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| The Beatles shed eDNA too |
In this series we have run up against long held and long disproved beliefs of some sometimes well meaning scientists who have upon occasion wanted to impose their beliefs on their students, readers, and the rest of us.
But we are not alone, those who came before us whose DNA is in the ground now had the same experience as we are having:
"Scientists long believed that it was impossible to extract DNA from the bones of Neanderthals. Before being excavated by archeologists, these bones had been lying in the deeper layers of moldy caves for at least 30,000 years, where prehistoric man once dwelled and died. Following the death of a Neanderthal, a host of bacteria, fungi, and other microbes infested the bones. It appeared extremely unlikely that a sufficient amount of original DNA remained intact ... Yet Svante Pääbo was able to prove the skeptics wrong ... Comparisons of their genome with that of humans today or with those of other extinct hominins and chimpanzees provide precise molecular biological answers to fundamental questions concerning our evolutionary origin."
(Svante Pääbo, emphasis added). As time goes on every once in awhile a new discovery is made which replaces the old one because accuracy and competence both can nearly always be improved upon (On The Origin of Genieology).
The research trend now is eDNA and aDNA, which can combine into aeDNA:
"Previous studies provided evidence that an important fraction of extracellular DNA can escape degradation processes, remaining preserved in the sediments ... This DNA represents, potentially, a genetic repository that records biological processes occurring over time ... In 2022, two-million-year-old eDNA genetic material was discovered and sequenced in Greenland, and is currently considered the oldest DNA discovered so far ..."
(Wikipedia, emphasis added). This kind of improvement is the result of overcoming certain "boundaries" that are not technically an archeology problem:
"... the field remains affected by substantial biases and skewness, particularly in geographical and temporal representation. This is in part due to the disproportionate allocation of research funding and archaeological activity ..."
(Science Direct). The concept of widespread disasters is also realistic but likely to be poo pooed (Population Discontinuity).
"Practice makes perfect" can apply when and only when belief systems give way to practice until competence increases:
"Here we report the successful isolation and nucleotide sequencing of segments of Bacillus sp. 16S ribosomal DNA from abdominal tissue of four specimens of the stingless bee Proplebeia dominicana (Apidae: Hymenoptera) in Dominican amber (Table 1) ... A total of 11 amber pieces with inclusions of P. dominicana were analyzed. All 11 samples originated from amber mines located in the Cordillera Septentrional between Santiago and Puerto Plata in the northern Dominican Republic. These mines are in the Altamira facies of the El Mamey Formation (Upper Eocene), which is estimated to range in age from 23 to 40 million years (Lower Miocene to Upper Eocene). The amber pieces were surface sterilized and cracked as described by Cano et al.. Tissues from the head, thorax, and abdomen of each of the 11 bees were collected separately and suspended in 300 ul of Glassmilk SpinBuffer from an RPM kit (Bio 101, La Jolla, Calif.). DNA extractions were carried out as described by Cano and Poinar. Extracted DNA was stored at -20°C until needed. DNAs were similarly extracted from alcohol-preserved tissues of the extant stingless bees Nogueirapis mirandula, Plebeia jatiformis, and Melipona panamica to provide amplifiable DNAs for comparative studies."
(Bacillus DNA in fossil bees, emphasis added). Other techniques have also increased research successes:
"In genetics, complementary DNA (cDNA) is DNA that was reverse transcribed (via reverse transcriptase) from an RNA (e.g., messenger RNA or microRNA). cDNA exists in both single-stranded and double-stranded forms and in both natural and engineered forms ... In engineered forms, it often is a copy (replicate) of the naturally occurring DNA from any particular organism's natural genome; the organism's own mRNA was naturally transcribed from its DNA, and the cDNA is reverse transcribed from the mRNA, yielding a duplicate of the original DNA. Engineered cDNA is often used to express a specific protein in a cell that does not normally express that protein (i.e., heterologous expression), or to sequence or quantify mRNA molecules using DNA based methods (qPCR, RNA-seq). cDNA that codes for a specific protein can be transferred to a recipient cell for expression as part of recombinant DNA, often bacterial or yeast expression systems. cDNA is also generated to analyze transcriptomic profiles in bulk tissue, single cells, or single nuclei in assays such as microarrays, qPCR, and RNA-seq."
(Complementary DNA). The beat goes on.
Today's appendices (Appendix 1, 2, 3) give another look at the DNA in the aeDNA from Greenland which was featured in a Nature Journal paper (A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA).
To check out the DNA, insert the Version Number into the GenBank site look-up page, which will bring up the GenBank .gbff file format.
Then load the FASTA format file by clicking on the FASTA link (the .gbff file format doesn't have the DNA of large files, so you need to load the FASTA format data).
Check out the short video below too.
The previous post in this series is here.
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