Tracking Host Trees: The Phylogeography of Endemic Psittacanthus sonorae (Loranthaceae) Mistletoe in the Sonoran Desert.

The host dependence of mistletoes suggests that they track the distributions of their hosts. However, the factors that determine the geographic distribution of mistletoes are not well understood. In this study, the phylogeography of Psittacanthus sonorae was reconstructed by sequencing one nuclear (ITS) and two plastid (trnL-F and atpB-rbcL) regions of 148 plants from populations separated by the Sea of Cortez. Divergence time and gene flow were estimated to gain insight into the historical demography and geographic structuring of genetic variation. We also described and mapped the spatial distribution of suitable habitat occupied by P. sonorae and its most common host Bursera microphylla in the Sonoran Desert, along with their responses to Quaternary climate fluctuations using environmental data and ecological niche modeling (ENM). We detected environmental and genetic differentiation between the peninsular and continental P. sonorae populations. Population divergence occurred during the Pleistocene, around the time of the Last Glacial Maximum. No signals of population growth were detected, with net gene flow moving from the continent to the peninsula. ENM models indicate decoupled responses by the mistletoe and its main host to past climate changes. For the Last Interglacial to the present, most models produce only partial areas of overlap on both the peninsula and the continent. Our results support a scenario of Late-Pleistocene isolation and divergence with asymmetrical gene flow between peninsular and continental P. sonorae populations. Continental populations migrated to the peninsula and the spatial isolation probably produced genetic differentiation under different environmental conditions.

A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

BACKGROUND: Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. RESULTS: Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate Bayesian Computation (ABC) analyses strongly supported a scenario of simultaneous divergence among the three groups isolated recently. CONCLUSIONS: Our results provide support for the predominant role of isolation and environmental factors in driving genetic differentiation of Mesoamerican parrot-flower mistletoes. The ABC results are consistent with a scenario of post-glacial mistletoe invasion, independent of host identity, and that habitat types recently isolated P. schiedeanus populations, accumulating slight phenotypic differences among genetic groups due to recent migration across habitats. Under this scenario, climatic fluctuations throughout the Pleistocene would have altered the distribution of suitable habitat for mistletoes throughout Mesoamerica leading to variation in population continuity and isolation. Our findings add to an understanding of the role of recent isolation and colonization in shaping cloud forest communities in the region.

Spatio-temporal evolution of Leucophyllum pringlei and allies (Scrophulariaceae): a group endemic to North American xeric regions.

The taxa of the Leucophyllum pringlei clade were used to understand the influence of the Neogene orogenesis and the Quaternary climate cycles on the diversification of the flora of the xeric regions of North America. This clade includes the five southernmost species of the genus: L. ambiguum, L. flyrii, L. pruinosum and L. ultramonticola, which are distributed throughout the Chihuahuan Desert north of the Trans-Mexican Volcanic Belt, and L. pringlei in the region of Tehuacán-Cuicatlán south of this mountain range. Here we test whether these species diverged during the pluvial periods of the Pleistocene, and whether L. pringlei diverged earlier from the other species during the uplift of the Trans-Mexican Volcanic Belt. Using three plastid regions (psbA-trnH, psbK-psbI, trnL-F) and a nuclear (ITS) marker, phylogenetic analyses were carried out, along with a reconstruction of their ancestral area. Trees retrieved the five species in a monophyletic group with the most recent common ancestor distributed in the Sinaloan dry forest during the Late Miocene (8.08Ma), from where it dispersed to the Chihuahuan Desert during the Late Miocene (6.35Ma). The secondary uplift of the Sierra Madre Occidental during the Late Miocene to Early Pliocene influenced a vicariance event. Divergence between L. pringlei and the species from north of the Trans-Mexican Volcanic Belt occurred during the second volcanic episode in the Late Miocene (7.5-3Ma). The most recent common ancestor of L. ambiguum, L. pruinosum and L. ultramonticola was widely distributed in the southern part of the Chihuahuan Desert during the Early to Late Pliocene (3.50Ma). The diversification of these three species occurred in the Middle Pleistocene (0.9Ma) during the pluvial and inter-pluvial cycles.

Origin and diversification of the Milla Clade (Brodiaeoideae, Asparagaceae): a Neotropical group of six geophytic genera.

The Milla clade currently comprises six genera of geophytic plants distributed from Arizona to Guatemala. Three genera (Behria, Jaimehintonia and Petronymphe) are monotypic while the remaining genera (Bessera, Dandya and Milla) contain from two to ten (Milla) species. Parsimony, Maximum Likelihood and Bayesian Inference analyses were conducted with plastid and nuclear DNA sequences from a total of 181 plants belonging to 15 species in all six genera. Molecular dating was performed under a relaxed clock model. We examined the phylogenetic relationships of the genera and species, estimated origin-divergence times for the clade and genera and determined the ancestral distribution area of the clade by optimizing ancestral areas given current biogeographic distributions. The phylogenetic results suggest that final decisions on limits of the six genera in the Milla clade will have to be established until further taxonomic work is completed for Milla, in particular for the group of populations included under the name M. biflora. The later genus is rendered polyphyletic by other genera of the family. The origin of the Milla clade is estimated at 15.8Ma. Ancestral area of the clade most likely was located in the California Floristic Province and dispersal occurred most likely to the Chihuahuan-Coahuila Plateaus and the Trans-Mexican Volcanic Belt and from there to Baja California and the Sierra Madre del Sur. Two hypotheses that need further testing are proposed to explain complex relationships of genera and polyphyly of Milla, one in relation to fragmentation of populations and pollinator shifts and another suggesting that populations remained in refugia in the Trans-Mexican Volcanic Belt.

Variation in traditional knowledge of culturally important macromycete species among three indigenous communities of Oaxaca, Mexico.

BACKGROUND: For centuries, wild mushrooms have been a forest resource of significant cultural value in several ethnic groups worldwide. In Mexico, extensive traditional knowledge on the use of fungal resources has been developed and deeply rooted. Mexico is the second country in the world in which the most species of wild mushroom are consumed, and it is considered a pioneer in ethnomycology. Nonetheless, there are still many indigenous groups in this country that have not been studied from an ethnomycological approach. The present study aimed to record the traditional knowledge on wild mushrooms in three indigenous groups of the state of Oaxaca, Mexico, and assess the variation in this knowledge within and across the studied groups. METHODS: The data were recorded from April to October 2022 within three communities belonging to the indigenous groups Chatino, Chontal, and Chinanteco. Through 84 interviews, information related to their knowledge of wild mushrooms was obtained. The cultural significance index of wild edible mushrooms was calculated for each community. Regression analyses, analysis of variance and covariance, t test, and non-metric multidimensional scaling analysis were performed to assess the distribution of traditional knowledge in the communities. RESULTS: A total of 32 culturally important mushroom species were recorded for the three indigenous groups (30 edible, 2 medicinal); 23 used by Chatinos, 16 by Chontales, and 6 by Chinantecos. Only Chatinos and Chinantecos use wild mushrooms in medicine. The cultural significance of wild edible mushrooms differed among groups. Traditional knowledge about wild mushrooms declines when the level of schooling increases and age decreases, especially in the Chatino group. This knowledge distributes more homogeneously in the Chontal and Chinanteco groups. Their age determines the difference in knowledge between men and women. CONCLUSION: Documenting how traditional knowledge differs among ethnic groups is relevant for preserving cultural and biological diversity. Factors such as level of schooling and age can affect traditional knowledge of wild mushrooms, but the effects of these factors vary within and across communities. Conducting studies encompassing a broader range of variables is of interest for a better understanding of the human-mushroom relationship.

The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes.

Geological events such as mountain uplift affect how, when, and where species diversify, but measuring those effects is a longstanding challenge. Andean orogeny impacted the evolution of regional biota by creating barriers to gene flow, opening new habitats, and changing local climate. B⁢o⁢m⁢a⁢r⁢e⁢a (Alstroemeriaceae) are tropical plants with (often) small, isolated ranges; in total, B⁢o⁢m⁢a⁢r⁢e⁢a species occur from central Mexico to central Chile. This genus appears to have evolved rapidly and quite recently, and rapid radiations are often challenging to resolve with traditional phylogenetic inference. In this study, we apply phylogenomics-with hundreds of loci, gene-tree-based data curation, and a multispecies-coalescent approach-to infer the phylogeny of B⁢o⁢m⁢a⁢r⁢e⁢a. We use this phylogeny to untangle the potential drivers of diversification and biogeographic history. In particular, we test if Andean orogeny contributed to the diversification of B⁢o⁢m⁢a⁢r⁢e⁢a. We find that B⁢o⁢m⁢a⁢r⁢e⁢a originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of mountain uplift. Furthermore, Andean lineages diversified faster than non-Andean relatives. B⁢o⁢m⁢a⁢r⁢e⁢a thus demonstrates that-at least in some cases-geological change rather than environmental stability has driven high species diversity in a tropical biodiversity hotspot. These results also demonstrate the utility (and danger) of genome-scale data for making macroevolutionary inferences.

Impact of urbanization on functional diversity in macromycete communities along an urban ecosystem in Southwest Mexico.

Macromycetes are a group of fungi characterized by the production of fruit bodies and are highly relevant in most terrestrial ecosystems as pathogens, mutualists, and organic matter decomposers. Habitat transformation can drastically alter macromycete communities and diminish the contribution of these organisms to ecosystem functioning; however, knowledge on the effect of urbanization on macrofungal communities is scarce. Diversity metrics based on functional traits of macromycete species have shown to be valuable tools to predict how species contribute to ecosystem functionality since traits determine the performance of species in ecosystems. The aim of this study was to assess patterns of species richness, functional diversity, and composition of macrofungi in an urban ecosystem in Southwest Mexico, and to identify microclimatic, environmental, and urban factors related to these patterns in order to infer the effect of urbanization on macromycete communities. We selected four oak forests along an urbanization gradient and established a permanent sampling area of 0.1 ha at each site. Macromycete sampling was carried out every week from June to October 2017. The indices used to measure functional diversity were functional richness (FRic), functional divergence (FDig), and functional evenness (FEve). The metric used to assess variation of macrofungal ecological function along the study area was the functional value. We recorded a total of 134 macromycete species and 223 individuals. Our results indicated a decline of species richness with increased urbanization level related mainly to microclimatic variables, and a high turnover of species composition among study sites, which appears to be related to microclimatic and urbanization variables. FRic decreased with urbanization level, indicating that some of the available resources in the niche space within the most urbanized sites are not being utilized. FDig increased with urbanization, which suggests a high degree of niche differentiation among macromycete species within communities in urbanized areas. FEve did not show notable differences along the urbanization gradient, indicating few variations in the distribution of abundances within the occupied sections of the niche space. Similarly, the functional value was markedly higher in the less urbanized site, suggesting greater performance of functional guilds in that area. Our findings suggest that urbanization has led to a loss of macromycete species and a decrease in functional diversity, causing some sections of the niche space to be hardly occupied and available resources to be under-utilized, which could, to a certain extent, affect ecosystem functioning and stability.

Comparison of diversity and composition of macrofungal species between intensive mushroom harvesting and non-harvesting areas in Oaxaca, Mexico.

Wild edible mushrooms have been collected and consumed by human groups for centuries, and today they represent a relevant source of food and income for many rural families worldwide. Preserving these non-timber forest products is of great interest, and there is concern about the damage caused by intensive mushroom harvesting on macromycete communities. The aim of this study was to evaluate variation in diversity and composition of macromycete species between areas regularly used for mushroom harvesting and non-harvested areas in the Mixteca region of Oaxaca, Mexico, as well as to assess the influence of microclimatic and environmental factors on this variation. We selected two harvested and two non-harvested sites within the study area. In each one, we established 10 permanent plots of 10 m × 10 m where we sampled all the observed fruit bodies weekly from June to October 2017. We recorded a total of 856 individuals corresponding to 138 species, and 23 of these were identified as edible. Overall macromycete diversity, edible species diversity and composition were similar in Sites 1 (non-harvested) and 3 (harvested), and in Sites 2 (non-harvested) and 4 (harvested). Variation of diversity and species composition along the studied area was mainly related to microclimatic variables, while most environmental variables and variables related to vegetation structure similarly affected macromycete species in the four sites. Our results indicate that intensive harvesting of wild edible mushrooms is not affecting the diversity and distribution of macromycete species in our study area. Knowledge on the sustainability of mushroom harvesting practices can help improve current regulations regarding the management of these valuable non-timber forest products.

Climate change and conservation in a warm North American desert: effect in shrubby plants.

BACKGROUND: Deserts are biologically rich habitats with a vast array of animals and plants adapted to xeric conditions, and most deserts are among the planet's last remaining areas of total wilderness. Among North American deserts, the Chihuahuan Desert has the highest levels of diversity and endemism. To understand the effect of future climate change on plants distributed in this arid land and propose effective conservation planning, we focused on five endemic shrubby species that characterize the Chihuahuan Desert and used an integrative approach. METHODS: Ecological niche-based modeling, spatial genetics and ecological resistance analyses were carried out to identify the effect of global warming on the studied five shrubby species. Key areas that need to be preserved were identified taking into account the existing protected areas within the Chihuahuan Desert. RESULTS: The extent of future distribution will vary among these species, and on average expansion will occur in the western part of the Chihuahuan Desert. For most species low environmental resistance to gene flow was predicted, while higher future resistance was predicted for one species that would lead to increased population isolation. The highest haplotype diversity was identified in three hotspots. Based on future suitability of habitat and in the haplotype diversity we suggest preserving two hotspots of genetic diversity in the Sierra Madre Oriental, located in areas without protection. The third hotspot was detected in the well preserved Tehuacán-Cuicatlán Man and Biosphere Reserve. CONCLUSION: Global climate change will have an effect in arid adapted plants, favoring expansion in the western of the Chihuahuan Desert however negatively affecting others with high ecological resistance disrupting gene flow. Two hotspots of genetic diversity in the Sierra Madre Oriental should be protected.

Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica.

BACKGROUND: Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. METHODS: Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. RESULTS: Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant variables or elevation. For elevational shifts, we found repeated change from low to high elevations. CONCLUSIONS: Our data suggest that representatives of Cyatheaceae main lineages migrated from Australia to Mesoamerican cloud forests in different times and have persisted in these environmentally unstable areas but extant species diverged recentrly from their ancestors.

The taxonomy of Psilocybe fagicola-complex.

Psilocybe fagicola comprises a complex of more than eight species, six of them in Mexico, and all of them possessing a long pseudorhiza, a characteristic not listed by Heim and Cailleux in 1959 in the original description of the type species, but described by Guzmán in 1978 and 1983. The description of Psilocybe fagicola s.s. is here emended to include the length of the cheilocystidia of (6-) 12-20 (-30) microm, as well as the absence or scarcity of pleurocystidia. Psilocybe xalapensis and P. wassoniorum are considered to be synonymous with P. fagicola s.s. However, Psilocybe banderillensis and P. herrerae from Mexico, P. columbiana from Colombia, and P. keralensis from India are considered to be valid species within this complex. Moreover, P. novoxalapensis and P. teofilae, both from Mexico, are described as new species. Length of spores, presence or absence of pleurocystidia and their variations, and type of cheilocystidia constitute the principal defining characteristics of the species. Setaceous hyphae at the base of the stipe, as well as caulocystidia, lack taxonomic value, as do other morphological characteristics, including pileipellis and subpileipellis. A key to the eight considered species is also presented within the paper.