Ch. 26 Connecting Classification to Phylogeny

International Code of Zoological Nomenclature (ICZN)

-contains the rules of zoological nomenclature (naming animals) -the object of it and similar codes for plants, protists, fungi, and microbes, is to promote stability and universality in the scientific names of animals and other organisms

To trace phylogeny, biologists use

-evidence from paleontology, molecular data, comparative anatomy, and other approaches

Classification

-is one branch of taxonomy where various things (books, clouds, species, etc.) are identified and grouped together into groups -orders and ranks things into a series of hierarchical levels (species into genera, genera into families, and so on)

Cladogram

-is one way (but not the only way) to depict the phylogenetic tree -is constructed from a series of dichotomies -the sequence of branching resembles historical chronology of common ancestry

genus

-is the closest group to which a species belongs -the important thing about a genus name is that it is unique -we try to not use the same genus name for two organisms in different phylogenetic lineages

Systematics

-is the field of biology concerned with the identification of the evolutionary relationships among species through time -to some scientists, this term is a synonym for "classification", but some classification methods do not necessarily spell out evolutionary relationships

Phylogeny

-is the pattern and history of evolutionary descent of all the taxa used in a classification of organisms -is the history of descent of a group of organisms from their common ancestor

branch lengths may indicate

-the amount of evolutionary change in the taxon since divergence from another lineage -time; the point at which two branches diverge in a phylogenetic tree can be connected to fossil/geologic events

species

-the second part, the specific epithet, refers to one species within each genus -there can be specific epithets that are used for different species

steps of allopatric speciation

1. Geographical isolation 2.if the two populations are completely isolated so that no gene flow occurs between them, they may evolve into two distinct species

Cladogenesis

= branching evolution or divergent evolution -is the budding off ofone or more new species from a parental species that continues to exist and which may coexist with the 'daughter' species for some time

Anagenesis

= phyletic evolution -is the transformation of one entire species over time into another through time -Darwin's theory on gradual changes in a species (descent with modification) reflects this type of evolution

A hierarchical classification groups species into broader, more inclusive taxonomic categories:

Kingdom - Phylum - Class - Order - Family - Genus - Species

Cladogenesis is the type of speciation in which

branching of new species from an ancestral lineage occurs -leads to an increase in the diversity of species

why is it not surprising that cetaceans have horizontal tail flukes (move them up and down)

cetaceans evolved from land animals, and land vertebrates have a dorsoventrally flexible spine that is an adaptation for quadrupedal running

paraphyletic taxon

is one that excludes some species that share a common ancestor with the rest of the species of the group. In other words, some of the descendant species have been left out of the group, but not the common ancestor

polyphyletic taxon

is one where the members are derived from two or more ancestral forms not common to all members. Some descendant species are not included, and the common ancestor has also been left out

phylogeny

is the history of descent of a group of organisms from their common ancestor

The goal of most taxonomists

is to create an evolutionary classification scheme that reflects the evolutionary history of the listed organisms

Recall that life is viewed as a tree, and each extant species is like a

leaf on the tree.

homologous structures

may have a different function (or a similar function), but the underlying structure, development, and physiology are the same

Systematists infer phylogeny from

molecular evidence

another name for a clade

monophyletic group

Each higher taxonomic level is

more inclusive than the lower level -ex: all species of cats are mammals, but not all mammals are cats

Each branch or clade can be

nested within a larger clade

Is knowledge of evolutionary relationships among species necessary for taxonomy?

no, although most taxonomists try to use such data in classifying organisms.

Shared primitive characters are _________ in establishing a phylogeny

not as useful as shared derived characters

, species that share many analogous structures are

not necessarily closely related.

Allopatric speciation

occurs due to the physical separation of two populations of a species

sympatric speciation

occurs when a new species is formed within the range of the parent populations; reproductive isolation occurs without geographic isolation

tracing phylogeny is

one of the main goals of systematics, the study of biological diversity in an evolutionary context

The principles of taxonomy are also used to

order species into categories based on their similarities and differences in morphology, physiology, biochemistry, behavior, or genes.

A key step in cladistic analysis is

outgroup comparison

Taxonomy uses

a hierarchical system of classification

evolutionary reversal

a loss of an advanced trait and thus the organism reverts back to using a primitive trait -ex: most frogs lack teeth on their lower jaw, but the ancestors of frogs did have teeth. One genus, Amphignathodon, has re-evolved teeth in the lower jaw -ex: land snails (pulmonate ) snails evolved from gilled ancestors (prosobranchs), but some pulmonates have reinvaded freshwaters, and have evolved a new (neomorphic) gill

apomorphy, plesiomorphy, autapomorphy, synapomorphy, and symplesiomorphy are terms defined relative to

a particular node of the cladogram -means that a trait can be a synapomorphy and a symplesiomorphy if different nodes are considered

trinomial nomenclature

a third name used to indicate a specific subspecies -ex: the scientific name Homo sapiens sapiens refers to subspecies called "modern" humans

The first step in DNA comparisons is to

align homologous DNA sequences of the species being compared.

One tenet in science is that there is one phylogenetic tree where

all living species are descended from a common hypothetical ancestor.

A clade consists of

an ancestral species and all its descendants

Each nucleotide position along a stretch of DNA represents

an inherited character as one of the four DNA bases: A, G, C, and T

Anagenesis is the transformation of

an unbranched lineage of organisms to such an extent that it can be called a new species

flukes of fish and whales are _____________ structures

analogous

analogous structures

are very different structurally, but they are similar in function

bird wings and bat wings as as wings and as forelimbs

as wings: analogous structures as forelimbs: homologous structures

Molecular systematics makes it possible to

assess phylogenetic relationships that cannot be measured by comparative anatomy and other non-molecular methods

As a general rule, the more homologies that two species share

, the more closely related they are.

In a perfect classification hierarchy

-all of the species (both living and dead) that had a common ancestor would be grouped together -this classification then would describe the phylogeny of all organisms included in the classification

homoplasy may be due to either of two major events

1. convergent evolution 2.evolutionary reversal

apomorphy

is a specialized or derived trait

Each species has a two-part name

Genus species (italicized/ underlined)

taxon

The named taxonomic unit at any level -ex: Pinus is a taxon at the genus level, the generic name for various species of pine trees -ex: Mammalia, a taxon at the class level, includes all the orders of mammals

Why do we need taxonomy?

Without a set of international rules to follow, the naming of species would be confusing. ex: robin and jay refers to different birds for Americans and Europeans.

Two closely related species may differ only in

a change in a single nitrogen base in a few genes

humans and bacteria are thought to share

a common prokaryotic ancestor -humans and bacteria have been evolving and surviving for the same amount of time

Most molecular systematics is based on

a comparison of nucleotide sequences in DNA

synapomorphy

a derived trait shared by two or more groups in a clade

Through the process of convergent evolution, different organisms

come up with similar adaptations (the analogous structures) to specific environmental challenges

The fossil record suggests that cladogenesis is

common, because within a taxon, the number of species typically increases over time

outgroup comparison is used to

differentiate shared primitive characters from shared derived ones

Genera (plural of genus) are grouped into progressively broader categories:

family, order, class, phylum (the term division is used in place of phylum for plants), kingdom (and recently, we have added domain as a higher taxon)

taxonomy

field of biology that is involved in naming, describing and classifying organisms, both fossil (extinct) species and living (extant) species.

A phylogeny is determined by a variety of evidence including

fossils, molecular data, anatomy (morphology), and developmental patterns.

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

genus -For ex: the leopard, Panthera pardus, belongs to a genus that includes the African lion (Panthera leo) and the tiger (Panthera tigris). The domestic cat (Felis catus) is in a closely related genus.

Willi Hennig

helped to develop cladistics and many terms used in cladistics

Producing monophyletic clades is

important in taxonomy and phylogeny

For a complete phylogeny

in addition to showing which species are more closely related, the times at which each species diverges from other species also would be included

monophyletic taxon

includes the single ancestral species and all species descended from that ancestral species. No unrelated species are included, and hopefully no related species has been left out and included elsewhere

The sub- and super- prefixes

indicate lower or higher taxonomic categories, compared to the taxonomic category being classified -ex: one or more orders would be in a superorder; one or more suborders would be in a single order

Ancestral, primitive traits are not _______ or _______ compared to derived characters.

inferior or worse

autapomorphy

is a derived trait that is unique to one group in a clade

symplesiomorphy

is a shared primitive trait -cam be found not only in the groups of the clade being analyzed, but it may be found in other clades as well.

phylogenetic tree

provides information about the evolutionary relatedness of all extant (living) species, both to each other and to all extinct species -shows the order in which species 'split' from each other through time

plesiomorphy

refers to a primitive or ancestral trait

homoplasy

scientists use this term to refer to the similarity in appearance of two groups due to independent evolutionary

systematists must sort through homologous features or characters to separate

shared derived characters from shared primitive characters.

homoplastric traits are

similar for some reason other than inheritance from a common ancestor.

homology

similarities that are based on shared ancestry

Although the presence of a backbone is a shared character for all mammals, it is a character for other vertebrates as well, so the backbone is a ________ for mammals

symplesiomorphy

For all vertebrates as a whole, compared to the related invertebrate animals, the presence of vertebrae represents a __________ because vertebrates all share this trait, and a backbone presumably evolved in the ancestor common to all living vertebrates

synapomorphy

Our understanding of the process of evolution (especially the processes of allopatric speciation and cladogenesis) shows

that the lineages of related organisms can be viewed as branching 'trees'

example of a homoplasy

the Octotillo cactus (America) and the Allauidia euphorb (Africa), species in two desert plant families, are not closely related. They owe their resemblance to analogous adaptations

example of the sequence of branching in a cladogram resembling historical chronology of common ancestry

the last ancestor common to both the cat and dog families lived longer ago than the last common ancestor shared by leopards, tigers, lions, bobcats, and domestic cats

The more recently two species have branched from a common ancestor,

the more similar their DNA and amino acid sequences should be.

One goal for biology is to have the hierarchical classification of taxonomic groups reflect

the phylogenetic history as much as possible.

Many phylogenetic trees contain information that is represented by

the positions of the branches relative to each other -the points at which different branches join -the lengths of the branches

Systematists may compare hundreds or thousands of adjacent nucleotide positions and among 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 the observed mutations in DNA sequence

outgroup

the species or group that is related to the various species that we are studying, but known to be less closely related than any study-group members are to each other ex: of the following six taxa: lancelet, lamprey, tuna, salamander, turtle and leopard: the 5 vertebrates are the in-group and the lancelet is the outgroup

cladistics

the systematic methodology that sought to emphasize objectiveness and reproducibility (in order to minimize the subjectivity of individual taxonomists) and be consistent with what scientists would refer to as "true" evolutionary patterns

The distinction between homology and analogy often depends on

the taxonomic level examined

Shared derived characters are _______ in establishing a phylogeny

useful

The binomial nomenclature system

was proposed by Linneaus in "Systema naturae" in the 18th century

geographical isolation

where two populations of one species are separated from each other by a physical barrier (new mountain ranges, streams, lakes, roads) or when a population moves into another habitat -populations are exposed to two different environmental conditions and begin to adapt to the new conditions because the selective forces in the environments are different. -the two populations then evolve and the gene pools begin to diverge for each other over time