El análisis de componentes principales de tablas florísticas de presencia-ausencia como herramienta para análisis de gradientes ambientales. Un estudio de caso en la Quebrada de Vaquerías (Valle Hermoso, Córdoba)

La vegetación de la Quebrada de Vaquerías (Provincia Fitogeográfica Chaqueña, Distrito del Chaco Serrano) fue estudiada mediante el análisis de componentes principales sobre una base de datos correspondiente a 50 stands distribuidos a lo largo de un gradiente ambiental complejo. Los resultados muestran la influencia de la exposición y la latitud sobre la distribución de la vegetación. En comunidades con una alta β-diversidad, los datos de presencia-ausencia describieron los cambios de la vegetación en forma más eficiente que los datos cuantitativos. Cuando el análisis fue no centrado, los valores de los stands a lo largo del primer eje estuvieron altamente correlacionados con la diversidad del sitio, mientras que los ejes 2, 3 y 4 fueron similares a los tres primeros ejes resultantes de un análisis centrado. El análisis, de varianza mostró que (a) el primero de estos ejes está fuertemente relacionado con la exposición, (b) el segundo eje florístico está fuertemente asociado a la variación altitudinal de las pendientes con orientación S-SE, y (c) el tercer eje florístico está asociado con la variación altitudinal de las pendientes con orientación N-NW. En los dos últimos casos, un análisis de regresión múltiple por pasos mostró que la forma de la respuesta es lineal. El análisis del peso de cada especie en los resultados mostró que la mayoría de las especies con alto peso coinciden con las especies consideradas como diagnóstico mediante un análisis fitosociológico tabular. Las propiedades del análisis de componentes principales aplicado a datos de presencia-ausencia se discute a la luz de estos resultadosThe vegetation of the Quebrada de Vaquerias (Chaquean Phytogeographic Province, Chaco Serrano District) was estudied by Principal Components Analysis on data of 50 stands distributed along a complex environiental gradient. The results show the influence of aspect and altitude on the distribution of the vegetation. The analysis indicate that presence - absence data are more efficient than quantitative data in describing vegelational change in communities with a high 13-diversity. First axis stand scores of the non-centered analysis were highly correlated with site diversity. Axes 2, 3 and 4 of the non-centered analysis were .similar to aces 1, 2, and 3 of the centered procedure. An ANOVA showed that (a) the first of these axes is strongly associated with aspect, (b) the second floristic axis is strongly associated with the altitude vahies on llte S-SE slopes; and (c) the third florislic axis is associated with attitudinal variation on the N-NW slopes. For the last two cases, a .stepwise multiple regression analysis showed that che foro of the response is linear. Die analysis of the species-loading showed that inosl species with high loading, coincide with the diagnostic species singled by a phylosociological tabular analysis. The properties of principal components analysis when applied to presence-absence data are discussed from these results

Controls of plant diversity and composition on a desert archipelago

Aim: With the most robust floristic data set for any arid archipelago, we use statistical modeling to determine the underlying controls of plant diversity and species composition. Location: The study was undertaken in the Midriff Islands of the Gulf of California, Mexico. Methods: Using the area-diversity relationship we estimate the power coefficient z with generalized linear models (GLM). We tested eight predictors (area, human presence, habitat diversity, topography, distance to mainland, island type, precipitation, and seabird dynamics) using a step-wise process on the same GLM procedure. Plant species composition was assessed by conducting a non-standardized principal component analysis on a presence-absence matrix of the 476 (plant species) x 14 (islands). Finally, families were tested for over or under representation with a X-2 analysis subjected to a Bonferroni correction. Results: The classic species-area model explained 85% of the variance in island plant diversity and yielded a slope (z) of 0.303 (+/- 0.01). When the effect of area is removed, four additional factors were shown to account for observed variation; habitat diversity (34%), seabird dynamics (23%), island type (21%), topography (14%). Human presence and distance to mainland were not predictors of species richness. Species composition varies significantly with island area; small islands have a particular flora where certain families are overrepresented, such as Cactaceae, while the flora of larger islands is strongly dependent on the continental source. Main conclusions: The factors that control diversity levels are expressions of geology, landscape heterogeneity, and land-sea connections. Species assemblages in small islands are governed by copious marine nutrients in the form of guano that depress species diversity. Distance to mainland and human presence hold no predictive power on diversity. The results show these islands to be isolated arid ecosystems with functioning ecological networks.National Science Foundation; UC MEXUSOpen access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Functional variants of DOG1 control seed chilling responses and variation in seasonal life-history strategies in Arabidopsis thaliana.

The seasonal timing of seed germination determines a plant's realized environmental niche, and is important for adaptation to climate. The timing of seasonal germination depends on patterns of seed dormancy release or induction by cold and interacts with flowering-time variation to construct different seasonal life histories. To characterize the genetic basis and climatic associations of natural variation in seed chilling responses and associated life-history syndromes, we selected 559 fully sequenced accessions of the model annual species Arabidopsis thaliana from across a wide climate range and scored each for seed germination across a range of 13 cold stratification treatments, as well as the timing of flowering and senescence. Germination strategies varied continuously along 2 major axes: 1) Overall germination fraction and 2) induction vs. release of dormancy by cold. Natural variation in seed responses to chilling was correlated with flowering time and senescence to create a range of seasonal life-history syndromes. Genome-wide association identified several loci associated with natural variation in seed chilling responses, including a known functional polymorphism in the self-binding domain of the candidate gene DOG1. A phylogeny of DOG1 haplotypes revealed ancient divergence of these functional variants associated with periods of Pleistocene climate change, and Gradient Forest analysis showed that allele turnover of candidate SNPs was significantly associated with climate gradients. These results provide evidence that A. thaliana's germination niche and correlated life-history syndromes are shaped by past climate cycles, as well as local adaptation to contemporary climate

Reply to Cleveland et al.’s “Detecting (trans)gene flow to landraces in centers of crop origin: lessons from the case of maize in Mexico”

Cleveland et al. (2005, Environ. Biosafety Res. 4: 197–208) offer useful suggestions for monitoring transgenes in landraces of maize, but we disagree with their statement that the scientific conclusions of our paper (Ortiz-García et al., 2005, Proc. Natl. Acad. Sci. USA 102: 12338–12343) are not justified. First, contrary to their perception, our survey was not designed to evaluate transgenes in the whole State of Oaxaca, but rather to monitor a specific portion of the District of Ixtlán de Juárez where the presence of transgenes had been reported previously by Quist and Chapela (2001, Nature 414: 541–543). Second, our paper described two methods for estimating frequencies of undetected transgenic seeds, while Cleveland et al. recommend a third approach that explicitly estimates effective population size. They argue that the effective population size of our seed samples is smaller than we assumed, leading to false claims about our detection accuracy. However, we employed a robust statistical approach to compensate for possible bias by using numbers of maternal plants, in addition to numbers of seeds, to provide a conservative estimate of the minimum number of independent samples. When we re-analyzed our 2004 data using effective population sizes, our conclusion that transgenic seeds were “absent or extremely rare” did not change, nor did the general range of possible frequencies of undetected transgenic seeds. Unlike Cleveland et al., we advocate using combined probability tests to analyze data across localities. Third, our critics argue that we accepted the null hypothesis that transgenes were absent. Actually, we assumed that transgenes were present in local landraces, and we used parameter estimation methods to calculate the probability of failing to detect transgenic individuals at a range of frequencies. In agreement with Cleveland et al., we reiterate that there is a clear need for additional surveys with rigorous sampling methods to provide estimates of transgene frequencies over broad geographic areas in Mexico

Local Extinction and Unintentional Rewilding of Bighorn Sheep (Ovis canadensis) on a Desert Island

Bighorn sheep ( Ovis canadensis) were not known to live on Tiburón Island, the largest island in the Gulf of California and Mexico, prior to the surprisingly successful introduction of 20 individuals as a conservation measure in 1975. Today, a stable island population of ∼500 sheep supports limited big game hunting and restocking of depleted areas on the Mexican mainland. We discovered fossil dung morphologically similar to that of bighorn sheep in a dung mat deposit from Mojet Cave, in the mountains of Tiburón Island. To determine the origin of this cave deposit we compared pellet shape to fecal pellets of other large mammals, and extracted DNA to sequence mitochondrial DNA fragments at the 12S ribosomal RNA and control regions. The fossil dung was 14C-dated to 1476-1632 calendar years before present and was confirmed as bighorn sheep by morphological and ancient DNA (aDNA) analysis. 12S sequences closely or exactly matched known bighorn sheep sequences; control region sequences exactly matched a haplotype described in desert bighorn sheep populations in southwest Arizona and southern California and showed subtle differentiation from the extant Tiburón population. Native desert bighorn sheep previously colonized this land-bridge island, most likely during the Pleistocene, when lower sea levels connected Tiburón to the mainland. They were extirpated sometime in the last ∼1500 years, probably due to inherent dynamics of isolated populations, prolonged drought, and (or) human overkill. The reintroduced population is vulnerable to similar extinction risks. The discovery presented here refutes conventional wisdom that bighorn sheep are not native to Tiburón Island, and establishes its recent introduction as an example of unintentional rewilding, defined here as the introduction of a species without knowledge that it was once native and has since gone locally extinct

Strategic Actions to Value, Conserve, and Restore the Natural Capital of Megadiversity Countries: The Case of Mexico

Decisionmakers need updated, scientifically sound and relevant information to implement appropriate policy measures and make innovative commitments to halt biodiversity loss and improve human well-being. Here, we present a recent science-based synthesis on the biodiversity and ecosystem services of Mexico, intended to be a tool for policymakers. We describe the methodological approach used to undertake such an assessment and highlight the major findings. Organized into five volumes and originally written in Spanish (Capital Natural de México), it summarizes the available knowledge on the components, structure, and functioning of the biodiversity of Mexico; the threats and trajectories of anthropogenic impact, together with its conservation status; and the policies, institutions, and instruments available for its sustainable management. We stress the lessons learned that can be useful for similar exercises in other megadiverse developing countries and identify major gaps and strategic actions to conserve the natural capital in light of the challenges of the Anthropocene

A framework to assess the health of rocky reefs linking geomorphology, community assemblage, and fish biomass

The recovery of historic community assemblages on reefs is a primary objective for the management of marine ecosystems. Working under the overall hypothesis that, as fishing pressure increases, the abundance in upper trophic levels decreases followed by intermediate levels, we develop an index that characterizes the comparative health of rocky reefs. Using underwater visual transects to sample rocky reefs in the Gulf of California, Mexico, we sampled 147 reefs across 1200 km to test this reef health index (IRH). Five-indicators described 88% of the variation among the reefs along this fishing-intensity gradient: the biomass of piscivores and carnivores were positively associated with reef health; while the relative abundances of zooplanktivores, sea stars, and sea urchins, were negatively correlated with degraded reefs health. The average size of commercial macro-invertebrates and the absolute fish biomass increased significantly with increasing values of the IRH. Higher total fish biomass was found on reefs with complex geomorphology compared to reefs with simple geomorphology (r2 = 0.14, F = 44.05, P \u3c 0.0001) and the trophic biomass pyramid also changed, which supports the evidence of the inversion of biomass pyramids along the gradient of reefs\u27 health. Our findings introduce a novel approach to classify the health of rocky reefs under different fishing regimes and therefore resultant community structures. Additionally, our IRH provides insight regarding the potential gains in total fish biomass that may result from the conservation and protection of reefs with more complex geomorphology

Local Extinction and Unintentional Rewilding of Bighorn Sheep (Ovis canadensis) on a Desert Island

Bighorn sheep (Ovis canadensis) were not known to live on Tiburón Island, the largest island in the Gulf of California and Mexico, prior to the surprisingly successful introduction of 20 individuals as a conservation measure in 1975. Today, a stable island population of ~500 sheep supports limited big game hunting and restocking of depleted areas on the Mexican mainland. We discovered fossil dung morphologically similar to that of bighorn sheep in a dung mat deposit from Mojet Cave, in the mountains of Tiburón Island. To determine the origin of this cave deposit we compared pellet shape to fecal pellets of other large mammals, and extracted DNA to sequence mitochondrial DNA fragments at the 12S ribosomal RNA and control regions. The fossil dung was ¹⁴C-dated to 1476–1632 calendar years before present and was confirmed as bighorn sheep by morphological and ancient DNA (aDNA) analysis. 12S sequences closely or exactly matched known bighorn sheep sequences; control region sequences exactly matched a haplotype described in desert bighorn sheep populations in southwest Arizona and southern California and showed subtle differentiation from the extant Tiburón population. Native desert bighorn sheep previously colonized this land-bridge island, most likely during the Pleistocene, when lower sea levels connected Tiburón to the mainland. They were extirpated sometime in the last ~1500 years, probably due to inherent dynamics of isolated populations, prolonged drought, and (or) human overkill. The reintroduced population is vulnerable to similar extinction risks. The discovery presented here refutes conventional wisdom that bighorn sheep are not native to Tiburón Island, and establishes its recent introduction as an example of unintentional rewilding, defined here as the introduction of a species without knowledge that it was once native and has since gone locally extinct

Environmental variability and fishing effects on the Pacific sardine fisheries in the Gulf of California

Small pelagic fish support some of the largest fisheries globally, yet there is an ongoing debate about the magnitude of the impacts of environmental processes and fishing activities on target species. We use a nonparametric, nonlinear approach to quantify these effects on the Pacific sardine (Sardinops sagax) in the Gulf of California. We show that the effect of fishing pressure and environmental variability are comparable. Furthermore, when predicting total catches, the best models account for both drivers. By using empirical dynamic programming with average environmental conditions, we calculated optimal policies to ensure long-term sustainable fisheries. The first policy, the equilibrium maximum sustainable yield, suggests that the fishery could sustain an annual catch of ∼2.16 × 105 tonnes. The second policy with dynamic optimal effort, reveals that the effort from 2 to 4 years ago impacts the current maximum sustainable effort. Consecutive years of high effort require a reduction to let the stock recover. Our work highlights a new framework that embraces the complex processes that drive fisheries population dynamics yet produces simple and robust advice to ensure long-term sustainable fisheries.Published versio