|I'm not sure what type of paper you are doing so these may or may not be helpful to you, but I did a review paper on morphological and behavioral changes in domestic dogs for a class last year, below are some of the references I found on the topic. Some of these are more about behavior though as my paper was about both.
You also might find this link interesting, it shows historical photos of various breeds: http://www.messybeast.com/history/history.htm
The paper "Molecular origins of rapid and continuous morphological evolution" has some interesting information on changes in skull structure of some breeds over time, and associated genetic factors (mostly involving tandem repeats). If you want more references for this I also did a paper on tandem repeats and canine skull morphology for another class a few years ago and I can search up the references I found then if you're interested. I know that same paper was on that list too.
Akey JM, Ruhe AL, Akey DT, Wong AK, Connelly CF, Madeoy J, Nicholas TJ, Neff MW (2010) Tracking footprints of artificial selection in the dog genome. Proc Natl Acad Sci USA 107:1160-1165.
Case, L (2008) Perspectives on domestication: the history of our relationship with man's best friend. J Anim Sci. Nov;86(11):3245-51.
Cruz F, Vilà C, Webster MT (2008) The legacy of domestication:accumulation of deleterious mutations in the dog genome. Mol Biol Evol 2008;25:2331–6.
Drake AG, Klingenberg CP (2008) The pace of morphological change: historical transformation of skull shape in St Bernard dogs. Proc Biol Sci. 275(1630): 71-6.
Fondon JW, Garner HR (2004) Molecular origins of rapid and continuous morphological evolution. Proc Natl Acad Sci USA. 101(52): 18058–18063.
Fondon JW, Garner HR (2007) Detection of length-dependent effects of tandem repeat alleles by 3-D geometric decomposition of craniofacial variation. Dev Genes Evol. 217(1): 79-85.
Gácsi M, Gyoöri B, Virányi Z, Kubinyi E,Range F, Belényi B, Miklósi Á (2009)
Explaining dog-wolf differences in utilizing human pointing gestures: selection
for synergistic shifts in the development of some social skills. PloS ONE. 4: e6584.
Haworth KE, Islam I, Breen Putt MW, Makrinou Binns EM, Hopkinson D, Edwards Y (2001) Canine TCOF1; cloning, chromosome assignment and genetic analysis in dogs with different head types. Mamm Genome. 12(8): 622-629.
Haworth KE, Healy C, McGonnell IM, Binns M, Sharpe PT (2007) Characterisation of the genomic canine Fgf8 locus and screen for genetic variants in 4 dogs with different face types. DNA Seq. 18(3): 209-219.
Honeycutt RL (2010) Unraveling the mysteries of dog evolution. BMC Biol. Mar 9;8:20.
Savolainen P, Zhang Y, Luo J, Lundeberg J, and Leitner T (2002) Genetic Evidence for an East Asian Origin of Domestic Dogs. Science 298:1610–1613.
Sears KE, Goswami A, Flynn BJ, Niswandera LA, (2007) The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in Carnivora. Evol Dev. 9(6): 555-565.
vonHoldt BMJ, Pollinger P, Lohmueller KE, Han EJ, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, ones PG, Qian ZW, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898-U109.
Edited by author Tue Apr 10, '12 2:04am PST