Bio activity done

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Oct 30, 2023

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Lorenzo Angelus Fernandez Participation credit – species delimitation On Canvas, please download the file “Cyerce_COI_aligned.fas”, our original fasta file containing COI sequences from all Caribbean specimens of Cyerce . When I collected these specimens, they were all one nominal (named, or recognized) species called “ Cyerce antillensis ”. When I performed species delimitation, the results indicated this was actually a cryptic species complex, meaning a group of related but distinct species that no one had told apart yet. Using this file, follow along with the lecture and see how we can use two methods of species delimitation to group individuals into distinct bins, or clusters, that presumably correspond to what we would recognize as nameable “species”. 1] ABGD – automated barcode gap detection Go to the website: https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html Copy-paste the .fasta file contents (COI sequences) into the box. Choose a model of DNA substitution to correct your genetic distances. Change any parameters if you want (pmin, pmax, etc). Hit return. Question 1: How many species did it find? 7 species Partition 1 : found 7 groups (prior maximal distance P= 0.001000) Partition 2 : found 7 groups (prior maximal distance P= 0.001995) Partition 3 : found 7 groups (prior maximal distance P= 0.003979) Partition 4 : found 7 groups (prior maximal distance P= 0.007937) Partition 5 : found 7 groups (prior maximal distance P= 0.015832) Partition 6 : found 7 groups (prior maximal distance P= 0.031581) Partition 7 : found 7 groups (prior maximal distance P= 0.062996) Click on “ here ” to see your results. 1 1
Question 2: Based on the histogram, what would you estimate is the barcoding gap – that is, the gap between intra-specific and inter-specific genetic distances? Does that agree with the gap calculated by ABGD? The barcoding gap is roughly ~0.058 or 5.8%, which does seem to agree with the calculations of ABGD and 7 groups/species. Click on one of the yellow dots to see the (a) barcoding gap, (b) grouping of individuals into species or “Groups”. Question 3: Based on the groups, are all named specimens grouping together? Are any specimens in groups that don’t match their names? Yes, the named species are grouping together. Tampa and Tarpon are grouped together in one group. Group 1 has over 5 species and outlier individuals Cy_antillensis_07SSal01 Cy_antillensis_10Bim01 Cy_antillensis_KM879888 Cy_antillensis_TXID1582513 Cy_antillensis_TXID1460625 in it. 2 2
Question 4: Now go back and change the pmin and pmax values to something else, or change the model of DNA substitution, and run a new analysis. Tell me the new parameters you used, and whether you got different results? New parameters: Partition 1 : found 7 groups (prior maximal distance P= 0.001000) Partition 2 : found 7 groups (prior maximal distance P= 0.001911) Partition 3 : found 7 groups (prior maximal distance P= 0.003652) Partition 4 : found 7 groups (prior maximal distance P= 0.006980) Partition 5 : found 7 groups (prior maximal distance P= 0.013338) Partition 6 : found 7 groups (prior maximal distance P= 0.025490) Partition 7 : found 7 groups (prior maximal distance P= 0.048714) The P value changes to varying extents but the number of groups remains the same, and the results on the histogram also appear to be the same. 2] ASAP – Assemble Species by Automatic Partitioning Go to the website: https://bioinfo.mnhn.fr/abi/public/asap/asapweb.html Upload the .fasta file contents (COI sequences) by clicking the “Choose a file” button. Choose a model of DNA substitution to correct your genetic distances. Hit return. Question 5: How many species did ASAP find in the top-scoring partition? What was the P-value associated with this result? 29 9.60e-01 Click on “ list ” (at the right-most column) to download a text file with your results, including the individuals sorted into groups (=species). Partition 10 3 3
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