Reconstructing and using phylogenies

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Presentation transcript:

Reconstructing and using phylogenies Chapter 16 Reconstructing and using phylogenies

16.1 All of life is Connected through is Evolutionary History Evolutionary biologists believe that all life is connected to a common ancestor Phylogeny-the evolutionary history of a particular group of organisms or their genes Phylogenetic tree-a diagram that shows the phylogenies of a group of organisms or their genes

Phylogenetic tree

The trees used to be constructed based on physical structures and behaviors They are now created based on genes and are considered more accurate A series of ancestor and descendant populations form a lineage (straight line) When a lineage splits (speciation), it creates a node and each line is a new lineage

Phylogenetic tree Node

May portray thee evolutionary history of all life forms, a group, closely related species, or the history of individuals, populations, or genes within a species Common ancestor forms the root of the tree Splits either show speciation events, gene duplication events, or transmission events

Taxon-any group of species that we designate with a name (ex Taxon-any group of species that we designate with a name (ex. Vertebrates) Any taxon that consists of all the evolutionary descendants of a common ancestor is a clade Two species that are each other’s closest relatives are called Sister species Any two clades that are each other’s closest relatives are sister clades

http://www.talkorigins.org/faqs/comdesc/phylo.html

Phylogenetic trees are the basis of comparative biology Biologists use phylogenies to make comparisons and predictions about shared traits across genes, populations, and species There are tens of millions of species on earth, 1.8 million species classified Phylogenetic analyses are constantly reviewed and revised

The phylogenetic tree of life allows us to make predictions about species that we have not studied in detail based on comparisons Any features shared by two or more species that have been inherited from a common ancestor are said to be homologous Examples: DNA sequences, protein structures, and anatomical structures Vertebral column is homologous in all vertebrates

Homologies

Derived traits provide evidence of evolutionary relationships Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait) Derived traits that are shared are used as evidence of common ancestry in a group are called synapomorphies Example the vertebral column

derived characteristic primitive characteristic

Not all similar traits show relatedness They can develop in other ways: 1. Convergent evolution-Independent evolution of similar features from different ancestral traits Example: wings of bats and birds are not homologous because they evolved independently from the forelimbs of different nonflying ancestors

Convergent Evolution vs. Divergent Evolution Convergent: same traits evolved in unrelated species

2. evolutionary reversal-when a character reverts from a derived state back to an ancestral state Example: the fins of dolphins and whales

Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies http://nodnacontrol.blogspot.com/2009/08/homoplasy-versus-recombination.html

16.2 Phylogeny can be reconstructed from traits of organisms In a phylogenetic study, the group of organisms of primary interest is called the ingroup Which is compared to the outgroup which is a species or group known to be closely related to but phylogenetically outside the group of interest The outgroup is used to determine which traits of the ingroup are derived and which are ancestral (figure 16.3)

Outgroup vs ingroup http://www.nescent.org/media/NABT/mega_workshop.php

Read page 319 & 320

Parsimony provides the simplest explanation for phylogenetic data Parsimony principle-the preferred explanation of observed data is the simplest explanation The best hypothesis under the parsimony principle is one that requires the fewest evolutionary changes (homoplasies) Phylogenetic trees represent scientist’s best estimates about evolutionary relationships, given the evidence available Modified a lot when new evidence arises

Hypothesis 1 is correct in accordance with the parsimony principle http://evolution.berkeley.edu/evolibrary/article/phylogenetics_08

Parsimony= simplest explanation is the most likely (Occam’s razor)– fewest evolutionary events is most likely

Phylogenies are reconstructed from many sources of data Any trait that is genetically determined can be used in a phylogenetic analysis Evolutionary relationships can be revealed through studies of morphology, development, the fossil record, behavioral traits, and molecular traits such as DNA and protein sequences

Morphology Morphology-the presence, size, shape, and other attributes of body parts Morphology still provides the most comprehensive data set available for many taxa Morphological features are usually specific to certain groups (example floral organs for flowering plants)

http://www.gns.cri.nz/Home/Our-Science/Earth-Science/Fossils/Research/Evolution-in-deep-time-and-shallow-seas

Extinct phylogenies are almost all done by morphological data The fossil record shows important data about ancestral traits and derived traits The fossil record also show when lineages diverged It is limited because some groups have few or no fossils and in some cases it is fragmented

Problems with morphology Some taxa a morphologically very similar even though they are a very different species (example leopard frogs) Few morphological traits can be compared across distantly related species Morphological differences can be environmental and not genetic Need more data

Development Developmental patterns may reveal evolutionary relationships Some organisms exhibit similarities in early developmental stages only Example: notochord

http://dtc.pima.edu/blc/182/lesson10/10step3/10step3page1.htm

Behavior Some behavioral traits are culturally transmitted, others have a genetic basis Bird songs, are often learned and may be inappropriate traits for phylogenies Frog calls are genetically determined and are acceptable for phylogenies

Molecular Data DNA sequences have become the most widely used sources of data for constructing trees Look at mitochondrial DNA and cytoplasmic DNA as well Also use nuclear gene sequences and amino acid sequences of proteins

Table 22.1 Molecular Data and the Evolutionary Relationships of Vertebrates

Biochemical Differences

Mathematical models expand the power of phylogenetic reconstruction Maximum likelihood-method that will identify the tree that most likely produced the observed data, given the assumed model of evolutionary change Most often used with molecular data Incorporate more info about evolutionary change than parsimony methods The disadvantage is that they are difficult to do and require in-depth models of evolutionary change

http://en.wikipedia.org/wiki/File:Sarraceniaceae_combined_maximum_likelihood_phylogeny.png

16.4 Phylogeny is the basis of biological classification The classification system that we use today was created in the 1700’s by Carolus Linnaeus It is called Bionomial Nomenclature, gives each species two names One identifies the genus (group closely related to species) and one identifies the species Example Homo sapiens (Genus species) Species name is underlined or in italics. First letter in genus is capitalized

http://www. tutorvista http://www.tutorvista.com/content/biology/biology-iii/modern-classification/binomial-nomenclature.php

Sometimes abbreviated (ex. C. lupus) Any group of organisms that is treated as a unit in classification is called a taxon Kingdom>Phylum>Class>Order>Family>Genus>Species Biologists today recognize the tree of life for biological classification Use evolutionary relationships as the basis for classifying organisms. (do not always use Linnaean groups)

Taxonomy Hierarchy

Evolutionary history is the basis for modern biological classification Taxa are expected to be monophyletic-the taxon contain an ancestor and all descendants of that ancestor, and no other organisms Also the definition of a clade Monophyletic group is a historical group of related species, or a complete branch on the tree of life

Monophyletic

Many mono- groups on a tree and these groups are smaller subset of larger mono- groups A group that does not include its common ancestor is polyphyletic A group that does not include all the descendants of a common ancestor is referred to as paraphyletic These groups are inappropriate taxonomic units because they do not reflect evolutionary history. These are now being eliminated

Polyphyletic and paraphyletic

Several codes of biological nomenclature govern the use of scientific names Biologists follow rules around the world so they can communicate about classification Common names are not good because their could be many for one species or refer to more than one species One rule is that each scientific name should be unique to a species

http://www.sms.si.edu/irlspec/namspecies.htm

Phylogeny Video

Modern classifications are based on phylogenetic trees (Linnaeus is dead) Another important point is that modern classifications are based on phylogeny. 51

Linnaean Hierarchy Kingdom Animalia Phylum Chordata Class Chondrichthyes Class Osteichthyes Class Amphibia Class Reptilia Class Aves Class Mammalia Traditional Linnaean classifications had a limited number of hierarchical levels—King Phillip chooses officer from good soldiers. If we applied this to our phylogenetic tree of vertebrates, we would have only three levels… 52

However, modern classifications recognize groups of organisms by common ancestry. 53

Trees and Classification Clade: Mammals That is, any group defined by a common ancestor—as shown here is called a clade, and can be recognized with a taxonomic name. 54

Trees and Classification Clade: Amniotes Likewise, more inclusive groups can be recognized. 55

Trees and Classification Clade: Tetrapods And this. In theory, there is no limit to how many of these groups could be recognized in a classification. 56

Classification Phylogeny Jawed vertebrates Bony vertebrates Tetrapods Amniotes Mammals Archosaurs In the case of our vertebrates, a phylogenetic classification might recognize six groups at five hierarchical levels. 57

Trees and Classification Not a clade: Fish The only limitation is that groups that contain some, but not all descendants of a common ancestor cannot be recognized. For instance, the common term “fish” has no phylogenetic meaning. We would call sharks and angelfish “fish”, but they are not a clade because their common ancestor down here also evolved into all these other forms. Another classic grouping that can no longer be recognized is the “reptilia”, because some reptiles like alligators are closer to birds than to other reptiles. 58

“…just as beginning students in geography need to be taught how to read maps, so beginning students in biology should be taught how to read trees and to understand what trees communicate.” O’Hara 1997. Zoologica Scripta 26:323 More importantly than the fact that study of phylogenetic trees addresses federal and state science standards is that understanding trees is now fundamental for all biologists, not just those studying evolution. This is reflected in this quotation… Phylogenetic trees are fundamental tools for organizing and interpreting all sorts of biological data. 59