On
the different concepts of homology
Homology
is a central concept in biology, and it refers to the correspondence
of morphological or molecular attributes due to common ancestry. It
is generally useful to sort and evaluate relationships among
organisms (Pinna 1991), depending on the field of study (Brigandt
2003). In comparative biology, it allows for effective
descriptions across species and unified morphological knowledge,
which provides comparisons that could be finely used for
classifications. In other branches of biology such as evolutionary
biology and phylogenetic systematics, it serves to explain the
adaptive modifications of characters and to characterize taxa,
respectively (Brigandt 2003). Given its diverse extents, there is
also a set of criteria to infer it, among them, the similarity in
molecular, structural detail and histology, the connectivity to
adjacent structures, correspondence of the developmental origin
(Patterson 1982; Patterson 1988) , and step-counting.
Regarding
the concepts of homology, (De Pinna 1991) made a distinction
between “primary” and “secondary” homology, treating the
first as an untested supposition that two parts are equivalent by
inheritance -definition that (Agnarsson & Coddington 2007)
pondered as the prior of a logical analysis or the background
knowledge that is not concerned to morphological data- , and the
second as the hypothesis that has passed the congruence test and thus
can be treated as a synapomorphy. A large discussion has been taken
upon this latter concept, as for authors like (De Queiroz 1985) it
does not equal homology, for he argued that homology applies to
instantaneous morphologies, while synapomorphy applies to ontogenetic
transformations that characterize monophyletic groups. On the other
hand, like (Eldredge, N, Cracraft 1980), like (De Pinna 1991),
considered these concepts as a single one. However, (Patterson 1982)
and (Rieppel 1980) assigned a certain hierarchical organization of
homologies, distinguishing between taxic (the feature of a
monophyletic group) and transformational (the change of a structure
into another) homology. Taking this into context, the radula of
molluscs or the radular teeth constitute a taxic homology, and the
classic example of the incus and the quadrate are a transformational
homology (Zelditch M.L., Fink W.L. 1995).
Patterson's
Test
A
main question that can be asked is how do we recognize a character as
homologous? One of the most outstanding processes was proposed by
Patterson (Patterson 1982), and it is an evaluation that
compresses three tests that a character needs to pass to be
considered as an homology in a phylogenetic analysis. These tests
are: similarity, which refers to the resemblance between structures
that could share a common ancestor and thus it is a first “candidate”
of homology; conjunction which evaluates that two different states of
a character can not be present within the same organism (angels are
definitely not an useful species to be included in an analysis using
this test); and congruence that is the final test that shows whether
a character most probably represents an homology.
Choosing
criteria of evaluation
A
question that arises when it comes to the evaluation of homology is
what test or what methodology to use. In theory, parsimony or other
criteria, could guide choice among competing homology hypotheses
before assessing their fit to a tree (Agnarsson & Coddington
2007). Testing the fit of data to trees using various optimality
criteria has been widely studied. However, the evaluation of the
initial criteria of similarity in the formation of homology
hypotheses, such as whether two structures should be considered
homologous, remains a key point of attention. The authors proposed an
index to make this initial assessment, weighting topology, function
and similarity equally, so that multiple points of comparison within
each criterion allow them to be averaged or down-weighted. Thence it
took each criterion into a comparable unit.
Although
morphological data present several points of special attention
(Patterson 1982), molecular data is a powerful source that
definitely has to be carefully analyzed. Mainly because it passes
through a test of similarity that could render wrong assumptions and
results. Taking into account that homologous sequences can be
orthologous -as divergent from a common ancestor- or paralogous -as
product of gene duplication-, as well as other mechanisms or
variations -like xenology- (Fitch 2000) we can not be sure that a
result from a similarity test will not come up as a convergence.
Another
issue to consider is the character optimization and analysis, which
basically have two different arguments: one that supports sequence
alignment as a crucial step (Simmons and Freudenstein, 2003), and
another that has proved that aligning base positions is not that
fundamental and the optimization can be directly done (Wheeler 2001;
Wheeler 2006). Wheeler introduced the concept of dynamic homology,
which states that nucleotide homologies are topology specific and can
be identified by optimization processes that determine nucleotide
correspondence and transformation via a specific criterion. This
method does not rely on a prior alignment, but analyses the
variation, rendering likely cladograms.
Overall,
it is evident that homology is a wide concept and its assessment is
rather complex. There are several types of potential information and
methods to analyze it properly. However, it is always necessary to
bring the evolutionary histology and biology principles into the
discussion, so one could be a little more positive about the obtained
phylogenies, which at the end, are hypotheses that should constantly
be evaluated until the phylogenetic relationships within a group are
considered to be clear. As (Patterson 1982) stated, homology can
be seen as a probability, as a result of any of the three tests,
interpreting them is always a delicate task assigned to biologists.
References
Agnarsson,
I. & Coddington, J.A., 2007. Cladistics Quantitative tests of
primary homology. , 23, pp.1–11.
Brigandt,
I., 2003. Homology in Comparative , Molecular , and Evolutionary
Developmental Biology : The Radiation of a Concept. Journal
of Experimental Zoology, 299, pp.9–17.
Eldredge,
N, Cracraft, J., 1980. Phylogenetic Patterns and the
Evolutionary Process,
Fitch,
W.M., 2000. Homology a personal view on some of the
problems. Homology, 16(5), pp.227–231.
Patterson,
C., 1988. Homology in Classical and Molecular Biology. Molecular
biology and evolution, 5(6), pp.603–625.
Patterson,
C., 1982. Morphological characters and homology.
Pinna,
M.C.C., 1991. Concepts and Tests of Homology in the Cladistic
Paradigm. Cladistics, 7(4), pp.367–394. Available at:
http://doi.wiley.com/10.1111/j.1096-0031.1991.tb00045.x.
De
Pinna, M.C.C., 1991. Concepts and Tests of Homology in the Cladistic
Paradigm. Cladistics, 7(4), pp.367–394. Available at:
http://doi.wiley.com/10.1111/j.1096-0031.1991.tb00045.x.
De
Queiroz, K., 1985. The ontogenetic method for determining character
polarity and its relevance to phylogenetic systematics. Syst.
Zool., 34, pp.280–299.
Rieppel,
O., 1980. Homology, a deductive concept? Journal of
Zoological Systematics and Evolutionary Research, 18(4),
pp.315–319.
Wheeler,
W., 2001. Homology and the Optimization of DNA Sequence
Data. Cladistics, 17(1), pp.S3–S11. Available at:
http://doi.wiley.com/10.1006/clad.2000.0154 [Accessed October 30,
2014].
Wheeler,
W.C., 2006. Cladistics Dynamic homology and the likelihood criterion.
, 22, pp.157–170.
Zelditch
M.L., Fink W.L., S.D.L., 1995. Morphometrics, Homology, and
Phylogenetics: Quantified Characters as Synapomorphies. Syst
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