@article {191,
	title = {Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans-Mexican Volcanic Belt},
	journal = {Journal of Biogeography},
	volume = {42},
	year = {2015},
	month = {2015/09/01/},
	pages = {1586 - 1600},
	abstract = {Aim(1) To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans-Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism.
Location
Mexico.
Methods
We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co-occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high-elevation taxa.
Results
The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky-island dynamic through climate fluctuations, allowing for long-term in~situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co-occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low-latitude mountains can facilitate both the long-term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events.
Main conclusions
Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate{\textendash}volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region.
},
	keywords = {Genetic diversity, glacial periods, Mexican trout, Neogene, phylogeography, Pleistocene, tropical mountains, volcanism},
	isbn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12546/abstract},
	author = {Mastretta-Yanes, Alicia and Moreno-Letelier, Alejandra and Pi{\~n}ero, Daniel and Jorgensen, Tove H. and Emerson, Brent C.}
}
@article {mastretta-yanes_biodiversity_2015,
	title = {Biodiversity in the Mexican highlands and the interaction of geology, geography and climate within the Trans-Mexican Volcanic Belt},
	journal = {Journal of Biogeography},
	volume = {42},
	number = {9},
	year = {2015},
	pages = {1586{\textendash}1600},
	abstract = {Aim (1) To synthesize data on the physical and phylogeographical history of the Mexican highlands, with a focus on the Trans-Mexican Volcanic Belt (TMVB), and (2) to propose approaches and analyses needed for examining the interaction of climate and volcanism. Location Mexico. Methods We performed a literature and data survey of the climatic, geological and phylogeographical history of the Mexican highlands. We then assessed how the expected effects of topographic isolation, co-occurring palaeoclimatic fluctuations and volcanism can be tested against the distribution of genetic diversity of high-elevation taxa. Results The Mexican highlands present a complex biogeographical, climatic and geological history. Montane taxa have been exposed to a sky-island dynamic through climate fluctuations, allowing for long-term in~situ population persistence, while also promoting recent divergence and speciation events. Volcanic activity transformed part of the Mexican highlands during the Pleistocene, mainly in the TMVB, leading to co-occurring climate and topographical changes. The TMVB highlands provide a suitable template to examine how low-latitude mountains can facilitate both the long-term persistence of biodiversity as well as allopatric and parapatric speciation driven by climatic and geological events. Main conclusions Climate fluctuations, together with recent volcanism, have driven the diversification and local persistence of biodiversity within the Mexican highlands. The climate{\textendash}volcanism interaction is challenging to study; however, this can be overcome by coupling genomic data with landscape analyses that integrate the geological and climatic history of the region.},
	keywords = {Genetic diversity, glacial periods, Mexican trout, Neogene, phylogeography, Pleistocene, tropical mountains, volcanism},
	issn = {1365-2699},
	doi = {10.1111/jbi.12546},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12546/abstract},
	author = {Mastretta-Yanes, Alicia and Moreno-Letelier, Alejandra and Pi{\~n}ero, Daniel and Jorgensen, Tove H. and Emerson, Brent C.}
}
@mastersthesis {186,
	title = {Modelaci{\'o}n y Caracterizaci{\'o}n Ambiental del {\'A}rea de Distribuci{\'o}n Potencial de Oncorhynchus chrysogaster (Needham y Gard, 1964) en las Cuencas de los R{\'\i}os Sinaloa y Culiac{\'a}n},
	year = {2015},
	month = {2015/01//},
	pages = {1-74},
	school = {Centro de Investigaci{\'o}n en Alimentaci{\'o}n y Desarrollo, A.C.},
	address = {Mazatl{\'a}n, Sinaloa, M{\'e}xico},
	abstract = {Regarding the Mexican golden trout Oncorhynchus chrysogaster, salmonid nativeto Mexico which distribution has been restricted to river basins Fuerte, Sinaloa,
Culiacan in the Sierra Madre Occidental (SMO). However, this study focused on
modeling the potential distribution of this species in the basins of Sinaloa and
Culiac{\'a}n rivers, bounded at altitudes >= 1500 m, being little studied in relation to the
distribution of this species. There are few historical records of the species,
extending to the present study with 11 new records obtained in four samples taken
during the investigation. The environmental information required for the modeling
process comes from the bioclimatic variables WorldClim and Compound
Topographic Index HYDRO1k project. Based on this information and the records of
the species, the potential distribution of the species with BIOCLIM, GARP and
MAXENT methods that relate common occurrence data (geographical location) of
one species with the set of environmental variables was modeled. The three
models agree in locating distribution sites above 1500 m, which is considered as
altitudinal limit, however there are differences in the extent and final distribution
area, having higher affinity to the results obtained with GARP and MAXENT,
compared with results generated with BIOCLIM. To assess the predictive ability of
different modeling methods mentioned before a statistical method known as
Jackknife resampling, which is appropriate when you have fewer than 25 records
of occurrence was applied. The model validation GARP places as the method has
a higher predictive success, followed by MAXENT.
Con relaci{\'o}n a la trucha dorada mexicana Oncorhynchus chrysogaster, salm{\'o}nido
nativo de M{\'e}xico cuya distribuci{\'o}n se ha restringido a las cuencas de los r{\'\i}os
Fuerte, Sinaloa y Culiac{\'a}n, en la Sierra Madre Occidental (SMO). A pesar de ello,
el presente estudio se centr{\'o} en el modelado de la distribuci{\'o}n potencial de esta
especie en las cuencas de los r{\'\i}os Sinaloa y Culiac{\'a}n, acotadas a altitudes >= 1500
msnm, por estar escasamente estudiadas con relaci{\'o}n a la distribuci{\'o}n de esta
especie. Dentro de esta {\'a}rea se cuenta con pocos registros hist{\'o}ricos de
presencia de la especie, ampli{\'a}ndose con el presente estudio con 11 registros
nuevos obtenidos en cuatro muestreos realizadas durante la investigaci{\'o}n. La
informaci{\'o}n ambiental requerida para el proceso de modelado procede de las
variables bioclim{\'a}ticas de WorldClim y el {\'I}ndice Compuesto Topogr{\'a}fico del
proyecto HYDRO1k. Con base en dicha informaci{\'o}n y con los registros de la
especie, se model{\'o} la distribuci{\'o}n potencial de la especie con los m{\'e}todos
BIOCLIM, GARP y MAXENT, que en com{\'u}n relacionan datos de presencia
(posici{\'o}n geogr{\'a}fica) de una especie con el conjunto de variables ambientales.
Los tres modelos coinciden en ubicar los sitios de distribuci{\'o}n por arriba de los
1500 msnm, que se ha considerado como l{\'\i}mite altitudinal, sin embargo existen
diferencias en cuanto a la extensi{\'o}n y {\'a}rea de distribuci{\'o}n final, existiendo mayor
afinidad en los resultados obtenidos con GARP y MAXENT, comparativamente
con los resultados generados con BIOCLIM. Para evaluar la capacidad predictiva
de los diferentes m{\'e}todos de modelaci{\'o}n mencionados anteriormente se aplic{\'o} un
m{\'e}todo estad{\'\i}stico de remuestreo conocido como Jackknife, el cual es apropiado
cuando se tiene menos de 25 registros de ocurrencia. La validaci{\'o}n de los
modelos coloca a GARP como el m{\'e}todo que presenta un mayor {\'e}xito predictivo,
seguido por MAXENT.
},
	keywords = {Mexican trout, Oncorhynchus chrysogaster, Sierra Madre Occidental, species distribution modelling},
	author = {Ram{\'\i}rez-Huerta, Alejandro Luis}
}
@article {177,
	title = {The interplay of riverscape features and exotic introgression on the genetic structure of the Mexican golden trout (Oncorhynchus chrysogaster), a simulation approach},
	journal = {Journal of Biogeography},
	volume = {45},
	year = {2018},
	month = {2018///},
	pages = {1500 - 1514},
	abstract = {Aim We explored the factors between riverscape features and exotic introgression of cultured rainbow trout (Oncorhynchus mykiss) that drive the current genetic structure in the endemic Mexican golden trout (Oncorhynchus chrysogaster) using a riverscape genetics simulator. Location Sierra Madre Occidental, Northwest Mexico, North America. Methods We created a system model for Mexican golden trout to test various scenarios for the effect of riverscape resistance and rainbow trout introgression on the native genetic structure of the Mexican golden trout. Individual genotypes were used to initialize the model and were based upon empirical allele frequencies from three genetically and spatially distinct groups in the study area. The geographical location of the simulated populations was defined using a species distribution model. We included hypotheses for movement of riverine distance and riverscape resistance. We evaluated model performance by conducting population and landscape genetics analyses on the simulation outputs. Results The most plausible scenario included riverscape resistance without introgression, which presented a spatial genetic structure matching the observed riverscape genetic structure and fitting expected general life-history patterns for high elevation trout streams. In addition, temperature, precipitation, hydrology and topography were the most important variables influencing species occurrence and dispersal. Main conclusion This work presents one of the first empirically derived simulation studies of introgression. It highlights the importance of considering riverscape resistance (i.e. hydroclimatic and topographical gradient effects) in models of spatial genetic structure and introgression. Moreover, our modelling suggests that what we characterize as riverscape resistance is acting as a boundary against exotic introgression. The results of this study could help to develop management strategies that preserve native gene pools.},
	keywords = {CDMetaPOP, exotic trout, Mexican trout, Oncorhynchus chrysogaster, rainbow trout, riverscape genetics, species distribution modelling, Truchas Mexicanas},
	isbn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13246},
	author = {Escalante, Marco Alejandro and Le{\'o}n, Francisco J. Garc{\'\i}a-De and Ruiz-Luna, Arturo and Landguth, Erin and Manel, St{\'e}phanie}
}
@mastersthesis {169,
	title = {Genetic Investigation Of The Pacific Trout Complex: From Pedigrees To Phylogenies},
	year = {2014},
	month = {2014/01/01/},
	pages = {164},
	school = {University of California Santa Cruz},
	address = {Santa Cruz, California},
	abstract = {Perhaps one of the world{\textquoteright}s most important groups of fish are the species within the Pacific trout complex, due to their harvest in fisheries and use in aquaculture. This dissertation consists of an in-depth evaluation of this group at different scales, from the assessment of biological traits throughout the reconstruction of pedigrees in two populations to a phylogeographic examination of multiple largely undescribed species. Here, a combination of novel molecular techniques allowed me to address critical ecological questions for the management and conservation of this group.In chapter one, I describe the discovery, characterization and development of single nucleotide polymorphisms for <italic>O. mykiss<italic> for the study of ecological interactions, phylogeography, and conservation status. These tools have great power for population genetic analysis, and for individual identification and pedigree reconstruction. The last allows the tracking of families, and an unprecedented level of evaluation of natural and hatchery populations.Chapter two expands the scope of these molecular tools to provide a powerful means of understanding of biological traits for steelhead hatchery programs in the Russian River, California. Reconstruction of cohort age distributions revealed a strong component of fish that spawn at age two, in contrast to program goals and distinct from naturally spawning steelhead. Correlations between family members in the day of spawning revealed a strongly heritable component to this life history trait and demonstrated the potential for selection to alter life history traits. These results demonstrate the promise of SNP-based pedigree reconstruction for providing biological inference in high-fecundity organisms.Chapter three describes how the molecular tools developed were applied to population genetics of trout inhabiting northwestern Mexico, to elucidate biodiversity, and evolutionary history, and measure introgression from hatchery rainbow trout. Here, I confirmed the vast genetic diversity present in northwestern Mexican trout and provided evidence that trout inhabiting the Sierra Madre Occidental correspond to independent lineages separated from <italic>O. mykiss<italic>. Introgression from non-native trout was detected, but the genetic integrity of native trout is still maintained. All the information presented in this document will help to guide effective conservation strategies for this globally important group of fishes.},
	keywords = {Conservation biology, Ecology, Genetics, Mexican trout, Microsatellites, Oncorhynchus, Pedigrees, Phylogenetics, Population genetics, Single nucleotride polymorphisms, Truchas Mexicanas},
	url = {http://escholarship.org/uc/item/4ks0b0sm},
	author = {Abad{\'\i}a-Cardoso, Alicia}
}
@mastersthesis {170,
	title = {Modelaci{\'o}n y Caracterizaci{\'o}n Ambiental del {\'A}rea de Distribuci{\'o}n Potencial de Oncorhynchus chrysogaster (Needham y Gard, 1964) en las Cuencas de los R{\'\i}os Sinaloa y Culiac{\'a}n},
	year = {2015},
	month = {2015/01//},
	pages = {1-74},
	school = {Centro de Investigaci{\'o}n en Alimentaci{\'o}n y Desarrollo, A.C.},
	address = {Mazatl{\'a}n, Sinaloa, M{\'e}xico},
	abstract = {Regarding the Mexican golden trout Oncorhynchus chrysogaster, salmonid nativeto Mexico which distribution has been restricted to river basins Fuerte, Sinaloa,
Culiacan in the Sierra Madre Occidental (SMO). However, this study focused on
modeling the potential distribution of this species in the basins of Sinaloa and
Culiac{\'a}n rivers, bounded at altitudes >= 1500 m, being little studied in relation to the
distribution of this species. There are few historical records of the species,
extending to the present study with 11 new records obtained in four samples taken
during the investigation. The environmental information required for the modeling
process comes from the bioclimatic variables WorldClim and Compound
Topographic Index HYDRO1k project. Based on this information and the records of
the species, the potential distribution of the species with BIOCLIM, GARP and
MAXENT methods that relate common occurrence data (geographical location) of
one species with the set of environmental variables was modeled. The three
models agree in locating distribution sites above 1500 m, which is considered as
altitudinal limit, however there are differences in the extent and final distribution
area, having higher affinity to the results obtained with GARP and MAXENT,
compared with results generated with BIOCLIM. To assess the predictive ability of
different modeling methods mentioned before a statistical method known as
Jackknife resampling, which is appropriate when you have fewer than 25 records
of occurrence was applied. The model validation GARP places as the method has
a higher predictive success, followed by MAXENT.
Con relaci{\'o}n a la trucha dorada mexicana Oncorhynchus chrysogaster, salm{\'o}nido
nativo de M{\'e}xico cuya distribuci{\'o}n se ha restringido a las cuencas de los r{\'\i}os
Fuerte, Sinaloa y Culiac{\'a}n, en la Sierra Madre Occidental (SMO). A pesar de ello,
el presente estudio se centr{\'o} en el modelado de la distribuci{\'o}n potencial de esta
especie en las cuencas de los r{\'\i}os Sinaloa y Culiac{\'a}n, acotadas a altitudes >= 1500
msnm, por estar escasamente estudiadas con relaci{\'o}n a la distribuci{\'o}n de esta
especie. Dentro de esta {\'a}rea se cuenta con pocos registros hist{\'o}ricos de
presencia de la especie, ampli{\'a}ndose con el presente estudio con 11 registros
nuevos obtenidos en cuatro muestreos realizadas durante la investigaci{\'o}n. La
informaci{\'o}n ambiental requerida para el proceso de modelado procede de las
variables bioclim{\'a}ticas de WorldClim y el {\'I}ndice Compuesto Topogr{\'a}fico del
proyecto HYDRO1k. Con base en dicha informaci{\'o}n y con los registros de la
especie, se model{\'o} la distribuci{\'o}n potencial de la especie con los m{\'e}todos
BIOCLIM, GARP y MAXENT, que en com{\'u}n relacionan datos de presencia
(posici{\'o}n geogr{\'a}fica) de una especie con el conjunto de variables ambientales.
Los tres modelos coinciden en ubicar los sitios de distribuci{\'o}n por arriba de los
1500 msnm, que se ha considerado como l{\'\i}mite altitudinal, sin embargo existen
diferencias en cuanto a la extensi{\'o}n y {\'a}rea de distribuci{\'o}n final, existiendo mayor
afinidad en los resultados obtenidos con GARP y MAXENT, comparativamente
con los resultados generados con BIOCLIM. Para evaluar la capacidad predictiva
de los diferentes m{\'e}todos de modelaci{\'o}n mencionados anteriormente se aplic{\'o} un
m{\'e}todo estad{\'\i}stico de remuestreo conocido como Jackknife, el cual es apropiado
cuando se tiene menos de 25 registros de ocurrencia. La validaci{\'o}n de los
modelos coloca a GARP como el m{\'e}todo que presenta un mayor {\'e}xito predictivo,
seguido por MAXENT.
},
	keywords = {Mexican trout, Oncorhynchus chrysogaster, Sierra Madre Occidental, species distribution modelling},
	author = {Ram{\'\i}rez-Huerta, Alejandro Luis}
}
@article {165,
	title = {Truchas Mexicanas},
	year = {2019},
	month = {2019/04/30/},
	abstract = {Global Biodiversity Information Facility. Free and Open Access to Biodiversity Data. Preliminary dataset published by http://truchasmexicanas.myspecies.info/},
	keywords = {Mexican golden trout, Mexican trout, Truchas Mexicanas},
	url = {http://truchasmexicanas.myspecies.info/},
	author = {Hendrickson, Dean A.}
}
@article {157,
	title = {Modelaci{\'o}n de la distribuci{\'o}n de truchas nativas de la Sierra Madre Occidental y su relaci{\'o}n con la estructura del paisaje adyacente},
	journal = {GBIF.org},
	year = {2020},
	month = {2020/03/30/},
	abstract = {El proyecto se centra en el estudio de truchas nativas de M{\'e}xico, que se distribuyen en la Sierra Madre Occidental. Se reconoce la existencia de la especie Oncorhynchus chrysogaster (Needham y Gard, 1964), denominada Trucha dorada mexicana (PISCES: Salmonidae), misma que est{\'a} reportada como especie end{\'e}mica amenazada en la NOM-059-SEMARNAT-2010 y como especie vulnerable en CITES (Conference on International Trade in Endangered Species). La situaci{\'o}n de riesgo es a{\'u}n m{\'a}s grave si se considera que estudios recientes indican que por la heterogeneidad gen{\'e}tica de este complejo de peces, es posible la identificaci{\'o}n de nuevas especies o subespecies de truchas nativas (Hendrickson et al., 2002, Hendrickson et al., 2006). Considerando lo anterior y tomando en cuenta que existen algunas iniciativas (particularmente realizadas por acad{\'e}micos estadounidenses y mexicanos), enfocadas al estudio sistem{\'a}tico y gen{\'e}tico de este grupo de peces, se propone complementarlas con el an{\'a}lisis espacial del paisaje del {\'a}rea de distribuci{\'o}n potencial de O. chrysogaster. Para ello se analizar{\'a}n los registros hist{\'o}ricos, los datos existentes con referencia geogr{\'a}fica espec{\'\i}fica y adicionalmente los datos que se generen a partir de este proyecto, para producir un modelo de distribuci{\'o}n de esta especie en la Sierra Madre Occidental. Dado el escaso registro con que se cuenta se considera indispensable la colecta con fines de ampliar dicho registro, pero particularmente con la intenci{\'o}n de validar en lo posible el modelo que se genere. Se aplicar{\'a}n t{\'e}cnicas de percepci{\'o}n remota que permitir{\'a}n identificar las caracter{\'\i}sticas ambientales de las localidades de registro (red hidr{\'a}ulica, altitud, pendiente, tipos de cobertura) y que podr{\'a}n ser incorporadas a un sistema de informaci{\'o}n geogr{\'a}fica (SIG), conjuntamente con informaci{\'o}n auxiliar (temperaturas promedio, precipitaci{\'o}n, geolog{\'\i}a, etc.). La identificaci{\'o}n de estas caracter{\'\i}sticas, en conjunto con datos de la presencia/ausencia de las truchas permitir{\'a} generar mapas de susceptibilidad de las {\'a}reas de distribuci{\'o}n de estas especies por medio de modelos del nicho ecol{\'o}gico, por ejemplo MAXENT y Mahalanobis.},
	keywords = {Mexican trout, Oncorhynchus chrysogaster},
	url = {https://www.gbif.org/dataset/90711430-4260-422f-aeb2-26ce7f72f56c},
	author = {Ruiz Luna, Arturo}
}
