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However, further phylogenetic analyses are needed to better understand the proposed duplication event.
In Arabidopsis, SROs were always present in pairs consistent with a previously proposed duplication event ([ 2, 34], Plant Genome Duplication Database http://chibba.agtec.uga.edu/duplication/index/home.
Analysis of the P. luminescens genome described here and by others shows essential outer membrane protein genes ompF, ompA and a proposed duplication of ompF.
In view of the large number of non- synonymous mutations (changes in amino acids), i.e., 59% identity in amino acid composition between P. luminescens ompF and plu1752, the proposed duplication may have been an ancient one.
The proposed duplication event leading to the emergence of two FAK family members is in agreement with chordate genome evolution in which one or several duplications occurred after the separation of craniates and cephalochordates, before the emergence of teleosts [ 64, 65].
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Alternatively, the proposed duplication-divergence model is more biologically motivated.
The first proposes duplication of the entire 6p25 locus followed by a number of single gene duplications at 18q21 [ 14].
The second proposes duplication of a single gene from 18q21 to 6p25, followed by successive duplications at both loci to derive the modern complement [ 15].
Two challenges to our hypotheses that a large-scale duplication event occurred early in the divergence of spiders and was important to the evolution of the silk glands is the fact that some gene families, including those directly involved with silk-production, like the spidroins, contain multiple duplication events and that some postdate the proposed ancient duplication event.
We argue that as many species as possible, with divergencies close in time to the proposed chromosome duplication events, should be included in the analyses to be able to date duplications and to reveal fluctuations of evolutionary rates among gene duplicates and across lineages.
Eight gene families had complications that precluded analysis (such as short sequence length or variable number of repeated domains) and another eight families did not support block duplications (because the paralogs in these families seem to have originated in another time window than the proposed genome duplication events).
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