| A rankless monograph: The current
monongraph is conducted without regard to taxonomic ranks and is strictly phylogenetic
(i.e., evolutionary) in philosophy and practice. The traditional Linnean system
for taxonomy suffers from a lack of explicit ties to evolutionary processes. Consequently,
use of Linnean ranking threatens a suite of misleading conclusions. Some of the
flaws are that ranks across organisms are incomparable (in size and age at least)
and the entities named and ranks need not be monophyletic.
There have
been many recent and tremendous efforts to explain the shortcomings of the Linnean
system and suffice it to say that I am in accord with the fundamentals of those
efforts (see http://persoon.si.edu/sbs/references.htm).
However, many of the recent contributions to the advancement of taxonomy do not
criticize the rank "species," with one notable exception (Mishler,
1999). Indeed "species" needs careful scrutiny for the same reasons
as any other taxonomic rank. In short, all ranks, including species, are flawed
and are in this monograph, entirely rejected (except in the treatment of synonymy).
The
current treatment --or phylomonograph-- is to my knowledge the first attempt to
avoid rank and work solely from a well-developed database and its phylogenetic
manifestations. The vocabulary chosen to describe branches in the phylogeny of
Mitthyridium are: Clade (designates a monophyletic group that contains
lineages) and Lineage (a single branch in the present phylogeny).
A
phylomonograph: Phylogeny is critical to monography. Yet, monographers
have taken two diametrically opposed approaches when incorporating a phylogeny
into their monograph: one approach starts with the alpha taxonomy (building circumscriptions
around a type specimen and assigning names); the other starts with the phylogeny
and deals with the taxonomy later. To take the former approach by first circumscribing
"species" (or other taxonomic entities) on some premise, be it phenetic/morphological,
biological, or otherwise and to build phylogenies later introduces biases to the
diagnosis of OTU's. The latter approach avoids the biasing effect by disregarding
prior taxonomic delimitations and by taking a "bottom-up" approach to
monography using phylogeny (and the inherent principle of evolution) as the the
backbone of subsequent taxonomy. This website is a manifestation of the
phylogenetic monograph of the genus Mitthyridium (one of at least three clades
in the paleotropical moss family Calymperaceae) built from the "bottom-up".
I collected hundreds of specimens from the Paleotropics including all major areas
where Mitthyridium is known to occur (see range map). I settled on 140 of these
specimens, but could obtain full data complements for 98 (see
table). That data complement includes over 2000 characters from 3 separate
genes (of the nucleus and chloroplast) and morphology (see
the data). When deciding on the specimens for data extraction, I did not consider
previous taxonomy (in the cases where herbarium specimens were used) and did not
attempt to name any of the taxa before conducting thorough phylogenetic analyses.
However, I used the breadth of morphological variation in the group to direct
a random stratified sampling regime, so that I would maximize the likelihood of
sampling every distinct lineage in Mitthyridium. Decisions to name were
based on two criteria (1.) Monophyly and (2) Practical diagnosability. The first
required sufficient support to establish robustness (via decay and bootstrap);
the second is guided by the individual collector’s capacity to rapidly identify
the clade using gross morphology and anatomy. I analyzed the 98 specimens
or operational taxonomic units (cf. semaphoronts (Hennig, 1966)) and their full
data under both parsimony and maximum likelihood-based phylogenetic algorithms.
My objective was to reconstruct THE phylogeny of Mitthyridium so that I could
correctly delimit natural taxonomic entities; entities that are the product of
evolution. Of these 98 specimens, 18 were genetically and morphologically identical
and thus were removed from subsequent phylogenetic analyses. The remaining 80
were analyzed phylogenetically and the resulting phylogeny was used to direct
the taxonomy (Here is the 80 taxon TOTAL EVIDENCE phylogeny).
However, the variation among the genes sampled varies considerably: glyceraldehyde
3-phosphate dehyrdogenase is the fastest, rps4 second, and trnL is the slowest
evolving (see figure on genetic variation). Many taxa
that differ genetically in glyceraldehyde 3-phosphate dehyrdogenase have identical
rps4 and trnL squence. Those specimens that are identical in sequence, specifically
in rps4 sequence, are also very difficult to distinguish morphologically. A second
and important criterion to the one underlined above that I chose at the outset
of this phylogenetic monograph was that the named entities be diagnosable in the
field or by quick examination under the microscope (rather than diagnosable by
sequence alone). Given this criterion, I removed those taxa with identical rps4
sequences and newly analyzed the data under parsimony. The resulting phylogenies
did not differ from the larger 80 taxon phylogeny and thus corroborated the consistency
of the general relationships within Mitthyridium. The reconstruction of
evolving lineages and their relationships is quite distinct from the procedure
of assigning phylogenetic names to monophyletic groups. Thus, my decision to remove
these taxa does not preclude the evolutionary importance of the unique lineages
discovered with the gene, glyceraldehye 3-phosphate dehyrdogenase. Those lineages
are indeed real and conferred the ability to demonstrate that Mitthyridium is
young and currently under the process of very rapid radiation that is on par with
text-book radiations in angiosperms and mammals and the first ever reported for
a moss group. For more information on the Age, Rate and Pattern of Diversification
in Mitthyridium (see Wall, Chapter 2). This website allows a researcher
to navigate through the 80 taxon phylogeny from the phylogeny of named and diagnosable
lineages to their internal "population" phylogenetic structure. This
is really the inverse procedure from the actual method by which I assigned names
(as described in text below) and thus a look at the methodological sequence behind
this phylogenetic monograph is provided in section 3: Phylo-monography Methods. | 
