Title: Phylogeny and Systematics
1Phylogeny and Systematics
2Taxonomy
- Taxonomy produces a formal system for naming and
classifying species to illustrate their
evolutionary relationship.
3Taxonomy Systematics
- Taxonomy
- Formal system for naming and classifying species.
- Systematics
- Broader science of classifying organisms based on
similarity, biogeography, etc. - Systematic zoologists have three goals
- To discover all species of animals.
- To reconstruct their evolutionary relationships.
- To classify animals according to their
evolutionary relationships.
4Taxonomy
- Introduction of evolutionary theory into animal
taxonomy changed taxonomists role from one of
classification to systematization. - Classification denotes the construction of
classes. - Grouping of organisms that possess a common
feature called an essence used to define the
class.
5Taxonomy
- Systematization places groups of species into
units of common evolutionary descent. - Character variation is used to diagnose systems
of common descent. - No requirement that an essential character be
maintained throughout the system for its
recognition as a taxon.
6Taxonomy
- In classification
- Taxonomist asks whether a species being
classified contains the defining feature of a
particular taxonomic class. - In systematization
- Taxonomist asks whether the characteristics of a
species confirm or reject the hypothesis that it
descends from the most recent common ancestor of
a particular taxon.
7Linnaeus and Classification
- Carolus Linnaeus designed our hierarchical
classification scheme. - Kingdom
- Phylum
- Class
- Order
- Family
- Genus
- Species
8Linnaeus and Classification
- All animals are placed in Kingdom Animalia.
- Names of animal groups at each rank in the
hierarchy are called taxa (taxon). - Each rank can be subdivided into additional
levels of taxa. - Superclass, suborder, etc.
9Linnaeus and Classification
10Linnaeus and Classification
- Binomial nomenclature is the system Linnaeus used
for naming species. - Genus and species
- Names are latinized and italicized, only the
genus is capatilized. - Sitta carolinensis
11Linnaeus and Classification
- A trinomial name includes a subspecies epithet.
- Ensatina escholtzii escholtzii
- E. e. klauberi
12Species
- Defining a species can be difficult.
- Criteria
- Common descent
- The smallest distinct groupings of organisms
sharing a pattern of descent. - Morphological molecular techniques
- Members of a species must form a reproductive
community that excludes other species.
13Species
- The geographic range of a species is its
distribution in space. - Evolutionary duration of a species is its
distribution in time. - A worldwide species is cosmopolitan.
- One with a very localized range is called endemic.
14Typological Species Concept
- The typological or morphological species concept
relies on type specimens that represent the ideal
form for the species. When trying to name a
specimen, the type specimens were compared.
- Scientists still name species by designating a
type specimen.
15The Biological Species Concept
- The biological species concept emerged during the
evolutionary synthesis. - A species is a reproductive community of
populations (reproductively isolated from others)
that occupies a specific niche in nature. Mayr
1982 - Sibling species fit this category, but can only
be differentiated with molecular techniques. - Lacks a temporal dimension.
- Degree of reproductive isolation necessary?
- Species that reproduce asexually?
16Evolutionary Species Concept
- The evolutionary species concept states that a
single lineage of ancestor-descendant populations
that maintains its identity from other such
lineages and that has its own evolutionary
tendencies and historical fate. - Definition accommodates both sexual and asexual
forms as well as fossils.
17Phylogenetic Species Concept
- The phylogenetic species concept is defined as an
irreducible (basal) grouping of organisms
diagnosably distinct from other such groupings
and within which there is a parental pattern of
ancestry and descent. - Both asexual and sexual groups are covered.
18Phylogenetic Species Concept
- Main difference in practice between the
evolutionary and phylogenetic species concepts - The latter emphasizes recognizing as separate
species the smallest groupings of organisms that
have undergone independent evolutionary change. - Discerns the greatest number of species but may
be impractical. - Disregards details of evolutionary process.
19Investigating the Tree of Life
- A major goal of systematics is to infer the
evolutionary tree or phylogeny the evolutionary
history of a species or group of related species.
20Phylogeny
- Phylogenies are inferred by identifying
organismal features, characters, that vary among
species. - Morphological
- Chromosomal
- Molecular
- Behavioral or ecological
21Phylogeny
- Shared characters that result from common
ancestry are homologous. - Independent evolution of similar characters that
are NOT homologous is called homoplasy.
22Sorting Homology from Analogy
- A potential misconception in constructing a
phylogeny is similarity due to convergent
evolution, called analogy, rather than shared
ancestry.
23Sorting Homology from Analogy
- Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages.
24Sorting Homology from Analogy
- Analogous structures or molecular sequences that
evolved independently are also called
homoplasies.
25Shared Primitive and Shared Derived
Characteristics
- A shared primitive (ancestral) character
- Is a homologous structure that predates the
branching of a particular clade from other
members of that clade. - Is shared beyond the taxon we are trying to
define. - Example mammals all have a backbone, but so do
other vertebrates.
26Shared Primitive and Shared Derived
Characteristics
- A shared derived character is an evolutionary
novelty unique to a particular clade. - All mammals have hair, and no other animals have
hair.
27Phylogeny
- The form of the character that was present in the
common ancestor of the entire group is called
ancestral. - Variant forms of the character arose later and
are called derived character states. - Determining polarity of a character involves
determining which state is ancestral.
28Phylogeny
- Polarity is determined by using outgroup
comparison. - An outgroup is closely related, but not part of
the group being examined (the ingroup). - If a character is found in both the study group
and the outgroup, it is considered ancestral for
the study group. - Character groups found in the study groups but
not the outgroups are derived.
29Phylogeny
- Clades are organisms or species that share
derived character states and form a subset within
a larger group. - A synapomorphy is a derived character shared by
the members of the clade. - A clade corresponds to a unit of evolutionary
common descent. - A nested hierarchy is formed by the derived
states of all characters in a study group.
30Phylogeny
- Ancestral character states for a taxon are called
plesiomorphic. - Sharing these ancestral characters is called
symplesiomorphy. - Symplesiomorphies, unlike synapomorphies, do not
provide information on nesting of clades groups
with derived characters get left out.
31Phylogeny
- The nested hierarchy of clades can be represented
as a cladogram that is based on shared
synapomorphies.
32Phylogeny
- A phylogenetic tree is another way of
representing evolutionary relationships. - Branches represent real lineages that occurred in
the evolutionary past. - Includes information about ancestors, duration of
evolutionary lineages, amounts of evolutionary
change that has occurred.
33Sources of Phylogenetic Information
- Characters used to construct cladograms can be
found using - Comparative morphology examine shapes and sizes
of organismal structures, including developmental
origins. - Comparative biochemistry examine sequences of
amino acids and nucleotides to identify variable
characters. - Comparative cytology uses variation in numbers,
shapes, and sizes of chromosomes and their parts.
34Taxonomy
- A theory of taxonomy allows us to rank taxonomic
groups. - Two popular theories
- Evolutionary taxonomy
- Phylogenetic systematics
- Both based on evolutionary principles, sometimes
results conflict.
35Cladistics
- A valid clade is monophyletic.
- Signifying that it consists of the ancestor
species and all its descendants.
36Cladistics
- A paraphyletic clade is a grouping that consists
of an ancestral species and some, but not all, of
the descendants.
37Cladistics
- A polyphyletic grouping includes numerous types
of organisms that lack a common ancestor.
38Traditional Evolutionary Taxonomy
- Evolutionary taxonomy utilizes common descent and
the amount of adaptive evolutionary change to
rank higher taxa. - Sometimes this type of classification includes
paraphyletic groupings.
39Phylogenetic Systematics
- Phylogenetic systematics, or cladistics,
emphasizes common descent and is based on
cladograms. - All taxa must be monophyletic.
- Cladistic taxonomists have moved chimpanzees,
gorillas, and orangutans into the family
Hominidae with humans. - Humans and chimps form a sister group, as do the
human/chimp group and gorillas.
40Theories of Taxonomy
- Both evolutionary and cladistic taxonomy
- Accept monophyletic groups.
- Reject polyphyletic groups.
- Differ on accepting paraphyletic groups.
- Traditional evolutionary taxonomy does.
- Phylogenetic systematics does not.
- Difference has important evolutionary
implications.
41Theories of Taxonomy
- Current State of Animal Taxonomy
- Modern animal taxonomy was established using
evolutionary systematics and recent cladistic
revisions. - PhyloCode
- New taxonomic system
- Being developed as an alternative to Linnean
taxonomy. - Replaces Linnean ranks with codes that denote the
nested hierarchy of monophyletic groups conveyed
by cladograms. - The terms primitive, advanced, specialized
and generalized are used for specific
characteristics and not for groups as a whole.
42Maximum Parsimony and Maximum Likelihood
- Systematists can never be sure of finding the
single best tree in a large data set. - Narrow the possibilities by applying the
principles of maximum parsimony and maximum
likelihood.
43Parsimony
- Among phylogenetic hypotheses the most
parsimonious tree is the one that requires the
fewest evolutionary events to have occurred in
the form of shared derived characters. - Occams Razor
44Parsimony
- The principle of maximum likelihood states that,
given certain rules about how DNA changes over
time, a tree can be found that reflects the most
likely sequence of evolutionary events.
45Phylogenetic Trees as Hypotheses
- The best hypotheses for phylogenetic trees are
those that fit the most data morphological,
molecular, and fossil.
46Molecular Systematics
- Much of an organisms evolutionary history is
documented in its genome. - Comparing nucleic acids or other molecules to
infer relatedness is a valuable tool for tracing
organisms evolutionary history.
47Major Divisions of Life
- Aristotles two kingdom system included plants
and animals. - One-celled organisms became a problem
- Haeckel (1866) proposed Protista for
single-celled organisms. - R.H. Whittaker (1969) proposed a five-kingdom
system to distinguish prokaryotes and fungi.
48Major Divisions of Life
- Woese, Kandler and Wheelis (1990) proposed three
monophyletic domains above kingdom levelEucarya,
Bacteria and Archaeabased on ribosomal RNA
sequences.
49Major Division of Life
- More revisions are necessary to clarify taxonomic
kingdoms based on monophyly. - Protozoa
- Neither animals nor a valid monophyletic taxon.
- Protista
- Not a monophyletic kingdom.
- Most likely composed of seven or more kingdoms.
50Major Subdivisions of the Animal Kingdom
- Traditional groupings based on embryological and
anatomical characters - Branch A (Mesozoa) phylum Mesozoa,
the mesozoa - Branch B (Parazoa) phylum Porifera,
the sponges and phylum Placozoa - Branch C (Eumetazoa) all other phyla
51Major Subdivisions of the Animal Kingdom
- Branch C (Eumetazoa) all other phyla
- Grade I (Radiata) phyla Cnidaria, Ctenophora
- Grade II (Bilateria) all other phyla
- Division A (Protostomia) Protostome
characteristics - Acoelomates phyla Platyhelminthes,
Gnathostomulida, Nemertea - Pseudocoelomates phyla Rotifera, Gastrotricha,
Kinorhyncha, Nematoda, Nematomorpha,
Acanthocephala, Entoprocta, Priapulida,
Loricifera - Eucoelomates phyla Mollusca, Annelida,
Arthropoda, Echiurida, Sipunculida, Tardigrada,
Onychophora.
52Major Subdivisions of the Animal Kingdom
- Division B (Deuterostomia) Deuterostome
characteristics - phyla Phoronida, Ectoprocta, Chaetognatha,
Brachiopoda, Echinodermata, Hemichordata, Chordata
53Major Subdivisions of the Animal Kingdom
- Recent molecular phylogenetic studies have
challenged traditional classification of
Bilateria. - Grade II Bilateria
- Division A (Protostomia)
- Lophotrochozoa phyla platyhelminthes, Nemertea,
Rotifera, Gastrotricha, Acanthocephala, Mollusca,
Annelida, Echiurida, Sipunculida, Phoronida,
Ectoprocta, Entoprocta, Gnathostomulida,
Chaetognatha, Brachiopoda - Ecdysozoa phyla Kinorhyncha, Nematoda,
Nematomorpha, Priapulida, Arthropoda, Tardigrada,
Onychophora, Loricifera - Division B (Deuterostomia)
- phyla Chordata, Hemichordata, Echinodermata
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