Fish Taxonomy and Systematics
Lecture 3:
The Evolutionary Relationships Among
Populations, Species And Higher Taxa
Why Systematics?
Organization
Basis for identification/ classification of life
Gives insight into biological processes:
speciation processes
adaptation to environment
Understanding relationships
Common language!
Systematics
Understand patterns of diversity
How? ...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 group
depends 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 populations
conventional definition until late 1980’s
includes genetic information
ignores hybridization
dependent on 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 tendencies
recognizes more than just genetic and
morphological differences
difficult 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 speciation
nothing is arbitrary
depends 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, behavioral
geographic
life history & development
habitat & feeding ecology
phylogenetics
evolutionary 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 traits
determine degree of similarity among groups based on
number of similar traits
operates 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 traits
classify each taxonomic group on basis of
presence or absence of each trait
determine 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.
Evolutionary approach
 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.
Cladistic 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 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 DNA
They are well organized, discrete units of inheritance
There are few recombination events
Uniparental 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 individuals
 Reconstructs pattern of
events leading to the
distribution and diversity of
life
 Often shown as a network or
tree
Understanding Trees
A
B
C
D
Time
Understanding Trees
A
B
C
D
“Root”: common ancestor
of organisms in the phylogeny
Understanding Trees
A
B
C
D
Internal branch:
common ancestor
of a subset of species
in the tree
Understanding Trees
A
B
C
D
“Node”: point of
divergence of two
species
Understanding Trees
A
B
C
D
“Leaf”: terminal
branch leading
to a species
Understanding Trees
A
B
C
D
Clade: group of
species descended
from a common
ancestor
Why study phylogenies?
It is useful to know how organisms are
related
Taxonomy
Character evolution and state prediction
Ecology
Co-evolution
Biogeography
Divergence times
Medicine
Uses of phylogenies: Taxonomy
 Similar organisms are
grouped together
 Clades share common
evolutionary history
 Phylogenetic
classification names
clades
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: 618622
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.
Uses of phylogenies: Character
evolution
Examine changes in particular traits
e.g. body plan in animals
Predict similar traits in related species
e.g. Taxol (a cancer drug) in the Yew tree
Correlation between 2 characters
e.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 behavior
Why 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 ecology
Evolutionary 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 are
Look at host switching
Evolutionary arms races
Traits in one group track traits in another
group
e.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 species
Understand geographic origin and spread of
species
e.g. origin of modern humans in Africa
Look at similarities
organisms
between
unrelated
Understand repeated patterns in distributions
e.g. identifying glacial refugia
Uses of phylogenies: Estimating
Divergence Times
Estimate when a group of organisms
originated
Uses information about phylogeny and rates
of evolutionary change to place timescales on
tree
Needs calibration with fossils
Combined with mapping characters, correlate
historical events with character evolution
e.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_batsars
After: 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.