1. Integrated Principles of Zoology, 17th edition

2. Taxonomy and Phylogeny of Animals
CHAPTER 10
Taxonomy and Phylogeny of Animals
Copyright © McGraw-Hill Education.  All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.

3. Mollusc Shells
Molluscan shells from the collection of Jean Baptiste de Lamarck (1744–1829).

4. Order in Diversity Evolution and diversity
More than 1.5 million species of animals named with thousands being described each year
Less than 20% of all extant animals known
Less than 1% of extinct animals found
Animal diversity is not random and has definite order.
Natural system of order reflects relationships among animals in nature and outside of human context.
Darwin’s theory of evolution serves as a guide

5. Taxonomy
Taxonomy is a formal system for naming and classifying species following the principle of common descent.
Animals with recent ancestry share many common features and are grouped closer together.
Biologists have organized animal diversity in nested hierarchy of groups within groups based on shared features.
However, many taxonomic practices predate evolutionary biology, but are sometimes controversial to update.

6. Systematics
Systematics (comparative biology) is the broader science of classifying organisms based on studies of variation among populations that reveal their evolutionary relationships.
Needs to accommodate various alternative taxonomic viewpoints

7. Linnaeus and Taxonomy
Aristotle (384–332 BC)—Greek biologist/philosopher, who first classified organisms based on structural similarities
Carolus Linnaeus designed the current system of classification
Swedish botanist with extensive experience classifying objects, especially flowers
Published in his work, Systema Naturae, which used morphology to develop a classification system of animals and plants

8. Linnaean Taxonomy The Linnaean system of classification
Divided animal kingdom into species and gave each a distinctive name
Grouped species based on shared common essential properties into genera, genera into orders, and orders into classes, and so on.
Animals are arranged in an ascending series of groups with increased inclusiveness
His original classification scheme was very limited and has been drastically altered, but the basic principle is still followed today.

9. Taxa in Linnaean System
Taxa (taxon)—major animal groups at each level in the hierarchy
Taxonomic ranks—indicate the general degree of inclusiveness per group
The seven mandatory major ranks
Kingdom, phylum, class, order, family, genus, and species
All animals are placed in Kingdom Animalia.
Each major rank can be further subdivided into smaller levels of taxa such as superclass, suborder, and so on.
More than 30 taxonomic ranks are now recognized.

10. Taxonomic Categories

11. Systematization Versus Classification
Introduction of the evolutionary theory into animal taxonomy changed the taxonomist’s role from one of classification to that of systematization.
Classification denotes the construction of classes and grouping of organisms.
Groups possess a common feature called an essence which is used to define the group.
Static nature of groups are ill advised due to the constant evolution of species.

12. Systematization
Systematization places groups of species into units of common evolutionary descent.
Include the most recent common ancestor and its descendants
Character variation is used to diagnose systems of common descent.
Not required as an essential character to be maintained throughout the system for its recognition as a taxon
Each successive taxon represents the descendants of an earlier ancestor

13. Classification Differs from Systematization
Morphology and other features are used differently between classification and systematization.
In classification
Taxonomists ask 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.

14. Binomial Species Nomenclature
Linnaeus’s system for naming species is called binomial species nomenclature.
Scientific name of an animal consists of two words, normally in Latin.
Scientific name should be printed in italics or underlined if handwritten
First word is the genus and is capitalized
The second, the specific epithet, is written in lower case
For example, Homo sapiens
Latin is used in scientific nomenclature by scientists all around the world due to its precise description compared to “common” names that may vary both culturally and geographically.

15. Scientific Names Genus name Species epithet
Always a noun and must refer only to a single group of organisms
Species epithet
Usually an adjective that must agree in gender with the species and never used alone
Same name cannot be given to different animals
A species epithet may be used in different genera
Sita carolinensis (white-breasted nuthatch)
Poecile carolinensis (Carolina chickadee)
Anolis carolinensis (green anole lizard)

16. What Is a Species?
Thomas Henry Huxley (1825–1895) asked this famous question which still has no clear answer
There are numerous species concepts, which lead to numerous disagreements
Biologists have repeatedly used certain criteria for identifying species
Common descent
Smallest distinct groupings
Reproductive community

17. Criteria for Identifying Species
Common descent
Central theme to all modern concepts of species trace their ancestry to a common ancient population but not necessarily the same exact pair of parents
Smallest distinct groupings
Species are the smallest unit sharing patterns of ancestry and descent.
Morphology has been traditionally used but now supplemented with chromosomal and molecular characteristics.

18. Another Criteria for Identifying Species
Reproductive community
Species form reproductive groups that exclude other species
Sexually reproducing populations
Interbreeding is critical for maintaining a reproductive community
Asexually reproducing populations
Entails occupation of a particular ecological habitat in a particular place so that a reproducing population responds as a unit to evolutionary forces

19. Species Distribution
All species differ greatly in their distribution through space and time
Geographic range
Cosmopolitan—species having very large geographic ranges or worldwide distributions
Endemic—species with very restricted geographic distributions
Range can either be continuous or disjunct
Evolutionary duration
Distribution through time which is variable per species

20. Ensatina Geographic Variation
Figure 10.2 Geographic variation of color patterns in the salamander genus Ensatina.

21. Typological Species Concept
Before Darwin, a species was considered a distinct and immutable entity derived from divinely created patterns.
A type specimen was labeled and deposited in a museum.
New specimens were always compared to this previously described representative specimen.
Small differences from the type are considered accidental imperfections.
Large difference leads to description of new species.

22. Bird Specimens
Figure 10.3 Specimens of birds from the Smithsonian Institution (Washington, D.C.),

23. Typological Species Concept Today
Evolutionists have discarded the typological species concept, though some traditions remain.
Organismal morphology is still important in recognizing species.
However, species are no longer viewed as classes of organisms defined by possession of certain morphological features.
Type specimens serves only as a guide to general morphological features that one might expect to find in a particular species.
Variation is not viewed as an imperfect manifestation of an eternal “type.”

24. Biological Species Concept
Proposed by Theodosius Dobzhansky and Ernst Mayr
A species is a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.
Ability to successfully interbreed is central to the concept
Criteria of “niche” views members of a reproductive community to have common ecological properties

25. Biological Species Concept Today
Modernized version states that a species is an interbreeding population of individuals having common descent and sharing intergrading characteristics.
Expect to maintain genetic cohesiveness within similar species and discontinuous between different species
Sometimes species status can be evaluated directly by conducting breeding experiments.
However, controlled breeding experiments can be difficult to conduct so character variation is still used.

26. Identifying Biological Species
Variation in molecular characters is used to identify geographical boundaries of different reproductive groups.
Molecular studies may detect sibling species which can be too similar in morphology to be diagnosed as separate species by morphological characters alone.
Biological species is based on reproductive properties of populations rather than organismal morphology, but morphology can help us to diagnose biological species.

27. Problems of the Biological Species Concept
Several perceived problems with biological species concept
Lacks an explicit temporal dimension
Gives little guidance regarding the species status of ancestral populations relative to their evolutionary descendants
Disagreement on the degree of reproductive isolation necessary for considering two populations separate species
Boundaries between species may be difficult to locate
Interbreeding does not occur in asexual organisms which only do binary fission and budding

28. Evolutionary Species Concept
George Gaylord Simpson (1902–1984) proposed the evolutionary species concept in the 1940s.
An evolutionary species is 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.

29. Advantages of Evolutionary Species Concept
Definition accommodates both sexual and asexual forms as well as fossils.
Adds the evolutionary time dimension needed by the biological species concept
Allows the unbroken genealogical chain of populations to the point where sister species converge on their common ancestor

30. Cohesion Species Concept
The ability of geographic populations to evolve collectively as a single, genetically cohesive unit through evolutionary time is critical to the evolutionary species concept.
Alan Templeton updated the evolutionary species concept to form the cohesion species concept
The most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms
Definition includes genetic changes in the population caused by gene flow, genetic drift, and natural selection.

31. Phylogenetic Species Concept
A phylogenetic species is an irreducible (basal) grouping of organisms distinct from other such groupings and within which there is a parental pattern of ancestry and descent.
Both asexual and sexual groups are covered
Phylogenetic species is a single population lineage with no detectable branching and emphasizes common descent.

32. Evolutionary Versus Phylogenetic
Emphasis of the evolutionary/cohesion species concept compared to the phylogenetic species concept:
Places greater emphasis on historically separated populations having biological potential to merge into a single lineage
Groups geographically disjoint populations into single species that show phylogenetic divergence but have similar evolutionary tendencies
Permits future gene exchanges and possible merging of different populations

33. Phylogenetic Versus Evolutionary
Emphasis of the phylogenetic species concept compared to the evolutionary/cohesion species concept:
Views separate species as the smallest groupings of organisms that have undergone independent evolutionary change
Discerns the greatest number of species more readily but may become impractical
Guarantees strict monophyletic units at the species level
Disregards details of evolutionary process intentionally
Allows the description of species without the need for detailed studies

34. General Lineage Concept
General lineage concept is the common underlying principle of many different species concepts.
Species constitute a segment of the population level lineage
Emphasizes the common goal of identifying the phylogenetic history of population level lineages
Still has issues with contrasting species concepts that may differ in how many species are named

35. Dynamism of Species Concepts
Disagreement is a sign of dynamic research and should not be considered discouraging.
Cannot predict which species concepts will remain useful in the future
Possible disagreements regarding species boundaries may identify interesting cases of evolution in action.
No single concept is comprehensive or final but all need to be understood so as to understand future concepts.

36. DNA Barcoding of Species
DNA barcoding is a technique used for identifying species using standard gene sequences present in all animals.
Mitochondrial gene encoding for the cytochrome c oxidase subunit 1 (CO1) normally varies between animals but the variation within species is smaller than differences among species.
Allows for the identification of the origin of a specimen within a given population

37. Major Goal of Systematics
Major goal of systematics is to infer the evolutionary tree or phylogeny that relates all extant and extinct species.
Accomplished by identifying organismal features called characters that vary among species
Characters are any features used to study variation within and among species.
Identified by observing patterns of similarity in morphological, chromosomal, and molecular features
Sometimes, behavioral and ecological features are also used

38. Phylogenetic Analysis
Phylogenetic analysis depends upon finding shared features among organisms that are inherited from a common ancestor
Homology—character similarity resulting from common ancestry
Similarity may not always reflect common ancestry due to independent evolutionary origin on different lineages
Homoplasy—non-homologous similarities that may be found in various organisms

39. Using Character Variation
Character variation can be used to reconstruct phylogeny
First step is to determine which variant form of each character was present in the common ancestor of the entire group
Ancestral character—the character state present in the common ancestor
Evolutionarily derived character—all other variant forms of the character that arose later within the group
Find polarity of a character by identifying which one of its contrasting states is ancestral and which one(s) is derived

40. Determining Polarity
Method used to examine the polarity of a variable character is called outgroup comparison.
Outgroup—group that is phylogenetically close but not within the group being studied
Infer that any character state found both within the group being studied and the outgroup is termed ancestral
All character states found in study groups and absent from appropriate outgroups are considered derived.

41. Clades
A clade corresponds to a unit of evolutionary common descent that includes ancestral lineage and all descendants.
Synapomorphy—derived character shared by members of a clade
Synapomorphies are used as evidence of homology and infer that a particular group of organisms forms a clade.
Plesiomorphic character states are ancestral for a taxon.
Symplesiomorphy is the sharing of ancestral states.

42. Nested Hierarchies
Nested hierarchy of clades within clades forms patterns of derived states of characters within a study group.
By identifying all of the clades nested within the study taxon, some patterns of common descent can be formed.
Cladogram is a branching diagram of a nested hierarchy of clades.
Not similar to phylogenetic tree which represents real lineages in evolutionary history
Normally act as the first approximation of the branching structure of the corresponding phylogenetic tree

43. From Cladogram to Phylogenetic Tree
To go from a cladogram to phylogenetic tree, must add
Additional interpretation concerning ancestors
Duration of evolutionary lineages
Amount of evolutionary change within the lineage

44. Cladogram
Figure 10.5 A cladogram as a nested hierarchy of taxa among five sampled chordate groups.

45. Sources of Phylogenetic Information
Characters useful for constructing cladograms come from comparative morphology, cytology, and biochemistry.
Comparative morphology
Examines shapes, sizes, and development of organisms
Macroscopic and microscopic characters
Living specimens and fossils are used
Comparative biochemistry
Analyzes sequences of amino acids in proteins and nucleotides sequences in nucleic acids
Recent studies show comparative biochemistry can be applied to determine the age of fossils

46. Information Sources and a Timescale
Comparative cytology (Karyology)
Examines variation in number, shape, and size of chromosomes
Used almost exclusively on living specimens
To add an evolutionary time scale needed for a phylogenetic tree
Calibrate the evolution of proteins and DNA sequences by measuring their divergence between species whose common ancestor has been dated in the fossil record
The age of other branches can then be estimated by molecular calibration

47. Phylogenetic Tree
Figure 10.6 An early phylogenetic tree of representative amniotes
based on inferred base substitutions in the gene that encodes the
respiratory protein, cytochrome c.

48. Theories of Taxonomy
Taxonomic theories establish the principles to recognize and rank groups
Two currently popular theories:
Evolutionary (traditional) taxonomy
Phylogenetic systematics (cladistics)
Both are based on evolutionary principles but differ in how these are used
Evolutionary taxonomy predates phylogenetic systematics.

49. Relating Taxonomy to Phylogeny
Relationship between taxonomic group and phylogenetic tree can take one of three forms:
Monophyly
A monophyletic taxon includes the most recent common ancestor and all descendants of that ancestor.
Paraphyly
A taxon is paraphyletic if it includes the most recent common ancestor of all members of a group and some but not all descendants of that ancestor.
Polyphyly
A taxon is polyphyletic if it does not include the most recent common ancestor of all members of a group.
The group has at least two separate evolutionary origins.

50. Convexity
Monophyletic and paraphyletic groups share the property of convexity and distinguish these from polyphyletic group.
A group is convex if you can trace a path between any two members of the group on a cladogram without leaving the group.

51. Phylogenetic and Taxonomic Relationships
Figure 10.7 Relationships between phylogeny and taxonomic groups illustrated for a hypothetical phylogeny of eight species.

52. Evolutionary and Cladistic Taxonomy
Both evolutionary and cladistic taxonomy
Accept monophyletic groups
Reject polyphyletic groups
However, they differ on accepting paraphyletic groups which has important evolutionary implications

53. Evolutionary Taxonomy
Evolutionary taxonomy retains basic structure of Linnaean taxonomy.
Evolutionary taxa must have a single evolutionary origin, and must show unique adaptive features.
George Gaylord Simpson and Ernst Mayr were influential in the development and formalization of evolutionary taxonomy.
A particular branch on an evolutionary tree is considered a higher taxon if it represents a distinct adaptive zone.
“a characteristic reaction and mutual relationship between environment and organism, a way of life and not a place where life is led”

54. Adaptive Zones
Entering a new adaptive zone with new organismal and behavioral changes will allow populations to use environmental resources in a new way
A taxon that represents a distinct adaptive zone is a grade.
The broader the adaptive zone when fully occupied by a group of organisms is, the higher will be the rank given to it.

55. Challenges to Evolutionary Taxonomy
Evolutionary taxonomy has faced two main challenges:
Phenetic taxonomy
Uses a more easily measured feature; the overall similarity of organisms is evaluated without regard to phylogeny
Has contributed some useful analytical methods but did not have a strong impact on animal taxonomy; scientific interest in this approach has declined
Phylogenetic systematics/cladistics

56. Penguins and Petrels
Figure 10.8 (A) Penguin. (B) Diving petrel. Penguins and petrels were recognized as a distinct adaptive zone within birds because of their adaptations for submarine flight.

57. Anthropoid Primates
Figure 10.9 Phylogeny and family-level classification of anthropoid primates.

58. Phylogenetic Systematics/Cladistics
Stronger challenge to evolutionary taxonomy
Formulated by Willi Hennig (1913–1976)
Sometimes called Hennigian systematics
Emphasizes criterion of common descent and is based on the cladogram of the group being classified
All taxa recognized by this system must be monophyletic.

59. Current State of Animal Taxonomy
Modern animal taxonomy was established using evolutionary systematics and recent cladistic revisions.
PhyloCode is a new taxonomic system that is being developed as an alternative to Linnaean taxonomy.
Replaces Linnaean ranks with codes that denote the nested hierarchy of monophyletic groups conveyed by cladograms
Nevertheless, Linnaean ranks are still widely used by many other taxonomists.

60. Describing Patterns of Descent
When discussing patterns of descent, we must avoid the use of phrases that imply paraphyly such as “mammals evolved from reptiles.”
The terms “primitive,” “advanced,” “specialized,” and “generalized” must be avoided as all groups have a combination of all of the terms.
Can be used for specific characteristics and not for groups as a whole
We should avoid calling a living group or species “basal.”
Taxonomist must always be careful to specify whether they are referencing traditional evolutionary taxa or newer cladistics taxa.

61. Major Divisions of Life
Modern classification systems take phylogenetic relationships into account to construct evolutionary branches.
Woese, Kandler, and Wheelis proposed three monophyletic domains above kingdom level based on ribosomal RNA sequences.
Eucarya (all eukaryotes)
Bacteria (true bacteria)
Archaea (variant bacteria)
Traditionally, multicellular organisms are given the rank of kingdom.
Compatible with phylogenetic systematics
Traditionally, unicellular eukaryotes were placed in kingdom Protista.
This group is now recognized to be paraphyletic.

62. Three Domains
Figure Phylogenetic overview of the three domains of life, Archaea, Eucarya, and Bacteria, based on analysis of genes encoding ribosomal RNA.

63. Major Subdivisions of the Animal Kingdom
Phylum is the largest formal taxonomic category in the Linnaean classification of the animal kingdom.
There are other commonly used groupings of animal phyla:
Bilateria includes all animal phyla except Porifera, Placozoa, Cnidaria, and Ctenophora.
Bilateria is further divided into Protostomia and Deuterostomia.
Protostomia is further divided into Ecdysozoa and Lophotrochozoa.