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Re: primers


Thanks for the primers on cladistics - I am sure it will be very useful.

As a few other participants have observed, my question regarding dogs was in 
relation to dinosaur cladistics, so one would have to
exclude DNA studies as these are not available for non avian dinosaurs.

----- Original Message ----- 
From: "Jaime A. Headden" <qilongia@yahoo.com>
To: <dinosaur@usc.edu>
Cc: <john.bass@ntlworld.com>
Sent: Wednesday, December 01, 2004 3:11 AM
Subject: Re: primers

> John Hunt (john.bass@ntlworld.com) wrote:
> <I think I can see why cladistics and traditional systematics have a
> problem.  I recent thread made reference to dogs and I believe all
> domestic dogs are considered to be the same species as they can
> interbreed.  Would a cladistic analysis of domestic dogs make Great Danes
> and Jack Russels monophylitic?>
>   Certainly, several studies have sponsored a monophyletic relationship
> between all domestic canines, and a sister-group relationship with wolves
> (Canis spp.) in which it is offered that wolves and dogs are subspecies of
> a single species (Canis lupus subspp.) which are then further divided by
> varieties and races, then breeds. Other, more recent studies, show that
> modern dog diversity has arisen from several domestication events from
> similar "wolf" species, suggesting that instead of a single speciation act
> (brought on by domestication), there may have been upwards of three, or
> more. These analyses were all wrought cladistically, using various DNA and
> mtDNA sequences.
>   References:
>   Chen Y.-j.; Zhang Y-p.; Zou X.-m.; Dong F.-y.; & Wang J.-j. 2000.
>    [Molecular phylogeny of canidae using mitochondrial cytochrome b DNA
>    sequences] _Yi Chuan Xue Bao_ 27 (1): 7-11. [in Chinese]
>   Abstract:
>   "372 bp mitochondrial cytochrome b DNA of blue fox, red fox, raccoon
>    dog, and wolf were sequenced. Combined with the DNA fragments of dog,
>    simien fox, and African wild dog, sequences were aligned and analyzed.
>    There are 113 nucleotide sites substituted (30%). Molecular phylo-
>    genetic tree constructed by NJ method suggests that African wild dog is
>    the earliest divergent. Wolf, dog, and simien fox which belong to genus
>    Canis are combined into one branch which diverged earlier than raccoon
>    dog, red fox and blue fox. Red fox is more related to blue fox than the
>    other animals. The above result is in consistent with that of
>    morphology."
>   Wayne, R. K. 1993. Molecular evolution of the dog family. _Trends in
>    Genetics_ 9: 218-224.
>   Abstract:
>   "Molecular genetic tools have been used to dissect the evolutionary
>    relationships of the dog-like carnivores, revealing their place in the
>    order Carnivora, the relationships of species within the family Cani-
>    dae, and the genetic exchange that occurs among conspecific popula-
>    tions. High rates of gene flow among populations within some species,
>    such as the coyote and gray wolf, have suppressed genetic divergence,
>    and where these species hybridize, large hybrid zones have been formed.
>    In fact, the phenotype of the endangered American red wolf may be
>    strongly influenced by hybridization with coyotes and gray wolves.
>    Hybridization and habitat fragmentation greatly complicate plans to
>    conserve the genetic diversity of wild canids."
>   link: http://www.idir.net/%7Ewolf2dog/wayne2.htm
>   Savolainen, P.; Zhang Y.-p.; Luo J.; Lundeberg, J.; & Leitner, T. 2002.
>    Genetic Evidence for an East Asian Origin of Domestic Dogs. _Science_
>    298 [iss. 5598]: 1610-1613.
>   Abstract:
>   "The origin of the domestic dog from wolves has been established, but
>    the number of founding events, as well as where and when these oc-
>    curred, is not known. To address these questions, we examined the mito-
>    chondrial DNA (mtDNA) sequence variation among 654 domestic dogs re-
>    presenting all major dog populations worldwide. Although our data indi-
>    cate several maternal origins from wolf, >95% of all sequences belonged
>    to three phylogenetic groups universally represented at similar fre-
>    quencies, suggesting a common origin from a single gene pool for all
>    dog populations. A larger genetic variation in East Asia than in other
>    regions and the pattern of phylogeographic variation suggest an East
>    Asian origin for the domestic dog, ~15,000 years ago."
>   link: http://www.sciencemag.org/cgi/content/full/298/5598/1610
>   Vilà, C.; Savolainen, P.; Maldonado, J. E.; Amorim, I. R.; Rice, J. E.;
>    Honeycutt, R. L.; Crandall, K. A.; Lundeberg, J.; & Wayne, R. K. 1997.
>    Multiple and ancient origins of the domestic dog. _Science_ 276 [iss.
>    5319]: 1687-1689.
>   Abstract:
>   "Mitochondrial DNA control region sequences were analyzed from 162
>    wolves at 27 localities worldwide and from 140 domestic dogs repre-
>    senting 67 breeds. Sequences from both dogs and wolves showed consid-
>    erable diversity and supported the hypothesis that wolves were the an-
>    cestors of dogs. Most dog sequences belonged to a divergent monophyle-
>    tic clade sharing no sequences with wolves. The sequence divergence
>    within this clade suggested that dogs originated more than 100,000
>    years before the present. Associations of dog haplotypes with other
>    wolf lineages indicated episodes of admixture between wolves and dogs.
>    Repeated genetic exchange between dog and wolf populations may have
>    been an important source of variation for artificial selection."
>   link: http://www.sciencemag.org/cgi/content/full/276/5319/1687
>   In nearly all these analyses, the coyote was the outgroup, but you may
> notices that some used "dog" as a single specifier, rather than selecting
> from breeds and "races" of dog. Some incompatibility issues with some dogs
> may have a lot to do with relative size of breeds attempting to produce
> viable offspring, since one tiny and one large parent will produce two
> competing growth regimes that may come in conflict, restricting
> development of an embryo. Wayne also showed that the coyote may also be
> paraphyletic with regards to wolves and dogs, as much as Savolainen et al.
> and Vilà et al. argue the same is true for domestic dogs with respect to
> wolves alone. There may not be that much species delineation in play,
> despite the high diversity of physical features. Much of this can be
> accounted for by minor forms of gigantism and dwarfism in several species,
> selection favored by breeders (which produces wierd cats, pigeons, etc.,
> in addition to dogs, because of the desire to have certain abnormal babies
> produce more such abnormal babies), and so on and so forth.
>   Anways, a cladistic primer is online at:
> http://www.ucmp.berkeley.edu/clad/clad1.html, and you can check out _the
> Compleat Cladist_  by Leonard Krisktalka at
> http://www.amnh.org/learn/pd/fish_2/pdf/compleat_cladist.pdf, if you would
> like to know more. These are, btw, based more on molecular than
> morphological studies, and most morphological studies use smaller datasets
> than molecular does, as a whole, with regards to the same sampled group of
> species/taxa.
>   Cheers,
> =====
> Jaime A. Headden
>   Little steps are often the hardest to take.  We are too used to making 
> leaps in the face of adversity, that a simple skip is so
hard to do.  We should all learn to walk soft, walk small, see the world around 
us rather than zoom by it.
> "Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)
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