Tag: DNA

DNA Study of Birds, Extinction, and Demography

This paper by Smith, Gehara, and Harvey was released earlier this year (currently behind a paywall): The demography of extinction in eastern North American birds. Supplementary material can be viewed here. The DNA study included passenger pigeon and four other extinct bird species.

From the abstract:

We found extinct species harboured lower genetic diversity and effective population sizes than extant species, but both extinct and non-extinct birds had similar demographic histories of population expansion. These demographic patterns are consistent with population size changes associated with glacial–interglacial cycles. The lack of support for overall population declines during the Pleistocene corroborates the view that, although species that went extinct may have been vulnerable due to low diversity or small population size, their disappearance was driven by human activities in the Anthropocene.

Reference: Smith BT, Gehara M, Harvey MG. 2021 The demography of extinction in eastern North American birds. Proceedings of the Royal Society B: Biological Sciences Vol. 288, Issue 1944: 20201945.

The California Condor Genome

An interesting article on the California Condor (Gymnogyps californianus), which faced extinction but has so far survived. Analysis of its genome implies a relatively large population about 1 million years ago followed by a decline in population around 10,000 years ago (or very roughly, the end of the Pleistocene). Note that the techniques used do not allow an estimation of recent (less than 10,000 years) population history.

For a species that was briefly extinct in the wild, the California condor has unexpectedly high genome-wide diversity

p. 5

our results show that the turkey vulture was historically less abundant than the California condor, though it is the most abundant and wide-ranging New World vulture today.

p. 6

Though the history of the California condor shows evidence of past decline, it retains a high degree of ancestral variation and, perhaps, the potential for future adaptation. As exemplified by the passenger pigeon (Ectopistes migratorius) and Carolina parakeet (Conuropsis carolinensis), high genetic diversity is by no means a barrier to extinction, but the variation present in the California condor is nonetheless reassuring. The species continues to repro- duce naturally and expand its range in the wild

p. 6

Source:

Robinson et al., Genome-wide diversity in the California condor tracks its prehistoric abundance and decline, Current Biology (2021), https://doi.org/10.1016/j.cub.2021.04.035

Featured image: Don Graham, CC BY-SA 2.0 https://creativecommons.org/licenses/by-sa/2.0, via Wikimedia Commons

Caveat Lector: New-ish data on the Piltdown Man Hoax

So what’s the new thing I learned from the recent DNA-and-other-scientific-techniques analysis of the infamous Piltdown hoax fossils? Some people use the word “caveat” as a verb.

There it is, in the middle of the nicely open access article:

However, we caveat this by emphasizing that Bornean orang-utans have suffered from habitat loss and range fragmentation, two processes that can result in rapid shifts in the geographical distribution of genetic lineages (p. 7)

The internet helpfully tells me that the use of caveat as a verb in modern usage is considered awkward, and is most closely associated with Alexander Haig of “I am in control here” fame. Haig was a decade or two ahead of his time in his tendency to turn nouns into verbs.

There are a few caveats (“noun: a warning or proviso of specific stipulations, conditions, or limitations” -the OED) that may be worth keeping in mind regarding de Groote and colleagues’ article.

  • The DNA analysis of the orang-utan and human bones that comprise the “Piltdown Man” fossils was mostly unproductive, the only positive result being evidence that two of the orang-utan teeth likely came from the same individual ape, who likely lived in western Borneo (that’s the conclusion that they caveated – now I’m doing it, too).
  • Traditional morphometry (i.e, measuring the actual fossils) was more successful in confirming that the fossil teeth are actually from an orang-utan, and not from a different species of ape. I did not realize this was considered uncertain (there has been no doubt that the teeth are not hominin since the mid 1950s), and in fact a 1982 article in Nature they reference is titled “Piltdown Jaw Confirmed as Orang” but since the ape teeth were deliberately modified by the hoaxer, it’s good to get additional confirmation of the species identification
  • This is kind of nifty:

    In combination, the geometric morphometric analyses link the Piltdown I mandible and Piltdown II molar; traditional morphometrics link the mandible with the canine, and ancient DNA analysis links the canine and Piltdown II molar. Therefore, given the nature of the context, we consider it highly likely that the Piltdown hoaxer(s) used a single orang-utan specimen originating from southwest Sarawak to construct parts of both Piltdown I and II (p. 7)

  • Radiocarbon dating attempts were a complete failure (contamination and other issues – probably not a big surprise).
  • Microscopy and μCT scans provide some new details on modifications that were made to the bones.
  • All this new research doesn’t really change anything about what was already known about the Piltdown hoax. The authors accuse Charles Dawson of being the sole perpetrator, but, as they acknowledge, Dawson has been “the prime suspect since the fraud was exposed in 1953.” (p. 12) Despite headlines like Human Ancestor Hoax At Piltdown Finally Solved and Study reveals culprit behind Piltdown Man, their new analysis doesn’t provide any evidence that incriminates Dawson any more or less.

 

Reference:

DeGroote, I., et al.

2016  New genetic and morphological evidence suggests a single hoaxer created ‘Piltdownman’. R.Soc. Opensci.3:160328. http://dx.doi.org/10.1098/rsos.160328

Stupendous! The ROM is bringing its Passenger Pigeons out of Storage

New research question: Is it possible to write an article about passenger pigeons without using the adjective “stupendous”? This article in The Star uses it, while talking about the Royal Ontario Museum’s plan to put some of their 153 stuffed Ectopistes back on display, as well as how the DNA from one of their birds is being used in an ambitious plan to recreate the passenger pigeon.

ROM curator Mark Peck with specimens from the museum’s collection of extinct passenger pigeons. Source: Keith Beaty / Toronto Star.