Fish Taxonomy and Systematics

Lecture 3:

The Evolutionary Relationships Among Populations, Species And Higher Taxa

Why Systematics?

OrganizationBasis for identification/ classification of lifeGives insight into biological processes:

speciation processesadaptation to environment

Understanding relationshipsCommon language!

Systematics

Understand patterns of diversityHow? ...in the context of evolutionary and

ecological theory.trends in where fish groups are found (spatial

distribution)trends in emergence/extinction of evolutionary

groups

The Concept of “Relationship”

Morphological (Linnaeus): the smallest group of individuals that look different from each other.can misclassify based on differences that can be

maintained within an interbreeding groupdepends only on observable morphological

differences

The Concept of “Relationship”

Biological (Mayr): group of populations of individuals that are similar in form and function and that are reproductively isolated from other populationsconventional definition until late 1980’sincludes genetic informationignores hybridizationdependent on on geographic isolation geographic isolation to achieve

species status

The Concept of “Relationship”

Evolutionary (Wiley): a population or group of populations that shares a common evolutionary fate and historical tendenciesrecognizes more than just genetic and

morphological differencesdifficult to determine “evolutionary fate”how much diversity is allowed within a common

evolutionary fate? Nelson 1999 Reviews in Fish Biology and Fisheries

The Concept of “Relationship”

Phylogenetic: the smallest biological unit appropriate for phylogenetic analysis (process that rates traits as ancestral (plesiomorphes) or derived (apomorphies) and then looks for groupings based on similarities (shared, synapomorphies)does not infer modes of speciationnothing is arbitrarydepends on thorough phylogenetic analysis first

The Concept of “Relationship”

Usefulness of each concept depends on the use - for Endangered Species Act, use as much evidence as possible:morphological, physiological, behavioralgeographiclife history & developmenthabitat & feeding ecologyphylogeneticsevolutionary fate

Determining Relationships Between Taxa

Traditional:examine and list primitive to advanced,link groups based on a few arbitrary traits,generate lineage model based on these limited

data

Determining Relationships Between Taxa

Phenetics: multivariate statistical approach:assemble list of traitsdetermine degree of similarity among groups based on

number of similar traitsoperates on the assumption that the total phenotype

accurately reflects the genotype.has been largely a failure when applied to higher

organisms (Ernst Mayr -Evolution and the Diversity of Life, 1976, p. 429)

ignores evolutionary linkage of groups (convergence could put evolutionarily distinct lines into a single taxon)

Determining Relationships Between Taxa

Evolutionary approach:for the evolutionary systematist, relationship

means more than just kinship in a strictly genealogical sense

it also involves a measure of genetic change that may occur within a group subsequent to its divergence (branching) from an ancestral group.

Determining Relationships Between Taxa

Phylogenetic (cladistic):define relationship in a strictly genealogical sense

—the measure of phylogenetic relationship is the relative recency of common descent

assemble a list of traitsclassify each taxonomic group on basis of

presence or absence of each traitdetermine degree of similarity among groups

based on shared and unique traits:

Determining Relationships Between Taxa

Phylogenetic (cladistic), continued:determine degree of similarity among groups

based on shared and unique traits:1. shared traits = plesiomorphic traits (ancestral)2. unique traits = apomorphic traits (derived)3. shared unique traits = synapomorphic traits

monophyletic group of taxa (common origin) = clade

Advantage:– Classification reflects pattern of evolution– Classification not ambiguous

Imagine an ancestral species A that gives rise to three modern-day species, B, C, and D.

Imagine further that 15% of the genetic content of species B differs from that of species A, 10% of the genetic content of species C differs from that of species A, and 70% of the genetic content of species D differs from that of species A.

There is a maximum genetic difference of 25% between the genomes of B and C, but 80% between C and D.

The evolutionist would say B and C are more closely related than either is to D, because there is much less genetic difference or genetic change between them, that is, they have a much greater inferred amount of shared genotype.

Evolutionary approach

The cladist, in direct opposition to the evolutionary systematist, would conclude that C is more closely related to D than to B because of greater recency of common descent.

Over the years, the cladistic approach has become widely accepted over any alternative approach, so that today nearly everyone in the field of biosystematics is a cladist!

Cladistic approach

Cladistic Systematics

Some recent classifications attempt to show only evolutionary relationships among organisms, ignoring their degree of morphological similarity or difference.

The objective of cladistic systematics is to determine the evolutionary histories of organisms and then to express those relationships in phylogenetic trees.

A clade is the entire portion of a phylogeny that is descended from a single ancestral species.

The closeness of organisms on a cladogram indicates the presumed time since they diverged from their most recent common ancestor.

Because the goal is to show phylogenies, taxa in a cladistic classification are clades and are monophyletic, i.e., each taxon is a single lineage that includes all-and only-the descendants of a single ancestor.

Traits shared due to descent from a common ancestor are called ancestral traits.

Q. How can ancestral traits be recognized?

A good fossil record helps reveal ancestral traits.

For example, the excellent fossil record of horses shows that modern horses, which have one toe on each foot, evolved from ancestors that had multiple toes.

A trait, such as the modern horse's single toe, that differs from the ancestral trait in the lineage is called a derived trait.

To erect classification systems that accurately reflect phylogenies, it is necessary to be able to distinguish ancestral from derived traits.

Therefore, cladists devote much effort to gathering and interpreting evidence to determine which traits are really ancestral and which are derived in different groups of organisms.

To erect classification systems that accurately reflect phylogenies, it is necessary to be able to distinguish ancestral from derived traits.

Therefore, cladists devote much effort to gathering and interpreting evidence to determine which traits are really ancestral and which are derived in different groups of organisms.

Study of Mitochondrial and Chloroplast genomes

DNA in these two organelles is useful in evolutionary studies because:Genomes have a relatively small size, especially when

compared to nuclear DNAThey are well organized, discrete units of inheritanceThere are few recombination eventsUniparental inheritance (usually)Often high copy-numbers in the cell

(i.e. easy to work with)Mutation rates vary (useful to study many levels of diversity)

What is a phylogeny?A phylogeny is a type of

pedigree Shows relationships between

species, not individualsReconstructs pattern of

events leading to the distribution and diversity of life

Often shown as a network or tree

Understanding Trees

Time

A B C D

Understanding Trees

“Root”: common ancestor of organisms in the phylogeny

A B C D

Understanding Trees

Internal branch: common ancestor of a subset of species in the tree

A B C D

Understanding Trees

“Node”: point of divergence of two species

A B C D

Understanding Trees

A B C D

“Leaf”: terminal branch leading to a species

Understanding Trees

Clade: group of species descended from a common ancestor

A B C D

Why study phylogenies?

It is useful to know how organisms are relatedTaxonomyCharacter evolution and state prediction EcologyCo-evolution BiogeographyDivergence timesMedicine

Uses of phylogenies: Taxonomy Similar organisms are

grouped together Clades share common

evolutionary history Phylogenetic

classification names clades

Source: Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M. 2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the “ancient fish”. Molecular Phylogenetics and Evolution, 26: 110-120.

Source: Pryer, K.M., H. Schneider, A.R. Smith, R. Cranfill, P.G. Wolf, J.S. Hunt and S.D. Sipes. 2001. Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409: 618-622

Uses of phylogenies: Character evolution

Examine changes in particular traitse.g. body plan in animals

Predict similar traits in related speciese.g. Taxol (a cancer drug) in the Yew tree

Correlation between 2 characterse.g. fruit traits and dispersal mechanism in

plants

Example of correlated character evolution

After: Conner, J.K. 2002. Genetic mechanisms of floral trait correlations in a natural population. Nature 420: 407-410.Conner, J.K. 1997. Floral Evolution in Wild Radish: The Roles of Pollinators, Natural Selection, and Genetic Correlations Among Traits. Int. J. Plant Sci. 158(6 Suppl.): S108-S120.Conner, J. and S. Via. 1993. Patterns of phenotypic and genetic correlations among morphological and life history traits in wild radish, Raphanus raphanistrum. Evolution 47: 704-711.

Corolla and Filament length in Flowers

Uses of phylogenies: Ecology

Study the evolution of ecological interaction and behaviorWhy might two related species have a different

ecology? e.g. social vs. solitary, drought tolerant vs. mesophytic,

parasitic vs. free living, etc.What are the causes of these differences?Is the environment causing these differences?Can we infer which condition is ancestral?

Examples of phylogenetic ecologyEvolutionary ecology of mate choice in swordtail fish (genus Xiphophorus)M. R. MORRIS, P. F. NICOLETTO & E. HESSELMAN. 2003. A polymorphism in female preference for a polymorphic male trait in the swordtail fish Xiphophorus cortezi. ANIMAL BEHAVIOUR, 65, 45–52 doi:10.1006/anbe.2002.2042. G. G. Rosenthal, T. Y. Flores Martinez, F. J. Garcîa de Leo, and M. J. Ryan. 2001. The American Naturalist. vol. 158, no. 2 Shared Preferences by Predators and Females for Male Ornaments in Swordtails.G. G. ROSENTHAL AND C. S. EVANS. 1998. Evolution Female preference for swords in Xiphophorus helleri reflects a bias for large apparent size (sexual selection

Uses of phylogenies: Co-evolution

Compare divergence patterns in two groups of tightly linked organisms (e.g. hosts and parasites or plants and obligate pollinators)Look at how similar the two phylogenies areLook at host switching

Evolutionary arms racesTraits in one group track traits in another

groupe.g. toxin production and resistance in prey/predator or

plant/herbivore systems, floral tube and proboscis length in pollination systems

Example of host-parasite phylogeny

Source: Page, R.D.M., Cruickshank, R.H., Dickens, M., Furness, R.W., Kennedy, M., Palma, R.L., Smith, V.S. 2004. Phylogeny of “Philoceanus complex” seabird lice (Phthiraptera: Ischnocera) inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 30: 633-652.

Uses of phylogenies: Phylogenetic geography

Sometimes called historical biogeography or phylogeography

Map the phylogeny with geographical ranges of populations or speciesUnderstand geographic origin and spread of species

e.g. origin of modern humans in AfricaLook at similarities between unrelated

organismsUnderstand repeated patterns in distributions

e.g. identifying glacial refugia

Uses of phylogenies: Estimating Divergence Times

Estimate when a group of organisms originatedUses information about phylogeny and rates of

evolutionary change to place timescales on treeNeeds calibration with fossils

Combined with mapping characters, correlate historical events with character evolutione.g. Radiation of flowering plants in the Cretaceous

Uses of phylogenies: Medicine

Learn about the origin of diseases

Look for disease resistance mechanisms in other hosts to identify treatment and therapy in humans

Multiple origins of HIV from SIV (Simian Immunodeficiency Virus)From: Understanding Evolution. HIV: the ultimate evolver. http://evolution.berkeley.edu/evolibrary/article/0_0_0/medicine_04

Example of disease phylogeny

Sourc: Understanding Evolution: Tracking SARS back to it's source. http://evolution.berkeley.edu/evolibrary/news/060101_batsarsAfter: Wendong Li, et al. 2005. Bats Are Natural Reservoirs of SARS-Like Coronaviruses. Science 28 October 2005: Vol. 310. no. 5748, pp. 676 - 679. DOI: 10.1126/science.1118391

Phylogeny in medical forensics: HIV

A dentist who was infected with HIV was suspected of infecting some of his patients in the course of treatment

HIV evolves very quickly (10-3 substitutions/year) Possible to trace the history of infections among

individuals by conducting a phylogenetic analysis of HIV sequences

Samples were taken from dentist, patients, and other infected individuals in the community

Study found 5 patients had been infected by the dentist

Source: Ou et. al. 1992. Molecular epidemiology of HIV transmission in a dental practice. Science, 256: 1165-1171.