Phylogenetics exercises
The next set of exercise will involve you trying to (broadly) reproduce some of the results of a paper (Teeling et al. 2005 – see additional reading folder). Traditionally, it was thought that there are two suborders of bats, megabats and microbats. There are some key differences between the orders, including the ability of microbats to echolocate (megabats cannot do this). In the paper Teeling and colleagues argue that molecular evidence shows conclusively that microbats are not monophyletic (some of the bats classified as microbats actually cluster within the megabats on a phylogenetic tree). This would imply that either megabats lost the ability to echolocate or that the different lineages of microbats acquired this ability independently (which seems unlikely).
Constructing and viewing phylogenetic trees using Mega
1. Copy the sequences from the bottom of this document to a file on your computer. These sequences are from the adra2b gene (adrenergic receptor) from four microbats, two megabats and human (we will use the human sequence as an outgroup).
2. Construct an alignment from these sequences using ClustalW within BioEdit and save it in fasta format.
3. Start Mega. On the file menu select 'convert to mega format' and select the fasta file you saved in BioEdit.
4. Save the mega format file and then open the mega file (using 'open' on the file menu).
5. Infer pairwise genetic distances from the sequences using the default options. Notice that there are lots of options under the ‘Models’ menu. What pair of sequences are the most distantly related? The numbers in the lower left of the matrix are the distances; the numbers in the upper right part are standard errors of the distances.
6. Construct phylogenetic trees using the Neighbour Joining method (you will find this option under 'construct phylogeny' on the phylogeny menu). It's usually a good idea to view the unrooted tree first (the radiation tree under the view menu in Mega). Root the tree using the human sequence and again look carefully at the result.
7. Investigate the effect of radical changes in the nucleotide substitution model on the inferred tree topology. You can change the model using the options you are given when you select the neighbor-joining tree option on the phylogeny menu.
8. Construct phylogenetic trees again, this time using the bootstrapping re-sampling technique (you will find this option under the phylogeny menu - select bootstrap test of phylogeny and then neighbor-joining).
9. Open the sequence alignment in BioEdit . In the top left corner change the ‘Mode’ to ‘Edit’. Delete most of the sequence alignment - keeping just the first 100 nucleotides and save the alignment with a different name. Redo the Neighbor-Joining tree, again using the bootstrap. How do the tree topologies compare (are there any differences in tree topology?). How do the bootstrap values that you have calculated compare to the ones in you calculated earlier? Why do they differ in this way?
10. You can also use Mega to infer trees by maximum parsimony. Infer a tree using maximum parsimony and compare to the Neighbor-Joining tree. Try out different search parameters and compare results and how long the searches take. The differences may be particularly noticeable when you bootstrap.
Inferring a Maximum Likelihood phylogenetic tree using phyml
This section of this exercise is a little more difficult than the previous section. We are going to use a software package called phyml which is less user-friendly than Mega, but also quite a lot more powerful. You will be using phyml from a DOS command prompt. If you haven't used DOS or Linux before you will need to follow the following instructions carefully.
1. Make a folder on the C-drive of your computer called Phyml (the naming is not essential - you can call it what you like and adapt the following instructions accordingly).
2. Download the phyml executable from the course website and place it in the phyml folder.
3. To open a DOS window, click Start and select Run, then type command and press enter.
4. Open the adra2b alignment from the previous exercise in BioEdit and save it in phylip4 format in the phyml folder (use the filename adra2b.phy).
5. In the DOS window type cd C:\phyml. This will get your DOS window into the phyml folder.
6. In the DOS window type phyml and then press enter. This will start the phyml program.
7. Enter the filename of your phylip format file and press enter.
8. The menu that should now appear gives you a lot of analysis options. Type the letter to the left of an option to change that option. For now just change the T option (get the program to maximize over the transition:transversion ratio, rather than using a single value).
9. Once you have finished changing the options you type Y and press enter to get the program to run. The tree will be output to a file called adrab2.fasta_phyml_tree.txt. You can view this tree using Mega. Open Mega and on the phylogeny menu select "Display Newick Trees from file...". Take a look at the tree and compare to trees from the previous exercise.
10. Try out some other analysis options in phyml. In particular, work out how to run an analysis that uses a gamma distribution for the variation of evolutionary rate across sites, automatically estimating the appropriate value of the alpha parameter (which describes the shape of the gamma distribution) from the data.
Inferring a Maximum Likelihood phylogenetic tree using phyml
In this section of the exercise we will investigate the use of the program MrBayes for Bayesian inference of phylogeny. MrBayes is also a bit harder to use than phyml. It has a command-line interface which is quite similar to the interface of another well known phylogenetics package, PAUP. There are quite a lot of options in MrBayes and to use the package properly you should go through the manual carefully and understand what these options do. In the exercise below we will primarily accept default parameters. If you have time, experiment with changing some of these and see what the effect (if any) is on the trees you infer.
1. Copy the MrBayes executable to the folder you used in the previous exercise.
2. Open the alignment you used in the previous sections in BioEdit and export the alignment in PAUP format. (To do this, go to file -> export -> sequence alignment, and then select PAUP/Nexus). Make sure the name of the file into which you export the sequences has no spaces in it. Also note whether it has a file extension.
3. Double click on the MrBayes executable. Then type execute filename (where filename is the name you gave the nexus-format sequences you created in step two). This loads the sequences into MrBayes.
4. Now type help. This will give you the list of commands available in MrBayes. To get more information on a particular command type help command. We will use the command MCMC to run a Monte Carlo Markov Chain. This chain will sample trees according to their posterior probabilities. Get help on the MCMC command to see what your options are (and their default values). The syntax used by MrBayes is command parameter = value, where command is the command you want to run, parameter is the parameter value you want to adjust and value is the value you wish to give this parameter. Any parameters for which you do not specify a value will take default values. The default values are listed when you get help on the command.
5. Type MCMC 1000 and then press enter. This will set the MCMC going for 1000 generations (quite a small number in the context of MrBayes – check out what the default value is for Ngen).
6. Type no, when MrBayes asks you if you want to continue with the analysis. Note the warning you are given!
7. Type the command sumt. This command summarizes the trees that have been visited by the MCMC. Take a look at the information you are given. You can also display the trees you obtained using Mega. To do this open the file called filename.con, where filename is the name you gave your exported alignment, in a text editor (like notepad). Delete every line in that file, except the first line beginning with “tree con_50_majrule” (there may be a better way to do this, but Idon’t know it!). Go to Mega and select the phylogeny menu, then click ‘Display newick trees from file’ and select the filename.con file. This should open the tree. Once the tree is open, click view -> show/hide and then select stats/frequency. This will show you posterior probabilities for each of the internal branches of the tree. Internal branches of the tree define partitions of the taxa. These posterior probabilities represent the number of times the partition appeared in trees sampled by the MCMC. This gives an estimate of the posterior probability of the partition. See how the posterior probabilities compare with bootstrap values obtained previously.
8. Redo the MCMC but this time, lets try to do a better job. Use 100,000 generations and include some ‘burnin’. The burnin parameter of the sumt command gives the number of trees at the start of the chain to be discarded. Trees at the beginning of the chain are discarded because it takes the chain some time to ‘converge’. Only after a while does the chain begin to sample trees according to their posterior probabilities. Try using a burnin of 100 trees. Again view the tree and the posterior probabilities of the partitions. How do these compare with previous?
Bat Sequences
>Pteropus_rayneri_megabat
GCCATCGCTGCGGTCATCACCTTCCTCATCCTCTTCACCATCTTCGGCAACGCGCTTGTCATCCTGGCCG
TGTTGACAAGCCGCTCGCTACGCGCCCCGCAGAACCTGTTCCTGGTGTCGTTGGCCGCCGCCGACATCCT
GGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTGGGCTACTGGTACTTCCGGCGCACG
TGGTGCGAGGTGTACCTGGCGCTCGACGTGCTCTTCTGTACCTCGTCTATCGTGCACCTGTGTGCCATCA
GCCTGGACCGCTACTGGGCGGTGAGTCGCGCACTGGAGTACAACTCCAAGCGCACCCCACGTCGCATCAA
GTGCATCATCCTCACCGTGTGGCTCATTGCGGCTGTCATCTCGCTGCCACCCCTCGTCTATAAGGGAGAC
CAGGGCCCCCAGCCCCGCGGACGCCCGCAATGCAAGCTCAACCAAGAGGCCTGGTACATCCTGGCCTCCA
GCATTGGGTCCTTCTTTGCGCCCTGCCTCATCATGATCCTAGTCTACCTGCGCATCTACCTGATCGCCAA
GCGTAGCCACCGCAGAGGTCCCAGGGCCAAGGGGGGCCTCAGGGACAATGAGTCTAAGCAGCCTCACAGG
GTCCCTGGGGGACCATCAACCATGGCCTCTTGTTTGGCTGCCTCTGGAGAGGCCAGCAGACACTCCAAGC
CCACTGGSGAGAAGGAGCAGGGGGAGACCGAAGATCCTGRGAGCYCCGCCCTGCCACCCAGCTGGCCTGC
CCTTCCCCATGCAGGCCAGAGTCCGAAGGAAGCAGTTTGTGGGGTGTCTCTGGAGGAGGAGGKTGGGGAG
GAGGAGGATGAGTGTGAGCCTCAGGCCCTGCCAGCGTCCCCTGCCTCAGCCTGCAGCCCACCCCTGCAGC
AGCCACAGGGCTCCAGGGTGCTGGCCACCCTGCGTGGCCAGGTGCTCCTGGGCAGGGGCATGGGCACTGC
AGGTGGGCAGTGGTGGCGTCGGCGGGCTCAGCTGACCCGGGAGAAGCGGTTTACCTTTGTGTTGGCAGTG
GTCATYGGCGTCTTTGTTCTCTGCTGGTTCCCTTTCTTCTTCAGCTACAGCCTCGGTGCCATCTGCCCGC
AGCACTGCAAGGTGCCCCATGGCCTTTTC
>Homo_sapiens_adrenergic
ATGGACCACCAGGACCCCTACTCCGTGCAGGCCACAGCGGCCATAGCGGCGGCCATCACCTTCCTCATTC
TCTTTACCATCTTCGGCAACGCTCTGGTCATCCTGGCTGTGTTGACCAGCCGCTCGCTGCGCGCCCCTCA
GAACCTGTTCCTGGTGTCGCTGGCCGCCGCCGACATCCTGGTGGCCACGCTCATCATCCCTTTCTCGCTG
GCCAACGAGCTGCTGGGCTACTGGTACTTCCGGCGCACGTGGTGCGAGGTGTACCTGGCGCTCGACGTGC
TCTTCTGCACCTCGTCCATCGTGCACCTGTGCGCCATCAGCCTGGACCGCTACTGGGCCGTGAGCCGCGC
GCTGGAGTACAACTCCAAGCGCACCCCGCGCCGCATCAAGTGCATCATCCTCACTGTGTGGCTCATCGCC
GCCGTCATCTCGCTGCCGCCCCTCATCTACAAGGGCGACCAGGGCCCCCAGCCGCGCGGGCGCCCCCAGT
GCAAGCTCAACCAGGAGGCCTGGTACATCCTGGCCTCCAGCATCGGATCTTTCTTTGCTCCTTGCCTCAT
CATGATCCTTGTCTACCTGCGCATCTACCTGATCGCCAAACGCAGCAACCGCAGAGGTCCCAGGGCCAAG
GGGGGGCCTGGGCAGGGTGAGTCCAAGCAGCCCCGACCCGACCATGGTGGGGCTTTGGCCTCAGCCAAAC
TGCCAGCCCTGGCCTCTGTGGCTTCTGCCAGAGAGGTCAACGGACACTCGAAGTCCACTGGGGAGAAGGA
GGAGGGGGAGACCCCTGAAGATACTGGGACCCGGGCCTTGCCACCCAGTTGGGCTGCCCTTCCCAACTCA
GGCCAGGGCCAGAAGGAGGGTGTTTGTGGGGCATCTCCAGAGGATGAAGCTGAAGAGGAGGAAGAGGAGG
AGGAGGAGGAGGAAGAGTGTGAACCCCAGGCAGTGCCAGTGTCTCCGGCCTCAGCTTGCAGCCCCCCGCT
GCAGCAGCCACAGGGCTCCCGGGTGCTGGCCACCCTACGTGGCCAGGTGCTCCTGGGCAGGGGCGTGGGT
GCTATAGGTGGGCAGTGGTGGCGTCGACGGGCGCAGCTGACCCGGGAGAAGCGCTTCACCTTCGTGCTGG
CTGTGGTCATTGGCGTTTTTGTGCTCTGCTGGTTCCCCTTCTTCTTCAGCTACAGCCTGGGCGCCATCTG
CCCGAAGCACTGCAAGGTGCCCCATGGCCTCTTCCAGTTCTTCTTCTGGATCGGCTACTGCAACAGCTCA
CTGAACCCTGTTATCTACACCATCTTCAACCAGGACTTCCGCCGTGCCTTCCGGAGGATCCTGTGCCGCC
CGTGGACCCAGACGGCCTGGTGAGCCCGCCTGCGCTGCCCCTGTGGGGTTGGTGCGGTGGCGCCGGGGTC
ACCCTGCTTCTTGCCCTGCTGTGTGTGGCTGCCTCCCCTGGGCTTTCTGCTCCCTGCCCAGATCCTGTAG
GCCTCATCTTAGGAACCCCTTGGGAGGGGTGGGCAGGGGGGCTGCTAGCAAGGGTCCCAGTGAAGCTTCC
CCTTGCCGGCTTAGCTGTGGGGGACCCCTTCTCCACCCTCTCCCTGAGCACAGGCCGATGGAGGTGGTTC
AAATCCTCTGGAACATAGCCAAGACCAGGAGAAGAGAGAGCACTTTCTTCCCAGAGCCCCATGCTCTCCA
GACCAATGTCTGGGCTTCCCTTTCTTGAGGACCTTGTGTTCCTGGCAGGTCACTTGCTTGTGGTGTTTTC
GTTTCTTTTTCATCTCCCCCCCACCCACAAAGAGCACGGAGCCAGCCTTCCACTTTTCCCAGTGGGGCCT
GCTGCTGAGGGGGAGGAAGAAACGAAGACTGATCACCCACGCTAGGCACTCGCGGTCCCTGGCAGGCGCT
GGGATGGGGGCTTATGGGGTGGCATCGTCTCTGGGCCCTCCTTTCCCCCTTTGCCTGTTTTCGGATCTGT
GGTTCCTTTGAAAGCCAGAACAATGGATCGGCTTCCTTACCCAGCACCCCTCCGGTAGGTGGGTGGCCAC
GTGGATGCCTCGCTGGGGCGGTCTTGGAGGCCTGGTCTCTGCCTCGACGGGAGATCCCCGATCACTGGCA
TTCACCCCCTGCAAAAATCGGGGCGACAATAGCTCACTGCCTACTTGCTGCAGGGAGATGAAAGGCTTTG
CAGAAAGCTTTGAGCTCTGTGGGGGAACACACTAGAGAACCAAAAATGTGATTATATGGTGATATAAAAA
TCCCTTTCCTCTGTGTTTACCACCACCTGTCTTCCTGTAGACTTTTGTTCTGTCCCTGGGGTGTGTGAAT
TCCTACCCCGAACTGGAAGCCGGGAGTGGCAGACAGAATCACTATTTCAAGTTAAAGGATCTCTTTGAGA
ATGTGTTCTTCTGGCTGCAAAGGTCTGAGTTATTACGCTACATGACAACGTTTCGACATTTCACCGGCAA
CACCAAGAGGGTTTTTAGTGGCTTGGGTCTCCCCAGTGGGGGATAAGTCTTTTGTCATCAAGGAGGCAAA
TTGTCTCCCCAAGACAGCTCAAAATATCCACACCTCGGCAACAGTCTAAGATGAGAGCCTGTGACAGGTG
GCAGCGCCCCCAGGTGGGGTACTGGCATCAGAGCCTGGTGCGCCCCTAGGGGAGCCTCCCACTGGAGTGC
CCGGCCAGGTCTCCAAGCCCCAAATGAGTCCTTGTGAACCACAACTGATCCCCCCAGGTGGGTGCTTGTG
GACTGCCTCGGACCCAGCCACGCTGCTCCCCGCAATGCTGATGGGGCTGTGCATTGAGGACCCCTGCTTC
CTGGTTCTCAGTCCCACCCCAAAACCTGGCACCCAGAACAGTTGGAAGTGTGGAAAGGAGGTTTATCGGC
CTTCCCTTGGAGAGGGCCTGGCTTCAACATTGGGCCAGTAGGCATCTTAGCTTGGCAGGTGTCGGGGGAA
TGGGCCAGATGGACCTGCTAGATTTGGAAGGGCACCGAGGGAGTTTTCTGGGTGTAGAGAGAATGGAGGG
GACCAAAAAGAGTCCTTCCTGGGGTGTGGGAGGCTTCCCAGCTTGGTCCTCAGTGGGTTGTTGAGGCCAG
AGTATCGCCCTGGGATGTGGTGGGGAGCTGGGCCAGGAGAGGGACTGACTGTGACCCTCTGCTGGCCGGT
CTTGTGTGCGCCCCATGGGACCCCCAGTGTTCTTGCCTGTGACCTCTTATTGCGACATGCAGGTGGTGTT
TTTTTTTTTTTTAAACTCTGAGCTATTTTATCAATAAAGGATATTTTGTAATAAGAAAAAAAAAAAAA
>Nyctimene_albiventer_megabat_
GCCATCGCTGCGGTCATCACCTTCCTCATCCTCTTCACCATCTTCGGCAACGCGCTTGTCATCCTGGCGG
TGTTGACAAGCCGCTCGCTACGCGCCCCGCAGAACCTGTTCCTGGTGTCGTTGGCCGCTGCCGACATCCT
GGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTGGGCTACTGGTACTTCCGACGCACA
TGGTGCGAGGTGTACCTGGCGCTCGACGTGCTCTTCTGTACCTCGTCTATCGTGCACCTGTGTGCCATCA
GTTTGGACCGCTACTGGGCGGTGAGTCGCGCTCTGGAATACAACTCCAAGCGCACCCCGCGCCGCATCAA
GTGCATCATCCTCACCGTGTGGCTCATCGCGGCTGTCATCTCGCTGCCACCCCTCATCTATAAGGGAGAC
CAGGGTCCCCAGCCCCGTGGGCGCCCGCAATGCAAGCTCAACCAAGAGGCCTGGTACATCCTGGCCTCCA
GCATTGGGTCCTTCTTTGCACCCTGCCTCATCATGATACTAGTCTACCTTCGCATCTACCTGATTGCCAA
GCGTAGCCACCGCAGAGGTCCCAGGGCCAAGGGCGGCCTCAGGGACAGTGAGTCTAAGCAGCCCCACAGG
GTCCCTGGGGGACCGTCAACCCTGGCCTCTTGTTTGGCTACCTCTGGAGAGGCCAGCAGACGCTCCAAGC
CCACTAAGGAGAAGGAGCAGGGGGAAACTGAAGATCCTGGGAGCCCTGTCCTGCCACCCAGCTGGCCTGA
CCTTCCCCATGCAGGCCAGAGTCTGAAGGAAGCAGTTTGTGGGGTGTCTCTGGAGGAGGAGGTTGGGGAG
GAGGAGGTTGGGGAGGAGGAGGACGAGGGTGAGCCTCAGGATGCCCTGTCAGCATCCCCTGCCTCAGCCT
GCAGCCCTCCACTGCAGCAGCCACAGGGCTCCCGGGTGCTGGCCACCCTGCGTGGCCAGGTGCTCCTGGG
CAGGGGCATGGGCACTGCAAGTGGGCAGTGGTGGCGTCGGCGGGCTCAGCTGACCCGGGAGAAGCGGTTT
ACCTTTGTGTTGGCAGTGGTCATTGGTGTCTTTGTGCTCTGCTGGTTCCCTTTCTTCTTCAGCTACAGCC
TCGGTGCCATCTGCCCGCAGCACTGCAAGGTGCCCCATGGCCTTTTC
>Rhinolophus_creaghi_Rhinolophus_microbat
GCCATCGCTGCAGTCATCACCTTTCTCATTCTCTTCACCATCTTCGGCAACGCGCTGGTCATCCTGGCGG
TGTTGACGAGCCGCTCGCTCCGCGCCCCGCAGAACCTGTTTCTGGTGTCGTTGGCTGCAGCCGACATCCT
GGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTAGGCTACTGGTACTTCCGGCGCACT
TGGTGCGAGGTGTACCTAGCGCTCGACGTGCTCTTCTGTACCTCGTCCATCGTGCACCTGTGCGCCATTA
GCCTGGACCGCTACTGGGCCGTGAGCCGCGCGCTGGAGTACAACTCCAAGCGCACCCCGCGCCGCATCAA
GTGCGTCATCCTCACCGTGTGGCTCATCGCAGCTGTCATCTCGTTGCCACCCCTCGTCTATAAGGACGAC
CCTGGCCCCCAGCCCCGTGGGCGCCCACAGTGCAAGCTCAACCAAGAGGCCTGGTATATCCTGGCCTCCA
GCATCGCGTCCTTCTTCGCACCCTGCCTCATCATGGTCCTCGTGTACCTGCGCATCTACCTGATCGCCAA
ACGCAGCCACCGCAGAGGTCCCAGGGCCAAGGSGGGSGCTGGGAAGGATGAGTCTAAGCAACCCTGCAGG
GTTGCTAGGGGAGCATCAGCCAAACTGTCAACCCTGGCCTCTCATGAGGCAGCTTCCGGAGAGGACAACG
AGCACTCCAAGCCCAATGGGGAGAAGGAGCAGGGGGAGACCCCTGAAGATCCTGGGATCCCCACCTTGCC
ACCCATCTGGCCTGCCCTTCCCCACGCAGGCCAGGGTCCAACGGAAGGAGTTTGTGGGGCGTCTCCAGAA
GAGGACGCTGGCGAGGAAGAGGAGGATGAGTGTGAGCCTCAGGTCTTGCGGGTGTCACCTGCCTCAGCTT
GCAGCCCACCCCTGCAGCAGCCACAGGGCTCCCGGGTGCTGGCCACCCTGCGTGGCCAGGTGCTGCTGGG
CAGGGGCATGGGAGCTGCAGGTGGGCAGTGGTGGCGCCGACGGGCTCAGCTGACCCGAGAGAAGCGGTTC
ACCTTTGTGCTGGCAGTGGTCATTGGCGTCTTCGTGCTCTGTTGGTTCCCCTTCTTCTTCAGCTACAGCC
TGGGTGCCATCTGCCCACAGCACTGCAAGGTGCCCCATGGCCTGTTC
>Hipposideros_commersoni_Hipposideros_microbat
GCCATCGCTGCGGTCATCACCTTCCTCATTCTCTTCACCATCTTCGGCAACGCACTGGTCATCCTGGCAG
TGTTGACGAGCCGCTCGCTCCGTGCCCCGCAGAACCTGTTCCTGGTGTCGTTGGCCGCAGCTGATATCCT
GGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTAGGCTAYTGGTACTTCCGGCGCACT
TGGTGCGAGGTGTACCTGGCGCTCGACGTGCTCTTCTGTACCTCGTCTATCGTGCACCTGTGCGCCATCA
GCCTGGACCGCTACTGGGCCGTAAGCCGCGCGCTGGAGTACAACTCCAAGCGCACCCCGCGCCGCATCAA
GTGCATCATCCTCACTGTGTGGCTCATCGCAGCTGTCATCTCGCTGCCGCCCCTCGTCTATAAGGACGAC
CCCGGCCCCCAGCCCCGCGGGCGCCCACAGTGCAAGCTCAACCAAGAGGCCTGGTACATCCTGGCCTCCA
GCATCGGGTCCTTCTTCGCACCCTGCCTCATCATGATCCTCGTGTACCTGCGCATCTACCTGATCGCCAA
ACGCAGCCACCGCAGAGGTCCCAGGGCTAAGGGGGGCCCTGGGGAGGGTGAGTCTAAGCAGCCCCACCGG
GTCCCTAGGGGAGCATCGGCCAAACTGTCAACCTTGGCCTCTCATCAGGCTGCTTCCGGAGAGGCCAACG
GACACACCAAGCCCAATGGGAAGAAGGAGCAGGGGGAGACCCCTGAAGATCCTGGGAGCCCTACCTTGCC
ACCCACCTGGCCTGCCCTTCCCCATGCAGGCCAGGGTCCGAAGGAAGGAGTTTGTGGAGTGTCTCCGGAG
GAGGAAGCTGGTGAGGAAGAGGAAGATGAGTGTGAGCCTCAGGTCTTGCCAGCGTCCCCCGCTTCAGCTT
GCCGCCCACCCCTGCAGCAGCCACAGGGCTCCCAGGTGCTGGCCACCCTGCGTGGCCAGGTGCTGCTGGG
CAGGGGCATGGGCGCTGCAGGTGGGCAGTGGTGGCGTCGGCGGGCTCAGCTGACCCGAGAGAAGCGGTTC
ACCTTTGTGCTGGCGGTGGTCATTGGCGTCTTCGTGCTCTGTTGGTTCCCGTTCTTCTTCAGCTACAGCC
TGGGTGCCATCTGCCCACAGCACTGCAAGGTGCCCCATGGCCTTTTC
>Noctilio_albiventris_microbat_AJ419812.1_NAL419812_
GCCATCGCTGCCGTTATCACCTTCCTTATTCTCTTCACCATCTTCGGTAACGTGCTCGTCATCCTGGCGG
TGTTGACCAGCCGCTCGCTTCGCGCTCCGCAGAACCTGTTCCTGGTGTCGTTGGCCGCAGCCGACATCCT
GGTAGCCTCGCTCATCATCCCTTTCTCTCTGGCCAACGAGCTGCTGGGCTACTGGTACTTCCGGCGAACG
TGGTGCGAGGTGTACCTGGCGCTAGACGTGCTCTTCTGTACTTCTTCCAACGTGCATCTGTGCGCCATCA
GCCTGGACCGCTACTGGGCTGTGAGCCGCGCTCTGGAGTACAACTCCAAGCGTACCCCGCGCCGCATCAA
GTGCATCATCCTCACTGTGTGGCTCATTGCGGCTGTCATCTCGCTGCCGCCCCTCATCTACAAGGGTGAT
CAGGGCCCCCAGCCCCGCGGGCGTCCGCAGTGCAAGCTCAACGAAGAGGCCTGGTACATCCTGGCCTCGA
GTATCGGGTCTTTCTTTGCACCCTGCCTCATCATGATCCTCGTCTACCTGCGCATCTACCTGATTGCTAA
ACGTAGCCACCGAAGAAGTCCCAGGGCCAAGGGGAGCTCTGGGGAGGGTAAACCTAAGCAGCCCCACCCA
GTCCCTGGGGGAACCTCAGTCAAACTGCCAACCCTGGCCTCTCATTTGGCTGCTTCCGGAGAGGCCAATG
GACACTCTAAGTCCACCGGGGAGAAGGAGCAAGGGAGGACCCCTGAAGACCCTGGGAGCCCCACCTTGCC
ACCCAGCTGGCCTGCCCTTCCCCATGAGGGCCAGGGTCCAAAGGAAGGTGTTGGTGGGGTGTCTCCAGAA
GAAGAAGTTGGAGAGGAGGAGGAGGAAGAGGAGGACGACGACGATGAGTGTGAGCCTCAGGCCTTGCCAG
CATCCCCTGCCTCGGCTTGCAACCCATCCCTGCAGCAGCCGCAGGGCTCCCAGGTGCTGGCCACCCTTCG
TGGCCAGGTGCTTCTGGGCAAGGGTATGGGTGCTTCGGGTGGGCAGTGGTGGCGTCGGCGGGCTCAGCTG
ACCCGGGAGAAGAGGTTCACCTTTGTGCTGGCCGTGGTCATAGGCGTCTTTGTGCTCTGCTGGTTCCCCT
TCTTCTTCAGCTACAGCCTGGGTGCCATCTGCCCACAGCATTGCAAGGTCCCCCATGGCCTCTTC
>Antrozous_pallidus_microbat
GCCATCGCGGCGGTCACCTCCTTCCTCATCCTCTTCACCATCTTTGGCAACGCACTGGTCATCCTGGCGG
TGTTGACCAGCCGCTCGCTGCGCGCCCCGCAAAACCTGTTCCTTGTGTCCTTGGCTGCCGCTGACATCCT
GGTGGCCACGCTCATCATCCCTTTCTCGCTGGCCAACGAGCTGCTGGGCTATTGGTACTTCGGGCAAGCG
TGGTGTGAGGTGTACCTGGCTCTCGACGTGCTCTTCTGTACTTCGTCCATCGTGCACCTGTGTGCCATCA
GTCTGGACCGCTACTGGGCGGTAAGCCGCGCTCTGGAGTACAACACCAAGCGCACCCCGCGCCGAATCAA
GTGCATCATCCTCACTGTGTGGCTCATTGCAGCTGTCATCTCGCTGCCGCCCCTACTGTACAAGGGCGAC
CCGGGCCCCCAGCCCCGCGGACGCCCACAATGCCAACTCAACCAAGAGACCTGGTACATCCTGGCCTCCA
GCTTTGGGTCCTTCTTCGCACCCTGCCTCATCATGATCCTYGTCTACYTGCGTATTTACCTGATCGCCAG
ACGTAGCCACCAGAGAGGTCCCAGGGCCAAGAGGGGTTCTGGGGAGGGTGAATCTAAGCAGCCCTGCCGG
GTCCCTGGGGGAACGTCGGCCAAACTGCCGACCCTGGTCTCCCATTTGGTTGCTTCTGAAGAKGCCAATG
GACACTCTAAGCCCACTGGGAAGAAAGAGCAGGTAGGGACCCCTGAAGATCCTGGGAACCCAGCCTTGCC
ATCCAGCTGGCCTGCCCTCCCCCATGCAAACCAGGGTCCAAAGGAAGGTGTTTGTGGAGTGTCTCCAGAG
GAGGAAGTTGAAGAGGAGGAGGAGGAGGAGTGTGGACCTCAGGCCTTGCCAGTATCCCCTGCCTCCGCTT
GCAGCCCACCCCTGCAGCAGCCACAGGGCTCCCGGGTGTTGGCCACCCTGCGTGGCCAGGTGCTTCTGGG
CAGGGATATGGACGCTGCAAGTGGGAAGTGGTGGCGGTGGCGRAGGCGGGCTCAGCTGACCCGGGAGAAG
CGGTTCACCTTTGTGCTGTCTGTGGTCATAGGCGCCTTCATGCTCTGCTGGTTCCCCTTCTTCTTCAGCT
ACAGTCTGGGTGCCATCTGCCCGAAGCACTGCAAGGTGCCACAAGGCCTTTTC