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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