Download Ess | Rebekah Ess Biology Lab November 2, 2012 “Genomic DNA

Rebekah Ess
Biology Lab
November 2, 2012
“Genomic DNA sequence from mastodon and woolly mammoth reveal deep speciation of forest
and savanna elephants”
There has been much dispute over the taxonomic status of different elephants and their
relationships with each other. Rohland et al. take a deeper look into the speciation of forest and
savanna elephants using genomic DNA sequencing from the mastodon and woolly mammoth.
The current genus taxonomic status of the African elephant, Loxodonta, remains
controversial along with questions of the relationship of the modern day elephants to the
woolly mammoth. A large reason for this is that the woolly mammoth and the American
mastodon, who would be the closest out-group to elephants and mammoths, are to this day
extinct which makes it considerably harder to find material for genetic analysis. Rohland et al.
used “a combination of modern DNA sequencing and targeted PCR amplification to obtain a
large data set for comparing American mastodon, woolly mammoth, Asian elephant, African
savanna elephant, and African forest elephant.” While there have been many studies done, the
phylogenetic relationships between these mammals are still in debate.
There is complete mtDNA of genomes on all three of the elephantid classes that has
been compared to the mastodon outgroups. The problem that arises from using mtDNA is that
we only get it from our mothers and there is a possibility that it doesn’t represent the true
species especially because herds are matrilocal; it is rare that females ever disperse across
herds. Patterns of nuclear and mtDNA is what has led to the debate about the true taxonomic
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status that the African elephants hold. Rohland et al. state, “the study of large amounts of
nuclear DNA sequences has the potential to resolve elephantid phylogeny, but die to technical
challenges associated with obtaining homologous data sets from fossil DNA, no sufficiently
large nuclear DNA data set has been published to date.” With no way to change this situation
Rohland et al. completed shotgun sequencing of the DNA from the great American mastodon,
using the same DNA extract that they had used to complete the mtDNA sequence from the
mastodon. In comparison to the elephantid data, the data of the mastodon had a high error
rate which was expected from shotgun sequencing. Only 38% of the mastodon-elephantid
divergent sites were confirmed which are contributed from the mastodon-specific errors due to
ancient DNA. The other section for error is the sample rate, which is highly limited and the
mutation rate which Rohland et al. have confessed to be “poorly measured for the
elephantids.”
Through the entire DNA sequencing Rohland et al. established that the Asian elephant is
actually the sister species to the woolly mammoth. They also came to the conclusion that the
African savanna and the African forest elephants should be two different species (rather than
the argued two populations of the same species) for the reason that they have a divergence as
ancient as the Asian elephant and mammoth. Using the mtDNA, analysis has suggested that
the genetic divergence of mammoths and Asian elephants go as far back as 5.8-7.8 million years
ago (Mya), while the African elephants diverged from an earlier ancestor dating to 6.6-8.8 Mya
(note that “mtDNA represents a single locus in the genome and need not represent the true
species phylogeny since a single gene tree can differ from the consensus species tree of the
taxa in question”).
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It is difficult to give an answer for why there is so much diversity as there are not
enough samples of each taxon to find out. One reason thought to have caused diversity is the
idea that the forest elephant female herds saw repeated migration of the savanna elephant
bulls, displacing the gene pool in every wave; this could also be a cause of mtDNA discrepancy.
Rohland et al. hypnotized that a large part of the divergence could be due to the “widespread
distribution of elephants may have created an isolation barrier that separated savanna and
forest elephants, so that gene flow became common only much later, contributing to the
patterns observed in mtDNA.” The largest theories have to do with migration and gene flow.
Rohland et al. came to the conclusion that African forest and African savanna elephants
should be classified as different taxonomic species based on their divergence 6.6-8.8 Mya. The
Asian elephant has been determined to be the sister species of the woolly mammoth. While
these studies are new and eye opening to the taxonomic status, the accuracy may be off as the
use of mtDNA is only maternal and gives only one side of the genetic information/diversity.
When considering the evolution it is also important to keep in mind the size of populations
along with the gene flow that went through them. Every bull brought with him a new wave of
genetic information. All of the listed are of equal importance when looking at the divergence of
the different elephants we see today.
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Bibliography:
Rohland N, Reich D, Mallick S, Meyer M, Green RE, et al. (2010) Genomic DNA Sequences from
Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna
Elephants. PLoS Biol 8(12): e1000564. doi:10.1371/journal.pbio.1000564