An example of a haplotype network, used to show relatedness between populations based on shared haplotypes. In the case of haplotype convergence between populations, one might conclude from the haplotype network that these populations are more closely related than they are in reality. 
English: Title: Bulletin - Southern California Academy of Sciences Identifier: bulletinsouth11032011sout (find matches) Year: 1902 (1900s) Authors: Southern California Academy of Sciences Subjects: Science Publisher: Los Angeles : Southern California Academy of Sciences Contributing Library: Smithsonian Libraries Digitizing Sponsor: Biodiversity Heritage Library View Book Page: Book Viewer About This Book: Catalog Entry View All Images: All Images From Book Click here to view book online to see this illustration in context in a browseable online version of this book. Text Appearing Before Image: 144 SOUTHERN CALIFORNIA ACADEMY OF SCIENCES mu nzj Half Moon Bay Santa Barbara Los Angeles Oceanside Harbor Agua Hedionda San Dieguito Mission Bay San Diego San Diego Bay Tijuana Estuary Ensenada/Todos Santos Punta Banda Bahia Asuncion Bahia Magdelena Text Appearing After Image: Fig. 2. Paralichthys californicus. Statistical parsimony network for 375 cytochrome b sequences. Small squares specify missing haplotypes; colors signify collection location. Circles are proportional to the number of individuals containing the haplotype with the smallest circles representing one individual. protocols with the addition of 0.2 ;iM of each primer, and 10-100 ng DNA template. PCR amplifications were performed using the following cycling protocol: preliminary denaturing step for 2 min at 94-C, followed by 35 cycles of 30 s at 94°C, 45 s at 53°C, 45 s at 72 C, and a final continuous hold at 15 °C. Exonuclease I and shrimp alkaline phosphatase (ExoSAP) were used to eliminate non-incorporated oligonucleotide primers and excess dNTPs in successful amplification products. Direct sequencing of amplification products was performed in both directions using the PCR primers at the Hawai'i Institute of Marine Biology EPSCOR Sequencing Core Facility on an ABB 130 genetic analyzer. Sequences were trimmed to a common length and collapsed to single stranded sequences using Sequencher v. 4.1 (Sequencher® sequence analysis software. Gene Codes Corporation, Ann Arbor, MI USA), and aligned using Clustal X (Larkin, et ah, 2007) with default settings. A statisfical parsimony network of mtDNA haplotypes was created for P. californicus using the program tcs (Clement, et ai, 2000) under default settings (Fig. 2.). Hierarchical population structure was evaluated based on estimates of st for both the entire dataset and in a pairwise manner using Arlequin (v. 3.11; Excoffier and Lisher, 2010). Values of haplotype and nucleotide diversity were obtained through Arlequin. Departure from equihbrium conditions was assessed using Tajima's D and Fu's F, (Table 2) as well as with mismatch distributions as calculated in Arlequin. When Note About Images Please note that these images are extracted from scanned page images that may have been digitally enhanced for readability - coloration and appearance of these illustrations may not perfectly resemble the original work.'