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ancient dna from lake sediments bridging the gap between paleoecology and genetics古代dna从湖泊沉积物之间的鸿沟方面古生态学和遗传学
Anderson-Carpenter et al. BMC Evolutionary Biology 2011, 11:30
/1471-2148/11/30
RESEARCH ARTICLE Open Access
Ancient DNA from lake sediments: Bridging the
gap between paleoecology and genetics
1 1* 2 3
Lynn L Anderson-Carpenter , Jason S McLachlan , Stephen T Jackson , Melanie Kuch ,
Candice Y Lumibao1, Hendrik N Poinar3
Abstract
Background: Quaternary plant ecology in much of the world has historically relied on morphological identification
of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably
yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological
change. This will allow changes in census populations, estimated from fossils and associated sediment, to be
directly associated with population genetic changes.
Results: We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf
fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of
North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10
copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments
2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA
sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time.
Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to
macrofossils in sediments.
Conclusions: An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights
into t
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