phylogenetic trees

branch

a lineage evolving through time that connects successive speciation or other branching events

phylogeny

a visual representation of the evolutionary history of populations, genes, or species

speciation

when a population forms two populations that no longer can exchange genes, making it possible for them to diverge into two seperate species

node

a point in a phylogeny where a lineage splits( a speciation event or other branching event, such as the formation of subspecies)

internal nodes

a node that occurs within a phylogeny and represents ancestral populations or species

tip

the terminal end of an evolutionary tree, representing species, molecules, or populations being compared

clade

a single “branch” in the tree of life; represents an organism and all of its descendants

cladogram

when a phylogenetic tree shows only the relationship among species; branches do not measure the period of time it took between speciation events

orientation of phylogenetic tree

there are many ways to represent the same relationships, can rotate branches around their nodes, can flip orientation, can leave out taxa and include clades, etc

nested hierarchy

is the result of traits evolving along different lineages with new traits appearing in some lineages

taxa

a group of organisms that a taxonomist judges to be cohesive taxonomic unit, such as a species or order

monophyletic

describes a group of organisms that form a clade

ex) mammals

polyphyletic

describes a taxonomic group that does not share an immediate common ancestor and therefore does not form a clade

paraphyletic

describers a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor

ex) reptilia because it does not include birds

character

a heritable aspect of organisms that can be compared across taxa

synapomorphies

a derived form of a trait that is shared by a group of related species(that is, one that evolved in the immediate common ancestor of the group and was inherited by all of its descendants)

outgroup

a group of organisms that is outside of the monophyletic group being considered

be be used to infer the ancestral states of characters

data matrix

a spreadsheet-like display of data

a primitive state is denoted as a zero in the table; the derived state is denoted as an one

homoplasy

describes a character state similarity not due to shared descent

for example produced by convergent evolution or evolutionary reversal

convergent evolution

the independent origin of similar traits in separate evolutionary lineages

evolutionary reversal

describes the reversion of a derived character state to a form resembling its ancestral state

parsimony

a principle that guides the selection of the most compelling hypothesis among several choices; the hypothesis requiring the fewest assumptions or steps is usually the best

consensus tree

when multiple tree options are combined to represent both the resolved(monophyletic) and unresolved portions of the phylogeny

polytomy

describes an internal node of phylogeny with more than two branches( the order in which the branching occurred is not resolved)

fossils and phylogenys

incorporating fossils of extinct species allow to extract info about phylogenies and and allow to determine timing of evolution

if several fossils from same clade can provide constraints to clade’s history

horizontal gene transfer

describes the transfer of genetic material to another organism, sometimes a distantly related one, without reproduction; once material added to recipient’s genome, it can be inherited by decsent

monotremes

mammals that secrete milk through a network of glands instead of nipples; they also lay eggs; ex) platypus and echidna

therians

all mammals other than monotremes which bear live young; split into two branches: marsupials and eutherian mammals

marsupials

young crawl into a pouch on the mother’s belly after they’re born until they are big enough to survive

ex) opossums, kangaroos, and koalas

eutherian mammals

mammals that develop a placenta to feed embryos in the uterus

ex) humans and all other mammals

exaptations

a trait that initially carries out one function and is later co-opyed for a new function; the original function may or may not be retained

BRCA1

a tumor-suppressor gene that when mutations occur can dramatically increase a women’s risk of developing breast cancer

shows that alleles have their own genealogies

genealogy

a line of descent traced continuously from an ancestor

gene tree

the branched genealogical lineage of homologous alleles that traces their evolution back to an ancestral allele

coalescence

the process by which the genealogies of alleles merge together as you trace them back in time to their common ancestor.

determine is population has experienced major changes in size or natural selection

the rate of branches coalesce depends on the size of the population

ex) positive selection=shorter coalesce

ortholog

one of two or more homologous genes separated by a speciation event

ex)BRCA1

paralogs

a homologous gene that arise by gene duplication; together form a gene family

introgression

describes the movement of alleles from one species or population to another.

occurs when two species interbreed and the hybrid offspring survive to mate with the original species, introducing new genes back into their genomes

ex) neanderthals and homo sapiens interbreeding

incomplete lineage sorting

occurs when a genetic polymorphism persists through several speciation events.

when fixation of alternative alleles eventually occurs in the descendant species, the pattern of retention of alleles may yield a gene tree that differs from the true phylogeny of the species

tiktaalik

375 million year old bone that taught use that after an organism dies the DNA degrades and ancient DNA rarely survives more than 100,000 years

molecular homoplasy

more common than morphological homoplasy because each DNA based has only 4 states( A,T,G,C) and separate lineages may arrive at the same character state

maximum parsimony

a statistical method for reconstructing phylogenies that identifies the tree topology that minimizes the total amount of change, or the number of steps, required to fit the data to the tree

purifying/negative selection

removes deleterious alleles from a population; a common form of stabilizing selection

bootstrapping

a statistical method that allows for assigning measures of accuracy to sample estimates;used for estimating the strength of evidence that a particular nose in a phylogeny exists

distance-matrix method

a procedure for constructing phylogenetic trees by clustering taxa based on the proximity(or distance) between their DNA or protein sequences

places closely related sequences under the same internal branch, and estimate branch lengths from the observed distances between sequences

predicts closely related species will have more similarities than more distantly related ones

neighbor joining

a distance-matrix method in which scientists pair together the two least-distance species by joining their branches at a node; repeated until tree with smallest possible distances and branch length is found

maximum likelihood

an approach used to estimate paramater values for a statistical model

used in phylogeny reconstruction to find the tree topologies that are most likely given model for molecular evolution and particular data

bayesian methods

refer to tests that are similar to maximum likelihood; use statistical model to determine the probability of data given an evolutionary model and phylogenetic tree

microsatellite

a noncoding stretch of DNA containing a string of short( 1-6bp), repeated segments

the number of repetitive segments can be highly polymorphic, helping them compare populations and assigning relatedness among individuals