Lecture 4 - Taxonomy and Phylogeny

taxonomy

the system of organizing species into nested groups

how many taxonomic groups?

8

taxonomic groups in order

domain, kingdom, phylum, class, order, family, genus, species

do keep ponds clean or frogs get sick

what are the three domains

bacteria, archaea, eukaryota

taxon/taxa

a group of organisms, it can be of any rank and contain any number of species i.e. primates, mammals, insects

**taxa = plural

biologists say taxa as an easy way to refer to a unit of biodiversity without having to specify what rank it might be

downsides to the taxonomic rank system

there’s no rules about how many species must be in a genus, famil, et.c so some genuses have 1 species and others can have 1000

**it’s up to subjective decisions by individual scientists to decide where to draw the line at including more species in a given genus/family/etc.

splitters vs. lumpers

some scientists like to split everything up into more groups (splitters) and others like to put lots of things in a group (lumpers)

*this happens any time we need to classify something

*because there’s no single universally agreed definition of a species, scientists argue all the time about whether a taxon should be split or not

why is taxonomy important?

taxonomic decisions have real-world impact for management decisions

phylogenetics

aka tree thinking, or systematics

system of organizing species based on their proposed evolutionary relationships (degree of relatedness)

phylogeny vs. taxonomy

taxonomy and phylogeneteics are similar but there are many taxonomic groups that haven’t had any phylogenetic work done on them

phylogeny shows how species are related through common ancestry whereas taxonomy is the science of naming, describing, and classifying organisms into hierarchical categories

phylogeny

a hypothesis of the evolutionary relationships between taxa

also called a cladogram, phylogenetic tree, or tree for short

**bc it’s a hypothesis, this means it’s a proposed explanation and it could turn out to be wrong

the parts of a tree

trees are bifurcating —> each branch splits into exactly 2 new lineages at each node

sister taxa

two taxa that share a node aka the two descendants share a last common ancestor

when trying to figure out which taxa/species are mostly closely related, what do you do

when trying to figure out which taxa/species are mostly closely related, look at how many nodes are between them

when looking at sister taxa/species, look at nodes and where they’re connected, but this doesn’t necessarily mean they’re all exactly closely related

what happens if nodes get rotated?

the trees still tell the same info but if there are groups that get completely switched, not at a node, it’s a diff tree

steps to come up with a phylogeny

(1) define traits that are relevant for all the species/taxa of interest

• traits can be based on morphology (physical anatomy), genetics, or behavior

(2) for each taxon, decide if it has that trait (1) or not (0)

• create a character matrix

(3) use an optimization algorithm to decide what configuration of an evolutionary tree would mostly likely result in the distribution of traits found in the taxa

• typically done using parsimony

parsimony

choosing the phylogeny that is simplest, the one that requires the fewest evolutionary trait changes to explain the data

relatives of elephants

manatees, hyraxes, tapirs, rhinoceroses, horses, cetaceans, hippos, ruminants, pigs

**most closely related to manatees and hyraxes

homology/homologous characters

morphology that’s shared between groups bc it was inherited from a common ancestor

**not all similar morphologies are homologous

this means that just because they have similar physical traits doesn’t mean it’s because they had the same ancestor, it can happen for other reasons independently

when morphology does not equal homology

(1) convergent evolution

(2) homoplasy

ex: wings in birds and bats

tusks and big body size in elephants and hippos

homoplasy

a feature that has been gained or lost in separate lineages over time

convergent evolution

when two different species developed the same trait independently of one another and their last common ancestor didn’t have it