Homology is correspondence due to their shared ancestry. Homology assessment is a crucial step in phylogenetics analyses regardless of the type of data employed, since hypotheses of homology relate observations among taxa.
Every proposition of homology involves two stages which are associated with is generation and testing: the primary homology statement is conjectural based on similarity. The secondary level of homology is the outcome of a patter detecting analysis, the congruence test, and represents a test of the expectation that the observable match of similarities is potentially part of a retrievable regularity indicative of a general pattern (de Pinna, 1991).
When dealing with molecular data similarity guides primary homology -as in morphological characters- but there have been a tendency to believe that higher the similarity, the more likely that the sequences are homologous (Salemi and Vandamme, 2003; Patterson, 1988) where the fundamental homology statements are made at the level of the individual nucleotide bases. Conversely, the fundamental homology statement can be consider at the level of the sequence itself because the contiguous sequences are the homologous units that transform at prescribed costs among various states (Wheeler, 1999). Therefore Sequences themselves are treated as the fundamental units of homology and homology assessment is not consider a matter of aligning sequences and counting matches between them. Following “Direct Optimization’’ we can vary dynamically the primary homology hypotheses during tree search consequently the resulting hypotheses of homology are tested in conjunction with character congruence through parsimony (Wheeler, 2006). The testing of all characters against one another simultaneously constitutes the most severe test of congruence; In a phylogenetic context, the best alignment is the one that generates the most parsimonious tree when analyzed in conjunction with all relevant data (Philips, 2006).
The homology assessment have been shown to be influenced by the way we coding and the different interpretations of the criteria used to asses those statements demonstrating that the organismal variation is often conceptualized as characters and characters states in different ways (Scotland and Pennington, 2000). Even so, it is possible to have greater explicitness in the delimitation of morphological characters by detailed observation and the topologic criterion used, used in conjunction with special quality, and intermediate conditions of form (Rieppel and Kearney, 2002). In general, better guidelines concerning character conceptualization are required to help solving this.
Similarity and conjunction have proposed as tests for homology but only congruence serves to this respect. Similarity, as mentioned above, guides the assessment of the homology conjecture. Conjunction is an indicator of non-homology, but it is not specific about the pair wise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology (de Pinna, 1991).
Every proposition of homology involves two stages which are associated with is generation and testing: the primary homology statement is conjectural based on similarity. The secondary level of homology is the outcome of a patter detecting analysis, the congruence test, and represents a test of the expectation that the observable match of similarities is potentially part of a retrievable regularity indicative of a general pattern (de Pinna, 1991).
When dealing with molecular data similarity guides primary homology -as in morphological characters- but there have been a tendency to believe that higher the similarity, the more likely that the sequences are homologous (Salemi and Vandamme, 2003; Patterson, 1988) where the fundamental homology statements are made at the level of the individual nucleotide bases. Conversely, the fundamental homology statement can be consider at the level of the sequence itself because the contiguous sequences are the homologous units that transform at prescribed costs among various states (Wheeler, 1999). Therefore Sequences themselves are treated as the fundamental units of homology and homology assessment is not consider a matter of aligning sequences and counting matches between them. Following “Direct Optimization’’ we can vary dynamically the primary homology hypotheses during tree search consequently the resulting hypotheses of homology are tested in conjunction with character congruence through parsimony (Wheeler, 2006). The testing of all characters against one another simultaneously constitutes the most severe test of congruence; In a phylogenetic context, the best alignment is the one that generates the most parsimonious tree when analyzed in conjunction with all relevant data (Philips, 2006).
The homology assessment have been shown to be influenced by the way we coding and the different interpretations of the criteria used to asses those statements demonstrating that the organismal variation is often conceptualized as characters and characters states in different ways (Scotland and Pennington, 2000). Even so, it is possible to have greater explicitness in the delimitation of morphological characters by detailed observation and the topologic criterion used, used in conjunction with special quality, and intermediate conditions of form (Rieppel and Kearney, 2002). In general, better guidelines concerning character conceptualization are required to help solving this.
Similarity and conjunction have proposed as tests for homology but only congruence serves to this respect. Similarity, as mentioned above, guides the assessment of the homology conjecture. Conjunction is an indicator of non-homology, but it is not specific about the pair wise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology (de Pinna, 1991).
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