applied-bioinformatics / built-iab Goto Github PK

Thanks for developing this resource! I was just looking to assign the phylogeny section to students , and noticed one place where I think the language could be revised. I wasn't entirely sure if PR against the static version via the edit link would be the right way to go or if you'd prefer an issue.

Anyway here's the language in question:

"Entomologists have debated whether orb-weaving is a monophyletic trait (meaning that it evolved one time), or whether it is polyphyletic (meaning that it evolved multiple times, such as flight, which has evolved independently in birds, flying dinosaurs, insects, and mammals). If orb-weaving is monophyletic, it would mean that over the course of evolution, extant spiders which don't weave orb webs have lost that ability. Some researchers doubt this as it's a very effective means of catching prey, and losing that ability would likely constitute an evolutionary disadvantage. If orb-weaving is polyphyletic, it would means that in at least two different spider lineages, this trait arose independently, which other researchers consider to be very unlikely due to the complexity of engineering these webs. Examples of the evolution of monophyletic and polyphyletic traits are presented in Figures 3 and 4, respectively."

I think the usage of monophyly here is slightly non-standard, and that alternative language might be clearer. Monophyly by definition typically refers to a group of organisms that descend from a common ancestor. (I get only 947 google hits for "monophyletic trait" vs. many more for e.g. "homologous trait", "synapomorphy" or "convergently evolved trait")

See e.g. https://en.wikipedia.org/wiki/Monophyly and https://ucmp.berkeley.edu/glossary/gloss1/phyly.html

A group of species is monophyletic if it includes an ancestral organism and all it's descendants. Traits, however, can't strictly be monophyletic under this standard definition. I suggest using homologous vs. convergent for the trait (to denote a single evolutionary origin or multiple origins for orb-weaving), or editing the language lightly to make clear we're debating whether orb-weaving spider species are a monophyletic group or not. Another alternative, if orb-weaving were a shared derived characteristic of a group of spiders would be to call it a synapomorphy.

Here's an example taking the first suggestion:

"Entomologists have debated whether orb-weaving in spiders is a homologous trait (meaning that it evolved just once in these spiders), or whether it is an example of convergent evolution (meaning that it evolved multiple times, such as flight, which has evolved independently in birds, flying dinosaurs, insects, and mammals). If orb-weaving in spiders is a homologous trait, it would mean that, over the course of evolution, extant spiders which don't weave orb webs have lost that ability. Some researchers doubt this as it's a very effective means of catching prey, and losing that ability would likely constitute an evolutionary disadvantage. If orb-weaving evolved convergently it would means that in at least two different spider lineages, this trait arose independently, which other researchers consider to be very unlikely due to the complexity of engineering these webs. Examples of the homologous or convergently evolved traits are presented in Figures 3 and 4, respectively."

Anyway, hope that's useful! Apologies in advance for the maybe overly pedantic feedback.