Avaliaa o 1 PEMARF

Name: Caio Gueratto Coelho da Silva

Target-audience: Biology students capable of interpreting cladograms

Title: Historical reconstruction and its biological uses: a tool not an answer.

Introduction

Biology, at its core, is a historical research area (Mayr, 2007). Since Darwins time, naturalists cared
about the origin of traits in organisms. In fact, the canonical book On the origin of species is a proposition of
a theory that explains historical origins of characteristics in living beings, and it became the unifier theory
behind all biological areas according to Dobzhansky: the theory of Evolution through Natural Selection (Mayr,
2007).
Since the middle of the last century, biologists use historical reconstructions through graphical
representations called the phylogenetic trees. A phylogenetic tree, according to Baum & Offner (2008), is a
depiction of the inferred evolutionary relationships among a set of species (or other taxa). Recently, the trees
spread through all biological areas and researchers use them in many contexts, to support hypothesis coming
from different sources (Baum et al., 2005).
Although biologists widely use phylogenetic trees, probably most of them think about these trees as a
final goal achieved, as the answer to particular scientific questions. Here, I will explain three of the contexts in
which scientists use the historical reconstructions through phylogenetic trees, making clear that they are not
the answer, but an evidence to support hypothesis.

Development

Historical reconstruction helps us to understand the origin of

particular taxa (Baum et al., 2005). An interesting case is the
unraveling of the HIV virus origin (Gao et al., 1994). In this research,
after observing that the HIV-2 virus has similar structure to the SIV
virus (Simian Immunodeficiency Virus) (Hirsch et al., 1989), Gao et
al. sequenced the HIV and SIV genes, running a phylogenetic analysis
afterwards. The result is in Figure 01, indicating that the HIV-2 virus
clusters closely with SIV virus. So, the authors used the phylogenetic
tree as an evidence to support that the human virus has a simian
origin.
A different biological area that extensively uses historical
reconstruction through trees is biogeography. In this area, people
infer patterns of taxa diversification related with geological events
that happened in the past (Cox et al., 2016). In this approach,
researchers use areas as terminals instead of species and the
presence/absence of a specific taxon in those areas as the characters.
With this, is possible to create area cladograms inferring which
geological events caused the divergence of taxa in the past as well as
endemism areas for those particular taxa (Cox et al., 2016).
Figure 1 - HIV-2 (bold terminals) and SIV
phylogenies. Taken from Gao et al, 1994.
 A good biogeographical study example is
the harvestmen. They are so due to its low
dispersal capacity and their sensibility to
deforestation and pollution (Bragagnolo et al.,
2015). So, each species is restricted to a small
endemic area. A work on the genus Promitobates
from the coastal Sa o Paulo e Parana states
revealed that each analyzed species has its own
restricted distribution area as small as 100 km
(Fig. 02). Moreover, some geological events
explained perfectly the species divergence based
on molecular dating of the splitting events
(Bragagnolo et al., 2015). The authors created the
hypothesis explaining the diversification pattern
thanks to the possibility of reconstructing
historical events using morphological and
molecular characters.
The last and most important example of
phylogenetic tree usage is in Taxonomy. Since
Aristotle, there has always been a human need for
classification. Naturalists classified everything in
the natural world, from rocks to animals (Stevens,
2003). Linnaeus was the first to create a
standardized nomenclature for every living being,
using a binomial system. After him, every
naturalist started classifying based on this system.
However, the classification was quite arbitrary and
collector-dependent. In other words, each
collector could classify an organism in a different
way (Stevens, 2003). It was only in the 1950s that
scientists started building a philosophical and
methodological basis for taxonomy. After this formalization period, taxonomy adopted the philosophy that
Figure 2 - Part of the phylogeographic tree obtained in classification of living things should reflect their
Bragagnolo et al. (2015). BE, Bertioga; BO, Boracia; CB, Carlos evolution. With this rationale, building
Botelho; IB, Ilhabela; IP, Iper; MG, Mogi das Cruzes; PA, Paraty; phylogenetic trees became an important part of
UB, Ubatuba. the taxonomic process. This is because the
relationships hypothesis among taxa would help scientists to decide how to classify organisms. The union of
both Taxonomy and Phylogenetics received the name of Systematics (Stevens, 2003).
An example of how phylogenetic trees help scientists to organize lifes diversity is the gymnosperm
classification. Until the end of last century, Gymnosperma was considered a natural grouping, containing all
tree species that produce seeds without ovary enclosure. During 1980s, the idea that this was not a natural
grouping became popular and works supporting this hypothesis arouse. Today, most of the phylogenetic trees
generated separate the four major gymnosperm groups (Pinaceae, Gnetales, Cycads and other Conifers), as
we can see in Figure 03. To consider Gymnosperma a natural clade, the angiosperms must be included.
Therefore, the name Gymnosperma is still used as tradition, but it is not considered a natural grouping
 anymore (Burleigh & Mathews, 2004). And
these conclusions were based on evidences
provided by the historical reconstruction
coming from phylogenetic trees.
Conclusions

It is clear with these examples that any

biological area uses historical reconstruction
through phylogenetic trees. Moreover, these
trees are of great importance in biological
research and enrich arguments supporting
hypothesis. I hope that it became clear as well
that trees are a support for external
hypothesis. We are users of a method of
historical reconstruction. The only
researchers that have phylogenetic trees as
their final goal are the ones who develop new
methods, algorithms, optimizations, etc. of
phylogenetic inference. It is important to
make this clear once a lot of systematic works
only show the trees and do not extract any
conclusion of that, as if it was the answer they
wanted to achieve. If systematists keep in
mind that trees are not their final goal, but a
tool to support another hypothesis,
discussions regarding taxonomic and
Figure 3 - Seed plants molecular phylogeny. Taken from Burleigh & biogeographic matters tend to improve.
Mathews (2004).

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