Genetics to replace morphological examination?

Some cryptic species are well studied and are definitely distinct. Often they have different behavior or habitat, if not morphology.

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I think I get what you’re saying, but I wouldn’t word it this way.

In order reliably identify species, it is critically important to be aware of aspects of morphology that are independent of the qualities used to distinguish species. I also would not say that they are “not genetically based” as there is a degree to which all morphology is influenced by genetics. It’s more that they’re “not based in the aspects of genetics that differ between species”. But of course that’s a mouthful so I get why you worded it the way you did.

An example of this would be how, on oaks, there can be great differences in leaf shape between shade-grown leaves low to the ground, especially of seedlings, and leaves high up on a tree exposed to full sun. Often these differences are greater, at a glance, than the differences from one species to another. For example, both Quercus velutina and Quercus rubra will have deeper sinuses between lobes at the top of a tree and broad, full leaves with very shallow sinuses on shade-grown seedlings. So, you need to look for other aspects of the leaf in order to tell them apart.

So this stuff is relevant to species identification to the extent that you need to be aware of it and able to filter it out or ignore it.

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I unfortunately can’t find the article at the moment, but at some point over the past year I found an analysis of some oaks in a hybrid swarm, which had been trying to settle the question of the genetic composition. The researchers ended up concluding that the genetic analysis reinforced, but added nothing new to the conclusions reached by morphological examination of the individuals alone: i.e. that morphologically-intermediate individuals showed similarly intermediate genetics, and that examining the morphology was a reliable way of predicting the genetic relationships, like whether a particular individual was closer to one species or the other.

It is all sort of intuitive to me.

I think this reinforces that, at least with our current technology where genetic analysis is costly and labor intensive, examining morphology is still far more useful.

There may be some exceptions though, on species that are clearly distinct and do not hybridize, but are very hard to tell apart by morphology. I mostly focus on plants though and don’t often encounter them. It still seems harder and more involved to analyze the genetics in every case.

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For identification DNA is used in birds from poop or feathers/blood.

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Which is a sort of roundabout way of saying that you need to be aware that an observed variation is not relevant to species identification, I think.

Morphological (or behavioural or physiological etc.) variation that is not heritable is noise not information if the context is differentiating between species. Heritability is (with maybe some exceptions related to things like maternal effects, depending on how you define these things) about genetics.

The barcode tech is not prohibitively expensive and it is a useful tool in a bunch of contexts. It is one of a suite of DNA technologies that have emerged as tools for ecological and environmental work.

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If you are analysing DNA from faeces, how can you be sure the sequence you are looking at has come from the target organism and not from the gut microbes or the semi-digested food? I suppose you select a sequence that is unique to the target species, but doesn’t that rely on a huge knowledge of the genetics of all the other organisms that could be in the sample?

I’ve asked the same question of an archaeologist who was looking at neanderthal DNA, and his answer was that he didn’t know.

Yeah, it fully should rely on knowing what you’re looking for, but actually they look for fresh feces so there shouldn’t be much more han hwat is living inside the bird.

Currently most DNA sequencing methods do not look at one strand of DNA but many strands of DNA with the same sequence. To go from environmental DNA (with lots of random DNA from many different sequences) to one short sequence with many repeats a method called PCR is used. This amplifies specific segments of DNA by selectively binding a preselected primer. These primers are where the specificity of PCR comes from. Primers are between 15-30 base pairs long and because each base pair can be one of four options the specificity of the primer is very high (4^length of the primer).

For a gene to be interesting it has to be variable but the primer has to start in a conserved region. This is where primer design comes in. By using known sequences and sequences of closely related species primers can be designed to only amplify the desired sequence. On top of that if a read happens and DNA is amplified that has no relationship to what is expected it will be noticed, and attempts can be made to amplify the desired section by redesigning primers.

You know you’re sequencing the right sequence because PCR primers are highly specific and well designed, and because the read can be compared to existing reads from related organisms.

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Thanks very much.
John

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