Taxonomists opinions on genomics/molecular studies

[AdamWargon]

Welcome to the iNat Forum, Truman!

Graminoid taxonomist @sedgequeen had a lot to say about this topic in another thread. I will share some of her comments below:

@sedgequeen

Two issues here. First, can genetics replace morphology for deciding whether two populations are one species or two? Answer: Sometimes. After all, different species no longer interbreed; they no longer exchange genes. Genetic analyses may be able to determine whether that’s true or not. However, there is no amount of genetic differentiation that indicates two populations are one species vs. two. Sometimes, a small genetic difference makes two populations unable to interbreed to produce fertile offspring. Other times, one species is highly genetically variable.

Sometimes genetic incompatibility results from translocations (rearrangements of gene order on chromosomes) or polyploidy (variation in number of copies of each chromosome). These can cause virtually instantaneous speciation, with, at first, no or few detectable difference in DNA sequences. And sometimes even polyploidy doesn’t prevent (though it does reduce) gene flow between, for example, diploids and tetraploids.

Sometimes there is clearly small morphological and genetic differentiation between two populations and it clearly results from geographic separation. Are the two populations one species or two? Would the organisms interbreed if they met one another? That’s a judgement call, and it can not be resolved with more data, morphological or genetic. Also a judgement call: where do we draw the line between asexual species? How do we handle populations that seem to be in the process of becoming two species but haven’t completed that?

Genetic analysis provides data for deciding what are species. Important data. But not a simple replacement for looking at morphology, behavior, etc.

@sedgequeen

Second issue about genetic data: Once we’ve decided on the species boundaries (see above), can we rely on genetic data (including but not limited to DNA barcoding) for species identification? Can / will genetic analysis replace morphology, behavior, etc., for identification?

A note: DNA barcoding as I learned about it refers to using one gene or a few genes for identification. Could theoretically be simple. But which gene(s) work for a given group? For example, a gene that often provides species level identification of plants misses most of the species boundaries within the genus Carex. Probably other genes will work, and likely whole-genome sequencing would work, but it’s not going to be as simple as analyzing one snippet of DNA and getting species ID’s for all plants.

You probably know that a skilled birdwatcher, botanist, etc., familiar with the area can go in the field and (depending on the season) reliably identify most of the birds or plants or whatever by sight/sound and do so almost as quickly as he sees or hears the animals. (We can also ID many photos fast, too.) That’s great, it’s relatively cheap, and it doesn’t require handling the animal or crossing the creek to get a piece of that plant. The value of this skill will never go away.

There are problems with ID’s by morphology, behavior, etc., though. What about animals that are usually hidden? What about plants that aren’t out at the time you have to be in the field? What about molds and other organisms that nobody knows much about? What about cryptic species? In these cases, that DNA barcode reader could be a wonderful tool.

Another issue is the time it takes to master the identification. Becoming good at DNA analysis takes time. Becoming good at insect identification takes time. Becoming good at grass identification takes time. Learning to dissect insect genitalia and know what you’re looking at takes time. Most of these skills are highly specific to the group of organism and the place. DNA analysis can be generalized. IF IF IF IF IF somebody has worked out the taxonomy and found handy genetic traits to use to distinguish the species, a gene jock who can barely tell a heron from a sparrow can do the identification (assuming DNA samples are available).

So, I think genetic analysis is a useful tool and will only become more useful as the equipment and processes get cheaper and faster. But it won’t simply replace identification based on morphology.

@sedgequeen

Genetic analysis is great! It’s really helpful! But it’s not a cure-all. Genetics help figure out where the lines are between taxa. If the distinction is clear – if the taxa have been separate for a long time – genetic analysis can find the difference. But in most (not all) cases, morphology can find that difference, too. Where morphology gives unclear answers, genetics may – or may not.

In the unclear cases, genetics provides more evidence but it can’t give us simple answers because there are no simple answers. Two populations are diverging, becoming two species. Will they continue? Will they merge back together? At what point should we call them different species? Genetics can’t answer those questions.

Two populations are similar but differ slightly and don’t interbreed because they’re geographically separated. They probably would interbreed if they met, but they don’t meet Should they be called one species or two? The answer must be a matter of human judgement, nothing else. Genetics can’t provide the answer.

People sometimes seem to think that a certain amount of genetic differentiation makes two populations different species. That isn’t true. Sometimes a small genetic difference or a chromosome rearrangement with little genetic sequence change causes two populations to be reproductively isolated. In other cases, a single species with clearly interbreeding populations is genetically variable.

We treat species like nice, neat, mutually exclusive categories because that’s what we need our words to be. Animals, plants, and other organisms have no need for our neat words. Our learning to analyze genetics doesn’t change that.