More problems part duex - (subtitled _ HEY HARSHMAN this time respond

[Quark E]

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774700/
BMC Evol Biol. 2009; 9: 259.
Published online 2009 October 27. doi:
10.1186/1471-2148-9-259PMCID:
PMC2774700

Estimating the phylogeny and divergence times of primates
using a supermatrix approach

Within Primates, the relationships within and between various
families
and genera continue to cause debate, despite the numerous molecular
estimates of the phylogeny that have been presented over the past 10
to 15 years

One of the foremost debates in primate systematics has long concerned
the position of tarsiers. Traditionally viewed as being more closely
associated with lemurs and lorises, tarsiers were placed within a
suborder Prosimii, under the gradistic view of primate taxonomy [8].
Modern taxonomic schemes generally recognize their closer
affiliation
with monkeys and apes, grouping them with Haplorrhini [9]. The
majority of molecular evidence supports the latter grouping
[4,10-13],
although a large number of molecular studies still provide support
for
the Prosimii concept [14-18]. The question is succinctly reviewed by
Yoder [19] and is further examined by Eizirik et al. [18]. There is
now general agreement on the higher-level relationships within the
two
suborders [20], with Strepsirrhini comprising Lorisiformes (galagos
and lorises) and the sister-pairing of the monophyletic Lemuriformes
(lemurs) and Chiromyiformes (the aye-aye), and with Haplorrhini
consisting of Platyrrhini (New World monkeys) and Catarrhini (apes
and
Old World monkeys). Within these groups, however, there are numerous
disagreements over interfamilial relationships. Molecular evidence
has
sometimes favored Cheirogaleidae as sister group to Lemuridae,
although current evidence suggests that the four lemuriform families
(Lemuridae, Cheirogaleidae, Lepilemuridae and Indriidae) represent a
four-way split, which may be real [4,21,22]. Within Haplorrhini,
controversial taxonomic
issues remain. The paraphyly of an all-encompassing Cebidae with
respect to the tamarins and marmosets is widely recognized now
[9,23,24], but the branching order of the major lineages is still
questionable. Among the Old World monkeys, particularly within
Colobinae, intergeneric relationships are still unclear.

While there may be consensus regarding relationships across the main
primate clades, there is continued disagreement at the species, genus
and even family levels. One of the primary challenges in primate
molecular phylogenetics remains the issue that different markers
support conflicting trees

[John Harshman]

On 2/4/13 6:30 PM, Quark E wrote:

Sorry, I thought your position was that I was stupid and should shut up.

OK, I'm commenting. What's the problem here? You seem to think that if
science progresses, that shows that we know nothing. There are
unresolved questions. Those questions are decreasing in number. That's a
good thing.

Now, regarding the conflicting trees from different markers, there is a
simple and obvious biological explanation, called lineage sorting. Every
sequence difference begins as a mutation in a single individual. When a
mutation arises, it produces a polymorphism in the population (meaning
that different individuals have different variants). The fate of every
polymorphism is to become fixed for one variant, with all other variants
becoming lost from the population (unless there is balancing selection,
which we will ignore for now). Fixation, however, can take quite a long
time, sometimes millions of years. If speciation happens during that
time, both descendant lineages may carry the polymorphism, and may
eventually fix different alleles. If several speciations happen during
that time, fixations may sort out differently from the species history.
And that's called lineage sorting. Because of it, the true phylogeny of
some genes may not match the true phylogeny of the species. For example,
around 15% of genes put humans with gorillas, and another 15% put chimps
with gorillas. The other 70% put humans with gorillas, the true
phylogeny. The reason is that the split between chimps and humans came
not long after the split between the chimp/human ancestor and gorillas,
and some genes that were polymorphic in the first speciation had still
not settled down by the second. There is even a small percentage of
genes (about 1.5% if I remember) that make humans and orangutans closest
relatives. It can take a really long time for all polymorphisms to
settle out.

But this isn't a big problem if you consider a lot of data.

[Amy Guarino]

On Feb 4, 10:00�pm, John Harshman <jharsh...@pacbell.net> wrote:
> For example,
> around 15% of genes put humans with gorillas, and another 15% put chimps
> with gorillas. The other 70% put humans with gorillas, the true
> phylogeny.

Good explanation, thanks. But I think there may be an oops in there.

[Quark E]

Whoops.

Last should read:

"The other 70% put humans with chimps, the true
phylogeny."

Good catch.

[Quark E]

> OK, I'm commenting. What's the problem here? There are

> unresolved questions. Those questions are decreasing in number.

No they are not, they are increasing, IDIOT.

> Now, regarding the conflicting trees from different markers, there is a
> simple and obvious biological explanation, called lineage sorting.

Wow a word, however that does not accoutn for all the family grouping
problems.

>
> But this isn't a big problem if you consider a lot of data.- Hide quoted text -

They have a lot of data, and it does not match what evolutionary
theory claims how it occurred, which is why they are
trying to account for it.

Some even posited a 4 way split at the same time.

[John Harshman]

Oops indeed. But you know what I meant.

[I am not a chemist]

You have a problem with amy posting here?

[John Harshman]

No, but that wasn't Amy. It was Greg. I don't have a problem with Greg
either.

[Quark E]

Yes it was.

[John Harshman]

This could go on for quite a while.

[Quark E]

> This could go on for quite a while.- Hide quoted text -

doubtful:

http://groups.google.com/group/alt.drugs.psychedelics/msg/706dcbcb450406b6?hl=en&dmode=source

[John Harshman]

?