Question

Take as much time you need but please give me the answers

Note: You can find the article online you search the name of the Article. let me know if you cant then ill upload the images. thanks

the For the first set of questions, please read the paper “Phylogenomic evidence for multiple losses of flight in ratite birds” by Harshman et. al. posted on Canvas. Do your best to get through the paper, but do not spend a lot of time struggling through any methodological details that are unfamiliar to you. Focus more on the concepts presented in the paper.

Q: The authors constructed a phylogenetic tree using nucleotide substitutions as well as a tree built using indel information.  What relationships did each support; do they agree completely with each other?

Q:Why did the authors use an 8-bp deletion as a trait, but choose to ignore single nucleotide deletions?

Q: If the authors’ results are correct, how many times was flight lost in this clade of birds? Is it reasonable to assume that loss of flight could evolve many more times than the evolution of flight in the paleognaths? Why?
Q: Why might the use of morphology, used by previous studies for this group, give incorrect/different results from the genomic data?

Answer 1

1. Answer to this part of the question has been previously given.
2. Homoplasy is a character shared by a set of species but which was not present in their common ancestor. It means that homoplastic characters could only have originated because of convergence. Indel events (Insertions and deletions in the genome) are pretty rare in occurrence, which means it is less likely that an indel event could be found in different species because it occurred multiple times throughout evolution(convergence). This makes indels a valuable phylogenetic marker because they can be assumed to have derived from a shared ancestor. Indels in vertebrates consistently exhibit less homoplasy than nucleotide substitution. Since indels are rare by themselves, indels or longer segments of genome(8bp or 9bp) are correspondingly rarer to have occurred by convergence than indels that are 1bp long. A study revealed, that 1-bp indels are more than twice as likely to exhibit homoplasy than longer (≥5-bp) indels. Thus, the likelihood of homoplasy in a 1bp indel event is much higher than the combined likelihood of homoplasy in the two longer indels. This is why the authors chose to rely on the data from longer indels to map out the common ancestors while ignoring the data from 1bp indel.
3. According to this study by authors, flight was lost independently at least three times in this clade of birds; this happened in ostriches, rheas, and Australasian ratites. From previous avian evolutionary studies it is known that losses of flight in avian members are more likely to occur than an event of gain of flight. Flight has been lost in members of 18 extant bird families, many more times in extinct groups, and hundreds of times in the family Rallidae alone. If multiple losses of flight had not happened, then this character must have been inherited by the ratite members, which consequently means that the tinamous must have regained the ability to fly at some point to have its present form. But there are no examples of avian lineages that have lost and regained flight, so it will be a stretch to assume so for timanous. Thus it is reasonable to assume that loss of flight could evolve many more times than the evolution of flight in the paleognaths
4. Several morphological studies strongly support ratite monophyly which is in conflict with the data found in this study. But often, convergence of morphological features can mislead phylogenetic analysis, which means characters that may have been occurred by convergence are taken to have occurred by descent. Even for multiple event of loss of flight in these lineages, the parallel evolution of the characters of volant ancestors of ratites may have produced the characters found in present flightless birds independently, and not necessaily by descent. Thus the same morphological evidences that till now were considered monophyletic, could very well point to a polyphyletic origin.