CRANFILL, RAYMOND. Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA 94720-2465. - Phylogenetic utility of plastid ribosomal protein S4 (rps4) in land plants.
Nadot and colleagues (1994) were first to demonstrate that nucleotide
sequences of chloroplast ribosomal protein S4 (rps) were
phylogenetcally informative. In spite of early promise, rps4
has been largely ignored since. Comprehensive analysis of sequences
drawn from over 200 representatives of all extant lineages of
embryophytes demonstrates that this neglect is unwarranted. For a
plastid gene, rps4 exhibits a remarkable degree of nucleotide
substitution rate heterogeneity. The gene can be divided into five
regions based on nucleotide substitution rate. Slowly evolving first
(5' end), last (3' end) and middle regions exhibit substitution rates
similar to rbcL, and may be functionally constrained. The two
regions flanking either side of the middle region evolve at a much
faster rate. Furthermore, these regions are prone to insertion and
deletion, with some insertions exceeding 140 bp’s. Both insertions
and deletions can be phylogenetically informative, either individually
or in groups and sometimes define large clades with long evolutionary
histories (e.g., euphyllophytes, moniliforms (ferns + horsetails),
polypodiaceous ferns, and yew-conifers). Further phylogenetic
information can be culled from the spacer region immediately adjacent
to the 3' end of the gene. This region is highly variable in length
with different size classes characteristic of different major clades
of land plants. The spacers of the three “bryophyte” clades,
lycopsids and most seed plants are short (generally <50 bp), whereas
those of the moniliforms are considerably longer (generally >300 bp).
The spacer region evolves at a rate similar to ITS in ferns and
angiosperms and is generally useful for detecting radiations occurring
during the Tertiary (i.e., within “families” of tracheophytes).
Although rps4 is significantly shorter (and thus provides fewer
characters for analysis) than phylogenetically comparable plastid
genes, such as rbcL or atpB, the phylogenetic resolving
power of rps4 is often greater, providing both fuller and more
well supported resolution of radiations occurring from the Devonian to
the early Tertiary.
Key words: chloroplast, ferns, land plants, molecular systematics, phylogeny, rps4