@article{gomez-alpizar_carbone_ristaino_2007, title={An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies}, volume={104}, ISSN={["0027-8424"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-33847647990&partnerID=MN8TOARS}, DOI={10.1073/pnas.0611479104}, abstractNote={
            Phytophthora infestans
            (Mont.) de Bary caused the 19th century Irish Potato Famine. We assessed the genealogical history of
            P. infestans
            using sequences from portions of two nuclear genes (β-
            tubulin
            and
            Ras
            ) and several mitochondrial loci P3, (
            rpl
            14,
            rpl
            5, tRNA) and P4 (
            Cox1
            ) from 94 isolates from South, Central, and North America, as well as Ireland. Summary statistics, migration analyses and the genealogy of current populations of
            P. infestans
            for both nuclear and mitochondrial loci are consistent with an “out of South America” origin for
            P. infestans
            . Mexican populations of
            P. infestans
            from the putative center of origin in Toluca Mexico harbored less nucleotide and haplotype diversity than Andean populations. Coalescent-based genealogies of all loci were congruent and demonstrate the existence of two lineages leading to present day haplotypes of
            P. infestans
            on potatoes. The oldest lineage associated with isolates from the section Anarrhichomenun including
            Solanum tetrapetalum
            from Ecuador was identified as
            Phytophthora andina
            and evolved from a common ancestor of
            P. infestans
            . Nuclear and mitochondrial haplotypes found in Toluca Mexico were derived from only one of the two lineages, whereas haplotypes from Andean populations in Peru and Ecuador were derived from both lineages. Haplotypes found in populations from the U.S. and Ireland was derived from both ancestral lineages that occur in South America suggesting a common ancestry among these populations. The geographic distribution of mutations on the rooted gene genealogies demonstrate that the oldest mutations in
            P. infestans
            originated in South America and are consistent with a South American origin.
          }, number={9}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Gomez-Alpizar, Luis and Carbone, Ignazio and Ristaino, Jean Beagle}, year={2007}, month={Feb}, pages={3306–3311} }
 @article{avila-adame_gomez-alpizar_zismann_jones_buell_ristaino_2006, title={Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans}, volume={49}, ISSN={["1432-0983"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-31044446103&partnerID=MN8TOARS}, DOI={10.1007/s00294-005-0016-3}, abstractNote={The mitochondrial genomes of haplotypes of the Irish potato famine pathogen, Phytophthora infestans, were sequenced. The genome sizes were 37,922, 39,870 and 39,840 bp for the type Ia, IIa and IIb mitochondrial DNA (mtDNA) haplotypes, respectively. The mitochondrial genome size for the type Ib haplotype, previously sequenced by others, was 37,957 bp. More than 90% of the genome contained coding regions. The GC content was 22.3%. A total of 18 genes involved in electron transport, 2 RNA-encoding genes, 16 ribosomal protein genes and 25 transfer RNA genes were coded on both strands with a conserved arrangement among the haplotypes. The type I haplotypes contained six unique open reading frames (ORFs) of unknown function while the type II haplotypes contained 13 ORFs of unknown function. Polymorphisms were observed in both coding and non-coding regions although the highest variation was in non-coding regions. The type I haplotypes (Ia and Ib) differed by only 14 polymorphic sites, whereas the type II haplotypes (IIa and IIb) differed by 50 polymorphic sites. The largest number (152) of polymorphic sites was found between the type IIb and Ia haplotypes. A large spacer flanked by the genes coding for tRNA-Tyr (trnY) and the small subunit RNA (rns) contained the largest number of polymorphic sites and corresponds to the region where a large indel that differentiates type II from type I haplotypes is located. The size of this region was 785, 2,666 and 2,670 bp in type Ia, IIa and IIb haplotypes, respectively. Among the four haplotypes, 81 mutations were identified. Phylogenetic and coalescent analysis revealed that although the type I and II haplotypes shared a common ancestor, they clearly formed two independent lineages that evolved independently. The type II haplotypes diverged earlier than the type I haplotypes. Thus our data do not support the previous hypothesis that the type II lineages evolved from the type I lineages. The type I haplotypes diverged more recently and the mutations associated with the evolution of the Ia and Ib types were identified.}, number={1}, journal={CURRENT GENETICS}, author={Avila-Adame, C and Gomez-Alpizar, L and Zismann, V and Jones, KM and Buell, CR and Ristaino, JB}, year={2006}, month={Jan}, pages={39–46} }