developed by a German entomologist Willi Hennig to analyze the data

· A phylogenetic diagram or cladogram is constructed from a series of dichotomies.

· These dichotomous branching diagrams can include more taxa.

· The sequence of branching symbolizes historical chronology.

· The last ancestor common to both the cat and dog families lived longer ago than the last common ancestor shared by leopards and domestic cats.

· Each branch or clade can be nested within larger clades.

· A clade consists of an ancestral species and all its descendents, a monophyletic group.

· Groups that do not fit this definition are unacceptable in cladistics.

· Determining which similarities between species are relevant to grouping the species in a clade is a challenge.

· It is especially important to distinguish similarities that are based on shared ancestry or homology from those that are based on convergent evolution or analogy.

· These two desert plants are not closely related but owe their resemblance to analogous adaptations.

· As a general rule, the more homologous parts that two species share, the more closely related they are.

· Adaptation can obscure homology and convergence can create misleading analogies.

· Also, the more complex two structures are, the less likely that they evolved independently.

· For example, the skulls of a human and chimpanzee are composed not of a single bone, but a fusion of multiple bones that match almost perfectly.

· It is highly improbable that such complex structures matching in so many details could have separate origins.

· For example, the forelimbs of bats and birds are analogous adaptations for flight because the fossil record shows that both evolved independently from the walking forelimbs of different ancestors.

· Their common specializations for flight are convergent, not indications of recent common ancestry.

· The presence of forelimbs in both birds and bats is homologous, though at a higher level of the cladogram, at the level of tetrapods.

· The question of homology versus analogy often depends on the level of the clade that is being examined.

· Systematists must sort through homologous features or characters to separate shared derived characters from shared primitive characters.

· A shared derived character is unique to a particular clade.

· A shared primitive character is found not only in the clade being analyzed, but older clades too.

· Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

· For example, the presence of hair is a good character to distinguish the clade of mammals from other tetrapods.

· It is a shared derived character that uniquely identifies mammals.

· However, the presence of a backbone can qualify as a shared derived character, but at a deeper branch point that distinguishes all vertebrates from other mammals.

· Among vertebrates, the backbone is a shared primitive character because it evolved in the ancestor common to all vertebrates.

· Shared derived characters are useful in establishing a phylogeny, but shared primitive characters are not.

· The status of a character as analogous versus homologous or shared versus primitive may depend on the level at which the analysis is being performed.

· A key step in cladistic analysis is outgroup comparison which is used to differentiate shared primitive characters from shared derived ones.

· To do this we need to identify an outgroup:

· a species or group of species that is closely related to the species that we are studying,

· but known to be less closely related than any study-group members are to each other.

· To study the relationships among five vertebrates (the ingroup)—a leopard, a turtle, a salamander, a tuna, and a lamprey—on a cladogram, then an animal called the lancet would be a good choice.

· The lancet is closely related to the most primitive vertebrates based on other evidence and other lines of analysis.

· These other analyses also show that the lancet is not more closely related to any of the ingroup taxa.

· In an outgroup analysis, the assumption is that any homologies shared by the ingroup and outgroup must be primitive characters already present in the ancestor common to both groups.

· Homologies present in some or all of the ingroup taxa must have evolved after the divergence of the ingroup and outgroup taxa.

· In our example, a notochord, present in lancets and in the embryos of the ingroup, would be a shared primitive character and not useful.

· The presence of a vertebral column, shared by all members of the ingroup but not the outgroup, is a useful character for the whole ingroup.

· Similarly, the presence of jaws, absent in lampreys and present in the other ingroup taxa, helps to identify the earliest branch in the vertebrate cladogram.

· Analyzing the taxonomic distribution of homologies enables us to identify the sequence in which derived characters evolved during vertebrate phylogeny.

· A cladogram presents the chronological sequence of branching during the evolutionary history of a set of organisms.

· However, this chronology does not indicate the time of origin of the species that we are comparing, only the groups to which they belong.

· For example, a particular species in an old group may have evolved more recently than a second species that belongs to a newer group.

· Systematists can use cladograms to place species in the taxonomic hierarchy.

· For example, using turtles as the outgroup, we can assign increasingly exclusive clades to finer levels of the hierarchy of taxa.

· However, some systematists argue that the hierarchical system is antiquated because such a classification must be rearranged when a cladogram is revised based on new evidence.

· These systematists propose replacing the Linneaen system with a strictly cladistic classification called phylocode that drops the hierarchical tags, such as class, order, and family.

· So far, biologists still prefer a hierachical system of taxonomic levels as a more useful way of organizing the diversity of life.

3. Systematists can infer phylogeny from molecular data

· The application of molecular methods and data for comparing species and tracing phylogenies has accelerated revision of taxonomic trees.

· If homology reflects common ancestry, then comparing genes and proteins among organisms should provide insights into their evolutionary relationships.

· The more recently two species have branched from a common ancestor, the more similar their DNA and amino acid sequences should be.

· These data for many species are available via the internet.

· Molecular systematics makes it possible to assess phylogenetic relationships that cannot be measured by comparative anatomy and other non-molecular methods.

· This includes groups that are too closely related to have accumulated much morphological divergence.

· At the other extreme, some groups (e.g., fungi, animals, and plants) have diverged so much that little morphological homology remains.

· Most molecular systematics is based on a comparison of nucleotide sequences in DNA or RNA.

· Each nucleotide position along a stretch of DNA represents an inherited character as one of the four DNA bases: A (adenine), G (guanine), C (cytosine), and T (thymine).

· Systematists may compare hundreds or thousands of adjacent nucleotide positions from several DNA regions to assess the relationship between two species.

· This DNA sequence analysis provides a quantitative tool for constructing cladograms with branch points defined by mutations in DNA sequence.

· The rates of change in DNA sequences vary from one part of the genome to another.

· Some regions (e.g., rRNA) that change relatively slowly are useful in investigating relationships between taxa that diverged hundreds of millions of years ago.

· Other regions (e.g., mtDNA) evolve relatively rapidly and can be employed to assess the phylogeny of species that are closely related or even populations of the same species.

· The first step in DNA comparisons is to align homologous DNA sequences for the species we are comparing.

· Two closely related species may differ only in which base is present at a few sites.

· Less closely related species may not only differ in bases at many sites, but there may be insertions and deletions that alter the length of genes

· This creates problems for establishing homology.

4. The principle of parsimony helps systematists reconstruct phylogeny

· The process of converting data into phylogenetic trees can be a daunting problem.

· If we wish to determine the relationships among four species or taxa, we would need to choose among several potential trees.

· As we consider more and more taxa, the number of possible trees increases dramatically.

· There are about 3 x 10⁷⁶ possible phylogenetic trees for a group of 50 species.

· Even computer analyses of these data sets can take too long to search for the tree that best fits the DNA data.

· Systematists use the principle of parsimony to choose among the many possible trees to find the tree that best fits the data.

· The principle of parsimony (“Occam’s Razor”) states that a theory about nature should be the simplest explanation that is consistent with the facts.

· This minimalist approach to problem solving has been attributed to William of Occam, a 14th century English philosopher.

· In phylogenetic analysis, parsimony is used to justify the choice of a tree that represents the smallest number of evolutionary changes.

· As an example, if we wanted to use the DNA sequences from seven sites to determine the most parsimonious arrangement of four species, we would begin by tabulating the sequence data.

· Then, we would draw all possible phylogenies for the four species, including the three shown here.

· We would trace the number of events (mutations) necessary on each tree to produce the data in our DNA table.

· After all the DNA sites have been added to each tree we add up the total events for each tree and determine which tree required the fewest changes, the most parsimonious tree.

5. Phylogenetic trees are hypotheses

· The rationale for using parsimony as a guide to our choice among many possible trees is that for any species’ characters, hereditary fidelity is more common than change.

· At the molecular level, point mutations do occasionally change a base within a DNA sequence, but exact transmission from generation to generation is thousands of times more common than change.

· Similarly, one could construct a primitive phylogeny that places humans and apes as distant clades but this would assume an unnecessarily complicated scenario.

· A cladogram that is not the most parsimonious would assume an unnecessarily complicated scenario, rather than the simplest explanation.

· Given a choice of possible trees we can draw for a set of species or higher taxa, the best hypothesis is the one that is the best fit for all the available data.

· In the absence of conflicting information, the most parsimonious tree is the logical choice among alternative hypotheses.

· A limited character set may lead to acceptance of a tree that is most parsimonious, but that is also wrong.

· Therefore, it is always important to remember that any phylogenetic diagram is a hypothesis, subject to rejection or revision as more character data are available.

· For example, based on the number of heart chambers alone, birds and mammals, both with four chambers, appear to be more closely related to each other than lizards with three chambers.

· But abundant evidence indicated that birds and mammals evolved from different reptilian ancestors.

· The four-chambered hearts are analogous, not homologous, leading to a misleading cladogram.

· Regardless of the source of data (DNA sequence, morphology, etc.), the most reliable trees are based on the largest data base.

· Occasionally misjudging an analogous similarity in morphology or gene sequence as a shared derived homology is less likely to distort a phylogenetic tree if each clade in the tree is defined by several derived characters.

· The strongest phylogenetic hypotheses are supported by both the morphological and molecular evidence.

6. Molecular clocks may keep track of evolutionary time

· The timing of evolutionary events has rested primarily on the fossil record.

· Recently, molecular clocks have been applied to place the origin of taxonomic groups in time.

· Molecular clocks are based on the observation that some regions of genomes evolve at constant rates.

· For these regions, the number of nucleotide and amino acid substitutions between two lineages is proportional to the time that has elapsed since they branched.

· For example, the homologous proteins of bats and dolphins are much more alike than are those of sharks and tuna.

· This is consistent with the fossil evidence that sharks and tuna have been on separate evolutionary paths much longer than bats and dolphins.

· In this case, molecular divergence has kept better track of time than have changes in morphology.

· Proportional differences in DNA sequences can be applied to access the relative chronology of branching in phylogeny, but adjustments for absolute time must be viewed with some caution.

· No genes mark time with a precise tick-tock accuracy in the rate of base changes.

· Genes that make good molecular clocks have fairly smooth average rates of change.

· Over time there may be chance deviations above and below the average rate.

· Each molecular clock must be calibrated in actual time.

· Typically, one graphs the number of amino acid or nucleotide differences against the times for a series of evolutionary events known from the fossil record.

· The slope of the best line through these points represents the evolution rate of that molecular clock.

· This rate can be used to estimate the absolute date of evolutionary events that have no fossil record.

· The molecular clock approach assumes that much of the change in DNA sequences is due to genetic drift and is selectively neutral.

· If certain DNA changes were favored by natural selection, then the rate would probably be too irregular to mark time accurately.

· Also, some biologists are skeptical of conclusions derived from molecular clocks that have been extrapolated to time spans beyond the calibration in the fossil record.

· The molecular clock approach has been used to date the jump of the HIV virus from related SIV viruses that infect chimpanzees and other primates to humans.

· Investigators calibrated their molecular clock by comparing DNA sequences in a specific HIV gene from patients sampled at different times.

· From their analysis, they project that the HIV-1M strain invaded humans in the 1930s.

7. Modern systematics is flourishing with lively debate

· Systematics is thriving at the interface of modern evolutionary biology and taxonomic theory.

· The development of cladistics provides a more objective method for comparing morphology and developing phylogenetic hypotheses.

· Cladistic analysis of morphological and molecular characters, complemented by a revival in paleontology and comparative biology, has brought us closer to an understanding of the history of life on Earth.

· For example, the fossil record, comparative anatomy, and molecular comparisons all concur that crocodiles are more closely related to birds than to lizards and snakes.

· In other cases, molecular data present a different picture than other approaches.

· For example, fossil evidence dates the origin of the orders of mammals at about 60 million years ago, but molecular clock analyses place their origin to 100 million years ago.

· In one camp are those who place more weight in the fossil evidence and express doubts about the reliability of the molecular clocks.

· In the other camp are those who argue that paleontologists have not yet documented an earlier origin for most mammalian orders because the fossil record is incomplete.

· Between these two extremes is a phylogenetic fuse hypothesis.

· This hypothesis proposes that the modern mammalian orders originated about 100 million years ago.

• But they did not proliferate extensively enough to be noticeable in the fossil record until after the extinction of dinosaurs almost 40 million years later.