Construction of Phylogenetic Trees

 

Construction of  Phylogenetic Trees

 

Phylogenetic trees serve as visual representations illustrating the evolutionary connections and relatedness among the species depicted within the tree structure. Phylogenetic trees are essential tools in biology for understanding the evolutionary relationships between different species or groups of organisms. These trees depict the evolutionary history of organisms, showing the branching patterns that represent common ancestry. Constructing a phylogenetic tree involves several steps, including data collection, alignment, tree building, and interpretation. we will discuss each of these steps in detail.

1. Data Collection:

Ø  The first step in building a phylogenetic tree is to gather data, typically genetic sequences such as DNA or protein sequences.

Ø  DNA sequences from specific genes, like ribosomal RNA (rRNA) or mitochondrial DNA, are often used because they provide valuable information about evolutionary relationships.

Ø  Researchers may also use protein sequences or morphological characteristics, although genetic sequences are generally preferred due to their higher information content.

2. Sequence Alignment:

Ø  Once the data is collected, the next step is to align the sequences. Sequence alignment involves arranging the sequences in such a way that similarities and differences between them become apparent.

Ø  There are various alignment algorithms and software tools available for this purpose, such as ClustalW, MUSCLE, and MAFFT.

Ø  After alignment, gaps may be introduced to optimize the alignment, ensuring that homologous regions are properly aligned.

3. Phylogenetic Tree Building Methods:

Ø  There are several methods for constructing phylogenetic trees, each with its own advantages and limitations. Some common methods include:

1.      Distance-based methods: These methods calculate the genetic distance between sequences and use this information to build a tree. Examples include Neighbor Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean).

2.      Character-based methods: These methods analyze the discrete characters (e.g., presence or absence of specific traits) to infer evolutionary relationships. Parsimony and Maximum Likelihood are examples of character-based methods.

3.      Bayesian methods: Bayesian inference uses probability theory to estimate phylogenetic trees, taking into account prior knowledge and uncertainty in the data.

The choice of method depends on factors such as the nature of the data, computational resources available and the assumptions underlying the method.

4. Tree Evaluation and Interpretation: Once a phylogenetic tree is constructed, it needs to be evaluated to assess its reliability and interpret the evolutionary relationships it represents.

a.       Bootstrap analysis and support values: Bootstrap analysis involves resampling the data to generate multiple datasets, from which multiple trees are constructed. Support values, often expressed as bootstrap percentages, indicate the robustness of the branches in the tree.

b.      Consistency with known biology: The resulting tree should be consistent with what is known about the biology and evolutionary history of the organisms being studied. For example, closely related species should cluster together on the tree.

c.       Outgroup analysis: Including an outgroup—a species that is known to be distantly related to the taxa of interest—can help root the tree and provide additional context for interpreting evolutionary relationships.

 

  

Constructing phylogenetic trees is a complex but essential task in evolutionary biology. By collecting genetic data, aligning sequences and using appropriate methods for tree building, researchers can gain valuable insights into the evolutionary history of organisms. Interpreting phylogenetic trees requires careful consideration of the data, methodology, and biological context, but the resulting trees provide a framework for understanding the diversity of life on Earth.

 

STEPS OF MAKING A PHYLOGENETIC TREE

 

a.       Find and download the sequences to be included in the tree from the biological database (NCBI: http://www.ncbi.nlm.nih.gov), (EMBL: http://www.ebi.ac.uk/) and (DDBJ: http://www.ddbj.nig.ac.jp/)

For example the following sequences

1.

>NW_026129590.1:c715037-712204 Labeo rohita strain BAU-BD-2019 unplaced genomic scaffold, IGBB_LRoh.1.0 scaffold_66, whole genome shotgun sequence

GCAGCAATGATATAGTCGCATACATATTGGAGATCATGAACACCCAGGTGCTTAAAAAAGAAGACGCTGT

GCCGCGACTGCAGCTGTTTAATTGCGCTTATACTGAATGTGGCGCCACATTCACTCGTCGATGGCGTTTA

CAGGAGCACGAGACCGTGCATACTGGTGCAGTGAGTCGTATTCATATTTTCCCTTTTTTTAAAAAAAAGG

GGTAGTGTTTATCACGTGCTATTTTATTTATTTATGTAGCCATGATCCGTTTTTTTTTGTTTGTTTGTTT

GTTTGTTTGTTTGTTTGTTTGTTTTTTTGTTTTTTTTTTGTCTTCTGTTTTCTTCAGCGACCTCACAAGT

GTGTTGTAGCGGGGTGTGGACGCAGTTTCACCCGTAAATCGCACCTGAGCCGACATGCTTTGGTACACAG

CGGAGTGAAAAACTTCAAGTAATATGATTATTAATAACAACCAGTTTGACGTGTGTGTGTGTGTGTGTGT

GTGTGTTTTTGAGTGAGGCTTGTATAGGCTTGGTTATTTGGATCCATTTGCATGACCTACTTGGGTGAAC

CCTTTATAGTTTTATATTAAGTTATGGCATTGTATTAACTGAGAGGTTATGTAGAATGTTTATATTTAAA

ATGATCTGGCATGGCGGGAAGGCAATTGTGGTTTCATATTTGTGAATAACCATTTCCCTCCGTTTTGATC

ATCTGAGAATGCTGGTTTCTCGCTGAGCAGGTGCACTGCAGCCGCATGTAGCAAAAGCTTCTGCACCGCT

GATAAACTGAAGAGGCACGTGCGTTACGCTCACAGCGAGAAACGCGAATATTTCAAGGTTTGACCCTTTT

ATTTTTTTTTATTTTCTAAACATATTTATTGGCTGCTTTTTGCTATAAACAGGCTTTATGCTTGTAATTA

AAAAAAAAAAAATAAGACTGAGTGTTTTTCTTTCTTAGTGTAAAGATCCACAGTGCGCAAAGACTTTTAA

GAAACGGCGAGTGTTAAAGCTGCACCTGGCGACGCACGGTACATCAAGTTTCAGGTGCGTCTGCAGCCTG

GAAGTCTTTGTAACCAAGGGTTTATAACTGCTAAAAGTAAAATACAGTATATGTACCTGGGTGTTTTCTG

TTTAAGGTGCTTGAAAAGCGGCTGTGGAATGAGGTTTGAGTCTCACATTGCACGGAAAGCGCATGATAAA

AGGCATTCAGGTAAGGATACATTAACTCTGAAGTGTTTTATCGACTGGCATTAACTGTTTAACCCCAATA

TTTGATCAACATATGGTGATGCTCATTAGCTGTCATGTTAACATGTTACCCAGAGGTTAATCCCAAAGTC

TCTTTACTTGTTCACATTTTTGGTAAGTATGGGTGAACTTTTTTTTTTTTTTTTCCTCCCTTAAAACGAG

TAAAATGTAACTAACTGTTAAGTAACTTTTGTTTGGATGCTTTGGAGTTGAGATTTGCATTTTGAGGTCC

GTGCTACCTTAAAACAAGTTCACCATGCCCACTCAGTATTTGTTTCTTCAGGTTATCGCTGTCTTCATGC

TGAATGCCCCATCAGTGTGCACACCTGGAGGAATTTACAAAAACACATGGCAAGTCACCCAGGTAAACTG

GTGGAACCATCCGTGTTTTCTTATTGGCTGTAAACCGCTGTTTTTCATGAGTGGCATGTTCTTTTTGTGC

CCATGATGGTTTCCACAATAGGTCTACATTCTGTTTTGTTAACAGCATCATTCCCTTGTATGGTATGTAA

AAAGACTTTCAAGAAACGTGACTCTTTGAGGAGACACAAGCGGACGCATGCGTTGCAGAAGCCGGTTTTA

CTCTGTCCCAGTCAGGGCTGCCAGGCTTACTTTTCCACCACTTTCAACCTGCAGCATCATATTCGAAAGG

TCCATCTGCAGCTGCTCTCACACCGCTGTTCCTTCCCTGGCTGTGGCAAAAGTTTTGCCATGCGTGTGAG

TACATTTGAGGAACATGGAAAGGATGGTAAAATGGTCTCATGATATTTTGTGTCCTAAAGCCAAATGATG

TGAAATAAGTAACCAGTGGTTGAATTCTGCAAATCACAACTCCAGTTTTGGGGTGATGTTCAAGTCAGCA

TGTCTTTATAGGTCTGTGGTGTTTGCAGTGTTAGATTGTGAAAAAATTGTGCTAGTAACCCCTGCTTTAC

ATGTGCTGTTTTAACAGGAAAGCCTTGTCCGCCACATGTTACGTCATGAACCTGATGTGGCCAAACTCAA

GGTAGTTCTGTCCCTTAAAGTAGTATTTAAAGGGTTAAATGCTGGTTGGGCTTAATTAACAGCATCTGTG

GCATGTACGTAATCACACCGCTTAAGTTTCATTTCCTCAACTCTCTGGTTGTTTGTGTTGTTTAGCACCC

ACATAAACGGAGCAGCAAGAGCTGGCAGAAACGCTTGGAAGGGCGAAGTCGACGTCCTCTGGTTGAAGAC

CTTCGATCTCTCTTTTCGTTACGCATGAAGATCTCTCCTAGGGCCAAACTGGAAGCTGATCTGACGGGCC

TCTTTAATGAGCGTAAAATCCCCCACCACGTTGATCCGGAAGTAAACCTCAGAGATCTGTTTAATGTCCG

TCCAACTAAGGTGGTCGATAAATAGAATTGTCCAATACTCTTAACCCCCCCTTTTTTTGAATACTGGTGA

CATGCGTTTACCTTAACTGAAGAGAATTTTGTTTCAAGTGTTAGTACTAGAGGTACAGAATTACTTTATA

ACTGCTGAACTATGTTGTTTGAGAACCGTTGTTTGAGAAACAACTGAAATTTAAGTTCTGTATGATGAAA

ATAAAGGTGGTTTGGTTTTGTCAGTCTGGCCAAT

 

2.

>NC_015193.1:2861-3835 Labeo bata mitochondrion, complete genome

ATGCTAAACATCCTAATAACCCACCTAATTAACCCACTAGCCTACATCGTGCCTGTCCTACTAGCAGTAG

CTTTCCTAACACTAGTTGAACGAAAAGTACTAGGCTATATACAACTACGAAAAGGACCTAACGTAGTAGG

ACCTTACGGACTACTACAGCCCATCGCCGACGGAGTAAAATTATTTATTAAAGAACCAGTCCGCCCATCT

ACATCATCCCCATTCCTATTTCTAGCCACCCCAATACTCGCACTAACACTAGCCATAACCCTATGAGCAC

CTATACCAATACCCCACCCAGTAACTGACCTAAACCTAGGAATCCTCTTCATCCTAGCCCTATCAAGCCT

AGCAGTATATTCAATTTTAGGGTCAGGATGAGCATCAAATTCAAAATACGCACTAATTGGTGCCCTACGG

GCTGTAGCCCAAACAATTTCCTATGAAGTAAGTCTAGGACTTATTCTCCTCTCAGTAATCATCTTCTCTG

GTGGATATACACTACAAACATTTAATATTACCCAAGAAAGCATCTGATTACTCGTACCAGCCTGACCATT

AGCCGCAATATGATATATCTCAACACTAGCTGAAACAAACCGAGCACCATTCGACCTAACAGAGGGAGAA

TCAGAACTAGTATCTGGCTTCAACGTAGAATATGCAGGAGGACCCTTCGCCCTCTTTTTCCTAGCCGAAT

ATGCTAACATTCTACTAATAAATACCTTATCTGCCGTATTATTCCTAGGAGCCTCACACATCCCAAGCAT

TCCCGAACTAACCACAATTAACCTAATAACTAAAGCTGCACTATTATCAATTTTATTCCTATGGGTACGA

GCTTCCTACCCACGATTCCGATATGACCAACTAATACATTTAGTATGAAAAAATTTCCTCCCACTAACAC

TTGCCTTCGTACTATGACATACCGCCCTACCAATTGCACTAGCAGGGCTTCCCCCACAACTATAA

 

3.

>NC_016892.1:3796-4770 Catla catla mitochondrion, complete genome

ATGCTAAACATCCTAATAACTCACCTAATTAACCCCCTAGCCTACATTGTACCCGTTCTCCTAGCAGTAG

CTTTCCTAACATTAATTGAACGAAAAGTACTAGGTTATATACAACTACGAAAAGGCCCTAACGTAGTAGG

ACCCTACGGACTACTACAACCCATCGCCGATGGAGTTAAACTCTTTATTAAAGAACCAGTCCGCCCCTCC

ACATCATCCCCATTCTTATTCCTCGCCACCCCCATACTCGCACTAACCCTAGCCATAACCCTATGAGCAC

CAATACCCATACCTCACCCCGTAACGGACCTCAACCTGGGAATCCTATTTATCCTAGCCCTATCAAGCCT

AGCAGTATACTCAATCCTGGGGTCAGGATGAGCATCAAATTCAAAATACGCGCTAATCGGGGCCCTACGG

GCCGTAGCCCAAACAATTTCATATGAAGTAAGTCTTGGGCTAATCCTCCTTTCAGTAATCATCTTTTCAG

GAGGTTATACACTACAAACATTCAACACCACCCAAGAAAGCATCTGACTACTCGTACCCGCTTGACCCCT

AGCCGCAATATGGTATATCTCAACACTAGCCGAAACAAACCGAGCACCATTTGACCTAACAGAAGGAGAA

TCCGAACTAGTCTCTGGCTTCAACGTAGAATATGCAGGAGGGCCCTTCGCCCTATTCTTCCTAGCAGAAT

ATGCCAATATTCTACTAATAAACACACTATCAGCCGTACTATTCCTAGGAGCCTCACACATCCCAAGCAT

CCCTGAACTCACAACCATTAACCTAATAACCAAAGCTGCATTATTATCAATTTTATTCCTATGAGTACGA

GCCTCTTATCCACGATTCCGATATGATCAACTAATGCACTTGGTCTGAAAAAACTTCCTCCCCCTCACAC

TAGCCTTCGTTCTATGACACACCGCCCTACCAATTGCACTAGCAGGACTCCCCCCACAACTATAA

4.

>NC_027495.1:11963-13801 Botia lohachata mitochondrion, complete genome

ATGCACACAACAGCCCTAATCTTATCCTCCTCACTAGTACTAGTCCTCACAATCCTCACATACCCGCTAC

TAACCTCACTTAACTCAAAACCCTTAAACCCAAAATGAGCAACCTCTCACGTTAAAACAGCCGTAAGCTG

TGCCTTTTTCATTAGTTTAGTACCTCTCATAATTTTCTTAGACCAAGGGGCCGAAACTATCGTTACAAAC

TGACATTGAATAAATACATCAATATTTGACATCAACATTAGCTTTAAATTTGACCAATACTCCCTTATTT

TTACACCAATTGCTTTATATGTTACTTGATCAATTTTAGAGTTTGCATCATGATATATACACTCCGACCC

ATACATAAACCGTTTTTTCAAATATTTACTTCTATTCTTAGTAGCCATAATTATCTTAGTAACAGCTAAC

AACATATTCCAACTCTTCATTGGCTGAGAAGGGGTAGGAATTATATCATTTCTATTAATCGGATGATGAT

ACGGACGAGCAGATGCCAACACAGCAGCACTCCAAGCCGTACTATATAACCGAGTAGGAGATATTGGACT

AATTATATGCATAGCCTGACTTGCAATAAACATAAACTCATGAGAAATTCAACAAATCTTCTTCCTATCA

AAAAACTTTGACATAACCTTACCTCTCGTAGGACTAATCCTCGCAGCAACAGGAAAATCAGCACAATTTG

GGCTTCACCCGTGATTACCCTCCGCCATGGAGGGCCCCACACCAGTGTCTGCCCTACTTCACTCTAGCAC

AATAGTTGTTGCCGGAATTTTCTTACTTATCCGACTCCACCCCCTAATAGAAAACAACAAAACAGCCTTA

ACAATCTGTCTTTGCCTGGGAGCCCTAACCACATTATTTACAGCTGCTTGTGCCCTCACTCAAAACGACA

TTAAAAAAATTGTAGCTTTCTCAACATCAAGTCAGCTAGGTCTCATAATAGTTACAATTGGACTTAACCA

ACCACAACTAGCATTCCTACACATCTGTACCCACGCTTTCTTCAAAGCCATACTATTTCTATGTTCAGGA

TCAATTATTCATAGCCTAAACGACGAACAAGATATCCGAAAAATAGGGGGCCTACATAACCTAATACCAT

TTACCTCAACCTGCCTCACAATTGGCAGCTTAGCACTTACAGGCACTCCATTCCTAGCCGGCTTTTTCTC

CAAAGATGCCATCATTGAAGCCCTAAATACCTCACACCTAAACGCCTGAGCCCTAACCCTCACACTAATT

GCCACTTCATTTACCGCCGTATATAGCTTCCGAGTCGTATACTTCGTAACTATAGGAACACCACGATTCC

TACCCATATCCCCAATCAACGAAAACGACCCAGCAGTTATTAAACCCATCAAACGACTCGCCTGAGGAAG

CATTTTCGCAGGACTTCTCATCACCTCAAACTTTTTACCTACCAAAACACCCATCATAACTATACCAACA

ACCCTAAAAACAACCGCTCTGCTAGTTACAATTATAGGACTACTAATAGCCATAGGACTAACAGCCTTAA

CAAGTAAACAATTCAAAATCACTCCAACAATAACATCACACCATTTCTCCAACATACTAGGATATTTCCC

AGCAATCATACACCGATTTATTCCAAAGCTAAATTTAGTATTAGGACAATCAATTGCCACCCAACTAGTA

GACCAAACATGATTCGAAGCCGTAGGACCAAAAGGATCCACAGCCGCCCAACTAAAAATAGCCAAAATTA

CTAGTGATGCCCAACGAGGAATAATCAAAACATACTTAACCATTTTCTTCCTGACCCTAACCCTAGCAAC

CCTTTTAGCCACCCTTTAA

b.      Align the acquired sequences, check and trim the alignment using CLUSTALW

 

Then go to the  uniprot and paste the sequences to align

Then paste the sequences in fasta format and run alignment

 

Then download the alignment

 

 

c.       For Construct the phylogenetic genetic tree click on the Tree on the Uniprot

and download the result .

 

Primary Criteria for Constructing a Multiple Sequence Alignment (MSA):

1. Structural Homogeneity

2. Evolutionary Consistency

3. Functional Concordance

4. Sequence Alignment Precision

 

Key Applications of Multiple Sequence Alignment (MSA):

1. Phylogenetic Reconstructions

2. Pattern Recognition

3. Extrapolative Studies

4. Domain Mapping

5. Identification of DNA Regulatory Elements

6. Structural Predictions

7. PCR Primer Design