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Lecture 2.3_Phylogenetic Classification of Living Mammals

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hi there welcome back Professor Jared

rathel here and you have tuned in to

lecture 2.3 which is entitled

phylogenetic classification of living

mammals look I know you guys have

endured some brutally long lectures this

week hopefully you found them

entertaining but I know they've been

long so I've purposefully paired uh

these chapters down in the textbook I

noted this in canvas but for lesson 2.3

you're only going to be responsible for

chapter two which is of course methods

for studying mammals I only want you to

read the few pages under the section

heading DNA sequences

that's within the systematic methods

section so that's all you'll be

accountable for and then further for

this lecture I'd also like you to return

to chapter three which is entitled

phylogeny and diversification of mammals

uh and within that first section uh

that's entitled relationships and

classification of living mammalian

orders please read uh the paragraphs

under two headings the first is

Simpson's classification of mammals and

then the few paragraphs under the

section heading insectivores and so

again that's what you'll be responsible

for and these readings are noted as

always in canvas for most of its history

mammalian biology relied on the study of

whole animals or on their preserved

remains from Museum collections however

as our understanding of the biochemical

basis of heredity evolved across the

20th century from understanding that DNA

was the molecule of heredity to

identifying the double helix structure

so as this science evolved mammologists

have increasingly employed molecular

markers to study population genetics

speciation and phylogeny our topic of

Interest today

so for example the development of

polymerase Chain Reaction or PCR in the

late 1980s is going to bring DNA

sequence and fragment analysis to Labs

of evolutionary geneticists around the world

world

in PCR

a Target sequence of DNA is Amplified

tremendously Amplified by first

unraveling that double helix structure

using heat

okay so this is called denaturation then

we're going to anneal or fix primers to

specific Target regions

and then we're going to build homolog

strands using a thermostable DNA

polymerase like Tac that's taq which was

actually isolated from thermophilic

bacteria in Hot Springs from Yellowstone

at the completion of one cycle the

region of DNA between the primers has

now been copied and it's available to

serve as a template during the second cycle

cycle

okay so by repeating this process again

and again the number of copies of this

target sequence of DNA is going to

increase a geometrically okay so in 30

cycles of PCR it's sufficient to produce

a billion copies of a single template

molecule all right please put me on

pause for two minutes and 37 seconds and

hop on to Canvas and check out the

embedded video short it's a really nice

animation of polymerase Chain Reaction

so please check that out now

so the sensitivity of PCR has made it

possible to recover and then amplify and

analyze DNA sequences from the remains

of long dead even extinct mammals

including species like the woolly

mammoth the Stellar sea cow the

thylacine which we talked about last

lecture and then our cousins the

European Neanderthals

estimates of the Divergence between the

Neanderthals and Homo sapiens are

species range from about 315

000 years ago to some 800 000 years ago

so if we take a mean somewhere around 500

500

000 years ago the lineage which is to

produce the Neanderthals in Europe and

Homo sapiens in Africa splits

splits

between 60 and 90 000 years ago

a changing climate spurred humans to

leave our African Homeland and then between

between

43 and 48 000 years ago humans colonize

Europe from uh present-day Kazakhstan

the Cradle of humanity

on uh arriving in Europe uh these first

European humans encountered the

Neanderthals who had been there for

hundreds of thousands of years we now

have evidence that those humans

interbred with the Neanderthals as

approximately two percent of European

and Asian

genomes are actually Neanderthal genes

Africans like the song Bushman here they

have considerably less Neanderthal DNA

on the order of about 0.5 percent and

that intro aggression of Neanderthal DNA

into the African genomes likely occurred

as Europeans uh went back migrated back

into Africa here's a great two and a

half minute synopsis from a natural

history museum that's going to uh really

better explain that interaction between

neanderthals and humans and the genetic

evidence that we now have for interbreeding

many molecular studies in mammology are

going to focus on micro satellite

markers which are loci remember loci are

positions on chromosomes that show these

back to back repeats of about two to six

base pairs so for example here's an

individual maybe it's a bat from Reunion

Island so this is a recently published

study on uh the relatedness of a

population of bats from Reunion Island

and they use these micro satellite

markers so maybe individuals from this

bat Colony show four of these four nucleotide

nucleotide

short tandem repeats or str's here you

can see g-a-t-a g-a-t-a right so four

times whereas individuals from these

colonies show six of these strs these

short tandem repeats so great way to

look at population level problems in genetics

genetics

so the reason why uh this works so well

is because these loci are prone to these

slip strand missed pairings during DNA

replication so these strs they have a

high mutation rate that's going to

generate considerable variation

across individuals the most widely

studied sequence in mammology is the

mitochondrial DNA so you remember

mitochondria from your general Biology

one class those are the organelles that

are considered the power houses of the

cell so these are the organelles that do

cellular respiration for the larger

eukaryotic cell that is to say they

convert glucose into ATP

the mitochondria evolved through

endosymbiosis so billions of years ago

there was an aerobic prokaryote a

bacteria that was engulfed by a larger

host cell this larger cell instead of

consuming the bacteria it actually

incorporates it into its cellular

architecture in this ancient mutualistic relationship

relationship

so that means that each one of these

mitochondria is going to have its own

circular DNA the mitochondrial DNA which

looks a lot like bacterial DNA because

these were once Free Living bacteria but

this mitochondrial DNA is separate from

the nuclear DNA so it's really nice

because it's only about 16 000 base

pairs and then further the protein

coding genes in the mitochondria

mitochondrial DNA are highly conserved

meaning they don't mutate very often

that said there are other loci in the

mitochondrial DNA that evolve very

rapidly so this means mitochondrial DNA

is very uh diverse in terms of the scale

of the questions that you can ask you

can use mitochondrial DNA to ask

intra-specific questions so looking at

populations within a species all the way

up to intra ordinal questions and I

might point out that it was actually

mitochondrial DNA analysis uh that first

mapped out human migrations around the

globe and what's called the human

genographic project so looking at

mitochondrial DNA we will we were able

to determine uh that Africa was the

birthplace of humans the first wave

leaves Africa travels across southern

Asia there's India across Indonesia and

settles in Australia becoming the

Aboriginal Australians another wave as

we mentioned several slides ago settles

in Kazakhstan and then moves over into

Europe to encounter the Neanderthals

still another wave waves really uh

spread out across Asia eventually move

across the Bering land bridge populate

North America the Native Americans and

then down into South America so these

routes were all established looking at

increasingly evolutionary geneticists

are now employing next Generation

sequencing so this is a really powerful

method which is going to determine

millions of short and by short I mean

like 50 to 750 bases they're going to

determine millions of these sequence fragments

fragments

simultaneously these fragments are then

assembled into larger sequences by

linking them together using regions of

overlap using high-speed computational methods

methods

these reconstructed genomes are then

compared against a reference genome

reference genomes are really important

because they're going to make the

analysis of new genomic data sets much

easier and more robust

so I'm super stoked to report that there

are hundreds of these reference genomes

that are now uh openly available in Open

Access databases like the National

Institutes of Health they have Gene bank

and you can download uh and analyze this

data there's another project known as

zoonomia and you can see all of these

species for which uh reference genomes

exist it's a really wide variety from

carnivores like the arctic fox to the

III which is a lemur from Madagascar a

primate so a wonderful variety of

mammalian reference genomes that have

allowed us to build uh to build the most

uh precise

phylogenetic tree of mammalian

relationships to date all right let's

conclude with a bit of History

George Gaylord Simpson was a professor

of zoology at Columbia and a curator at

the American Museum of Natural History

he was a prominent evolutionary

biologist he contributed to the great

synthesis in biology he was a

paleontologist and a taxonomist in fact

George Gaylord Simpson he really laid

the taxonomic foundation for our modern

science of mammology with his Landmark

publication entitled the principles of

classification and a classification of

mammals which was published in 1945.

as you may recognize at right many of

the orders that George Gaylord Simpson

described uh are still in use today so

uh he recognized the order mono tremada

the marsupials the primates the

chiroptera road and slagomorphs

carnivores so on and so forth so these

orders have survived Decades of

subsequent research

so George Gaylord Simpson he didn't have

next Generation sequencers okay so he

realized at the time that some of his orders

orders

um like the order

insectivora here were and I quote

something of a scrap basket for small

animals of a generally primitive

character that are not clearly referable

to some more distinctive order so in

short he's going to lump the Hedgehogs

the shrews the ten racks the golden

moles he's going to put them all in this

catch-all order that he calls the

insectivora using modern molecular

methods phylogenetic systematists now

split the insectivora into the orders

macro Scalia day which includes the elephant

elephant

trues the order afro psoricidae which

includes the tenrex Shrew 10 Rex and

Otter shrews we'll be covering both of

those orders in our next lecture so

that's why we're covering classification

now as well as the EULA pot phyla which

is the selenodons true shrews moles

hedgehogs we'll cover them in week five

and then the order scandencia which are

the tree shrews and we'll cover

scandincia in week four this represents

the best phylogenetic tree of mammalian

orders that we have to date so this uh

has been presented before it's in

chapter three the phylogeny and

diversification of mammals this is figure

figure

3.1 but this is going to map out those

phylogenetic relationships and remember

Sister taxa they are most closely

related to each other so the macro

Scalia day and the afro-cericidae they

are what we would consider sister taxa

because they share a most recent common

ancestor here some 75 million years ago

so these are the orders that we're going

to be covering in ABS

470. we've already covered a good chunk

of them here's our monotreams and our

marsupials so you remember that new

world opossums

um the um

uh dazzy urads which includes the

Tasmanian devil and the thylacine so

these have already been covered and then

in our next lecture we're going to cover

these three uh orders within this super

order the

afrotheria so we're going to be coming

back to this figure again and again

because in uh mammology in all the

biological sciences it only makes sense

to see things through an evolutionary lens

lens

with that uh short lecture I told you it

was short

um just a handful of references cited in

this lecture and uh just one more

lecture to go in this module before your

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Lecture 2.3_Phylogenetic Classification of Living Mammals