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. MethodsWe 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. ResultsThe 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-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.

Diversity generally increases ecosystem productivity over short timescales. Over longer timescales, both ecological and evolutionary responses to new environments could alter productivity and diversity–productivity relationships. In turn, diversity might affect how component species adapt to new conditions. We tested these ideas by culturing artificial microbial communities containing between 1 and 12 species in three different environments for ∼60 generations. The relationship between community yields and diversity became steeper over time in one environment. This occurred despite a general tendency for the separate yields of isolates of constituent species to be lower at the end if they had evolved in a more diverse community. Statistical comparisons of community and species yields showed that species interactions had evolved to be less negative over time, especially in more diverse communities. Diversity and evolution therefore interacted to enhance community productivity in a new environment.

The effect of biodiversity on the ability of parasites to infect their host and cause disease (i.e. disease risk) is a major question in pathology, which is central to understand the emergence of infectious diseases, and to develop strategies for their management. Two hypotheses, which can be considered as extremes of a continuum, relate biodiversity to disease risk: One states that biodiversity is positively correlated with disease risk (Amplification Effect), and the second predicts a negative correlation between biodiversity and disease risk (Dilution Effect). Which of them applies better to different host-parasite systems is still a source of debate, due to limited experimental or empirical data. This is especially the case for viral diseases of plants. To address this subject, we have monitored for three years the prevalence of several viruses, and virus-associated symptoms, in populations of wild pepper (chiltepin) under different levels of human management. For each population, we also measured the habitat species diversity, host plant genetic diversity and host plant density. Results indicate that disease and infection risk increased with the level of human management, which was associated with decreased species diversity and host genetic diversity, and with increased host plant density. Importantly, species diversity of the habitat was the primary predictor of disease risk for wild chiltepin populations. This changed in managed populations where host genetic diversity was the primary predictor. Host density was generally a poorer predictor of disease and infection risk. These results support the dilution effect hypothesis, and underline the relevance of different ecological factors in determining disease/infection risk in host plant populations under different levels of anthropic influence. These results are relevant for managing plant diseases and for establishing conservation policies for endangered plant species.

Management of wild peppers in Mexico has occurred for a long time without clear phenotypic signs of domestication. However, pre-domestication management could have implications for the population's genetic richness. To test this hypothesis we analysed 27 wild (W), let standing (LS) and cultivated (C) populations, plus 7 samples from local markets (LM), with nine polymorphic microsatellite markers. Two hundred and fifty two alleles were identified, averaging 28 per locus. Allele number was higher in W, and 15 and 40% less in LS and C populations, respectively. Genetic variation had a significant population structure. In W populations, structure was associated with ecological and geographic areas according to isolation by distance. When LM and C populations where included in the analysis, differentiation was no longer apparent. Most LM were related to distant populations from Sierra Madre Oriental, which represents their probable origin. Historical demography shows a recent decline in all W populations. Thus, pre-domestication human management is associated with a significant reduction of genetic diversity and with a loss of differentiation suggesting movement among regions by man. Measures to conserve wild and managed populations should be implemented to maintain the source and the architecture of genetic variation in this important crop relative.

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. parviglumis and ssp. mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a follow up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.

Barriers to microbial migrations can lead adaptive radiations and increased endemism. We propose that extreme unbalanced nutrient stoichiometry of essential nutrients can be a barrier to microbial immigration over geological timescales. At the oasis in the Cuatro Ciénegas Basin in Mexico, nutrient stoichiometric proportions are skewed given the low phosphorus availability in the ecosystem. We show that this endangered oasis can be a model for a lost world. The ancient niche of extreme unbalanced nutrient stoichiometry favoured survival of ancestral microorganisms. This extreme nutrient imbalance persisted due to environmental stability and low extinction rates, generating a diverse and unique bacterial community. Several endemic clades of Bacillus invaded the Cuatro Cienegas region in two geological times, the late Precambrian and the Jurassic. Other lineages of Bacillus, Clostridium and Bacteroidetes migrated into the basin in isolated events. Cuatro Ciénegas Basin conservation is vital to the understanding of early evolutionary and ecological processes.

Aim To explore the genetic and phylogeographic structure of a temperate forest species, Pinus strobiformis Englem., in a subtropical region in the context of climate change during the Pleistocene. It is expected that the colder conditions during glacial stages favoured range expansions of P. strobiformis, thus promoting gene flow.Location Mexico and the United States.Methods Estimates of genetic diversity and structure were obtained using chloroplast microsatellite loci of 23 populations of P. strobiformis across its entire range, seven neighbouring populations of Pinus ayacahuite Ehrenb. ex. Schtdl, and one population of Pinus flexilis James. ResultsThe genetic diversity of P. strobiformis (H e = 0.856) was found to be high, especially in western populations, whereas eastern populations were less variable and more genetically similar to P. ayacahuite of central Mexico. We found evidence of significant phylogeographic structure (N ST = 0.444; P = 0.026), high genetic structure (R ST = 0.270), and isolation by distance. Pairwise R ST and samova (spatial analysis of molecular variance) results indicated an east-west partition of genetic variation, with populations within each group showing little differentiation and no isolation by distance. Main conclusionsThe phylogeographic structure of P. strobiformis across the entire range was pronounced, with two main genetic and geographic groups separated by the Chihuahuan Desert. However, within each of the two groups there was little population differentiation and no isolation by distance, suggesting genetic connectivity as a result of population expansions within these areas during glacial stages.

Abstract—Pinus subsection Cembroides comprises approximately 15 taxa distributed from the southwestern United States to south central Mexico. Despite previous phylogenetic studies based on morphology, nuclear ribosomal DNA, and plastid DNA, we still lack a robust phylogenetic hypothesis and clear delimitation for the closely-related species within the group. We studied the evolutionary relationships within subsection Cembroides and explored incomplete lineage sorting and reticulation using low-copy number nuclear genes. Concatenation and multispecies coalescent phylogenies were inferred from samples representing all taxa from subsection Cembroides and outgroups corresponding to the closely-related subsections Balfourianae, Nelsoniae, Gerardianae, and Krempfianae. The concatenation and coalescence-based trees mainly agreed with one another in recovering Pinus subsection Cembroides as monophyletic and in recovering similar relationships among species as in previous plastid DNA-based studies. Phylogenetic position and admixture analysis suggest that P. californiarum should be treated as a separate species from P. monophylla. Furthermore, our results support recognizing P. fallax as a species rather than as an infraspecific taxon of P. monophylla or P. edulis. The ASTRAL-III tree was consistent with the presence of very high levels of ILS in the group of pinyon pines with small cones. Analyses that account for both incomplete lineage sorting and reticulation identify some unexpected hybridization scenarios that were not reported in the literature.