Editing Phylogenetic tree (section)

== Limitations of phylogenetic analysis ==
{{More citations needed section|date=October 2012}}

Although phylogenetic trees produced on the basis of sequenced [[gene]]s or [[genome|genomic]] data in different species can provide evolutionary insight, these analyses have important limitations. Most importantly, the trees that they generate are not necessarily correct – they do not necessarily accurately represent the evolutionary history of the included taxa. As with any scientific result, they are subject to [[Falsifiability|falsification]] by further study (e.g., gathering of additional data, analyzing the existing data with improved methods). The data on which they are based may be [[signal noise|noisy]];<ref name=Townsend_2012>{{cite journal |vauthors=Townsend JP, Su Z, Tekle Y |title=Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny |journal=Genetics |volume=61 |issue=5 |pages=835–849 |year=2012 |doi=10.1093/sysbio/sys036 |pmid=22389443 |doi-access= }}</ref> the analysis can be confounded by [[genetic recombination]],<ref name=Arenas_2010>{{cite journal |vauthors=Arenas M, Posada D |title=The effect of recombination on the reconstruction of ancestral sequences |journal=Genetics |volume=184 |issue=4 |pages=1133–1139 |year=2010 |doi=10.1534/genetics.109.113423 |pmid=20124027 |pmc=2865913 }}</ref> [[horizontal gene transfer]],<ref name=Woese_2002>{{cite journal |author=Woese C |title=On the evolution of cells |journal=Proc Natl Acad Sci USA |volume=99 |issue=13 |pages=8742–7 |year=2002 |pmid=12077305 |doi=10.1073/pnas.132266999 |pmc=124369|bibcode = 2002PNAS...99.8742W |doi-access=free }}</ref> [[Hybrid (biology)|hybrid]]isation between species that were not nearest neighbors on the tree before hybridisation takes place, and [[conserved sequence]]s.

Also, there are problems in basing an analysis on a single type of character, such as a single [[gene]] or [[protein]] or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This is most true of genetic material that is subject to lateral gene transfer and [[Genetic recombination|recombination]], where different [[haplotype]] blocks can have different histories. In these types of analysis, the output tree of a phylogenetic analysis of a single gene is an estimate of the gene's phylogeny (i.e. a gene tree) and not the phylogeny of the [[taxa]] (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use a combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes),<ref>{{cite journal |doi=10.1016/j.gene.2019.143967 |pmid=31279710 |title=Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group |journal=Gene |volume=713 |pages=143967 |year=2019 |author1=Parhi, J. |author2=Tripathy, P.S. |author3=Priyadarshi, H. |author4=Mandal, S.C. |author5=Pandey, P.K. |s2cid=195828782 }}</ref> or genes that would be expected to evolve under different selective regimes, so that [[homoplasy]] (false [[homology (biology)|homology]]) would be unlikely to result from natural selection.

When extinct species are included as [[leaf node|terminal node]]s in an analysis (rather than, for example, to constrain internal nodes), they are considered not to represent direct ancestors of any extant species. Extinct species do not typically contain high-quality [[ancient DNA|DNA]].

The range of useful DNA materials has expanded with advances in extraction and sequencing technologies. Development of technologies able to infer sequences from smaller fragments, or from spatial patterns of DNA degradation products, would further expand the range of DNA considered useful.

Phylogenetic trees can also be inferred from a range of other data types, including morphology, the presence or absence of particular types of genes, insertion and deletion events – and any other observation thought to contain an evolutionary signal.

[[Phylogenetic network]]s are used when bifurcating trees are not suitable, due to these complications which suggest a more reticulate evolutionary history of the organisms sampled.