How do we apply evidence of Common Descent?

Moderator edit: Topic split from:Greg on the Forum
@gbrooks9

The two are not the same.

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The principle is the same, even some of the methods. What do you propose is not the same?

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First, he’s talking about using DNA as a way to identify an individual, as in a murder trial. That’s not how we arrive at an inference that groups of taxa share a common ancestor.

He probably meant paternity testing. But that’s not the same either. First, that relies on specific markers and what’s more important the method could be tested using known relationships. That’s not the case for inferring phylogenies.

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How do you arrive at this inference? Is an inference the same as an untested hypothesis?

How do you test that two taxa share a common ancestor if the common ancestor is not known? Do we infer it, hard stop.

@Mung

Wow… pretty cavalier interpretation of what i meant and how common descent is used and evidenced all around the world!

Please name the Two Things that are not the same. Thanks!

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We observe that siblings and cousins have the same endogenous retrovirus insertions due to common ancestry. The same logic applies to shared ERVs between humans and chimps, as well as to other primates.

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Hey guys, let’s not talk past one another. I thought this might be interesting if we can tear this down to basics.

Common Descent is the basis for DNA evidence, paternity testing, identification of relatives of a victim or culprit, YES?

How does this differ (if it does) from taxa with a common ancestor?

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The methods for using DNA in forensic contexts (e.g., paternity, criminal identification) are tested against known pedigrees and relationships, always within a species. That is not the case for nearly all phylogenetic inference, above the species rank, where the lineages are unknown.

This talk by Jeremy Brown of LSU, recorded last week, gives a good overview of the challenges faced in molecular phylogenetics, where data frequently disagree. The major problems reviewed by Brown begin at about the 23:00 minute mark:

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Here is Brown’s talk title and abstract:

The role of model fit in resolving the Tree of Life

More data alone will not resolve the Tree of Life. That statement encapsulates perhaps the most striking lesson of phylogenomics. While genome sequences provide us with an invaluably rich source of information about evolutionary history, our ability to properly interpret this information is sometimes flawed, which has led to protracted debates about some of the most interesting and enigmatic relationships across the Tree. However, phylogenetic inference now has a robust grounding in statistical inference. This grounding gives us tools to at least recognize the existence, and hopefully resolve the source, of errors when they occur. These tools are important and broadly applied in other areas of statistical inference, but have been slow to be adopted in phylogenetics. In this talk, I will cover some of the strategies that have been proposed for assessing model fit, some of the reasons for the slow adoption, and the challenges that remain.

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@pnelson

They dont have to be identical in scope to use the same comparative methods and to develop useful sets of probabilities.

Naturally, once we go beyond living samples, it is a very different process from using only anatomical comparisons.

But when the term “Common Descent” is dismissed with a wave of the hand… the mind behind the hand is going too far.

Common Descent is everywhere. And it doesnt always lead to Speciation.

Speciation is much more open to speculation.

Amateurs decry Common Descent… the knowledgeable researchers understand the diversity of factors that trigger Speciation.

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Phylogenies don’t form within populations since there is mixing between lineages. That would be the big difference. On a somewhat similar note, forensic geneticists are now using DNA samples submitted to genealogical sites to track down criminals. One of the more famous cases used DNA submitted to 23andMe to track down the Golden State Killer. I don’t know exactly how it is done, but I would think they use rare markers to join up two family trees, and where they meet is the suspect.

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Nor does it always lead to murder convictions! :slight_smile:

Are you familiar with the claim that if someone accepts the results of a paternity test they ought to accept the evidence for common descent?

But really, the two have nothing to do with each other. Do you agree?

The basics are the same. Shared DNA is due to common ancestry. I have yet to hear someone claim that a child was immaculately conceived through a process where God borrowed one person’s DNA and made a new child. However, the very same flawed argument is used for different species.

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I don’t know what you mean by “the basics.” There are established methods for inferring phylogenies (common descent) based on DNA. Are these methods the same as those used in paternity tests?

If I crack open a book on phylogenetic inference, will I find the claim that the methods of phylogenetic inference have been established as being correct and reliable because, you know, paternity testing works?

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It’s in the sentence right after it: Shared DNA is due to common ancestry.

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Can we talk about the methodologies involved? Are you familiar enough with them to discuss them?

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So, logically:

  1. DNA that is not shared is not due to common ancestry.

Or

  1. Shared DNA is due to common ancestry and taxonomically restricted (i.e., not shared) DNA is also due to common ancestry (such sequences have been modified via evolutionary processes). All DNA sequences, shared or unique, are due to common ancestry.

(1) or (2)?

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Something as simple as BLAST or KALIGN will do.

In common parlance, differences are due to mutations while shared sequence is due to common ancestry.