Integrating environmental, molecular, and morphological data to unravel an ice-age radiation of arctic-alpine Campanula in western North America

Phylogenomics and Biogeography of the Mammilloid Clade Revealed an Intricate Evolutionary History Arose in the Mexican Plateau

Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.

Plant-plant interactions determine natural restoration of plant biodiversity over time, in a degraded mined land

Restoration of degraded environments is essential to mitigate adverse impacts of human activities on ecosystems. Plant-plant interactions may provide effective means for restoring degraded arid lands, but little is understood about these impacts. In this regard, we analyzed the effects of two dominant nurse plants (i.e., Artemisia sieberi and Stipa arabica) on taxonomic, functional, and phylogenetic diversity across different ages of land abandonment (i.e., control, recent, and old ages) in a limestone mine site in Iran. In addition, we considered two spatial scales: i) the plot scale (i.e., under 1m2 plots) and ii) the vegetation-patch scale (i.e., under the canopies of nurse plants), to assess nurse plant effects, land abandonment ages, and their relative importance on biodiversity facets by performing Kruskal-Wallis H test and variation partitioning analysis. Our results indicated an increase in taxonomic, functional, and phylogenetic diversity at the plot scale, when considering the presence of nurse plants under old ages of land abandonment. Such significant differences were consistent with the positive effects of Artemisia patches on taxonomic diversity and Stipa patches on functional and phylogenetic diversity. In addition, we found a larger contribution from nurse plants than land abandonment age on biodiversity variation at both spatial scales studied. Therefore, these results indicate the importance of plant-plant interactions in restoring vegetation, with their effects on the presence of beneficiary species and their functional and phylogenetic relatedness depending on the nurse life forms under the stress-gradient hypothesis.

Assisted species migration and hybridization to conserve cold-adapted plants under climate change

Temperature rise due to climate change is putting many arctic and alpine plants at risk of extinction because their ability to react is outpaced by the speed of climate change. We considered assisted species migration (ASM) and hybridization as methods to conserve cold-adapted species (or the genes thereof) and to minimize the potential perturbation of ecosystems due to climate change. Assisted species migration is the deliberate movement of individuals from their current location to where the species' ecological requirements will be matched under climate projections. Hybridization refers to crossbreeding of closely related species, where for arctic and alpine plants, 1 parent is the threatened cold-adapted and the other its reproductively compatible, warm-adapted sibling. Traditionally, hybridization is viewed as negative and leading to a loss of biodiversity, even though hybridization has increased biodiversity over geological times. Furthermore, the incorporation of warm-adapted genes into a hybrid may be the only means for the persistence of increasingly more maladapted, cold-adapted species. If approached with thorough consideration of fitness-related parameters of the source population and acknowledgement of the important role hybridization has played in shaping current biodiversity, ASM and hybridization could help save partial or whole genomes of key cold-adapted species at risk due to climate change with minimal negative effects on ecosystem functioning.

The genetic differentiation of a cricket (Velarifictorus micado) with two modes of life cycle in East Asia after the middle Pleistocene and the invasion origin of the United States of America

The cricket Velarifictorus micado is widely distributed in East Asia and colonized the United States of America (the USA) in 1959. It has two life cycles: egg and nymph diapause. We aimed to investigate the biogeographic boundary between them and determine when and why V. micado diverged. Mitochondrial fragments including COI and CytB were used for haplotype network, demographic analysis, and divergence time estimation in individuals of East Asia. We selected several samples from the USA to find out the colonization origin. The haplotype network indicated there were three lineages based on COI, NE lineage (the egg diapause and mainly distributed in the northern regions), SE lineage (the egg diapause and mainly distributed in the southern regions), and SN lineage (the nymph diapause and mainly distributed in the southern regions). The molecular chronograms indicated that the first divergence of V. micado into two main lineages, NE and southern lineages (SE and SN), was essentially bounded by the Yangtze River. It occurred around ~0.79 Ma (95% HPD: 1.13-0.46 Ma) in the Middle Pleistocene Transition. This was followed by the divergence of the southern lineage into two sublineages, SE and SN lineage, occurred around ~0.50 Ma (95% HPD: 0.71-0.25 Ma), corresponding to the time of development of glaciers in various parts of the Qinghai-Tibet Plateau (QTP) (0.73-0.46 Ma). SE lineage might originate from southwestern China based on the comparison between the haplotype network based on COI and CytB. Our study suggested that divergences of lineages have twice co-occurred with tendency of cooling climatic in Asia after the Mid-Pleistocene, and the life-history strategy may play an important role in lineage diversification. Additionally, our results indicated that the USA populations were revealed at least twice separate Asian invasions. These both belonged to the egg diapause, which might provide a new perspective for invasion control.

Rapid speciation and ecological divergence into North American alpine habitats: the Nippononebria (Coleoptera: Carabidae) species complex

The climate-driven species pump hypothesis has been supported in a number of phylogeographic studies of alpine species. Climate-driven shifts in distribution, coupled with rapid demographic change, have led to strong genetic drift and lineage diversification. Although the species pump has been linked to rapid speciation in a number of studies, few studies have demonstrated that ecological divergence accompanies rapid speciation. Here we examine genetic, morphological and physiological variation in members of the ground beetle taxon Nippononebria, to test three competing hypotheses of evolutionary diversification: isolation and incomplete lineage sorting (no speciation), recent speciation without ecological divergence, or recent speciation with ecological divergence into alpine habitats. Genetic data are consistent with recent divergence, with major lineages forming in the last million years. A species tree analysis, in conjunction with morphological divergence in male reproductive traits, support the formation of three recognized Nippononebria taxa. Furthermore, both morphological and physiological traits demonstrate ecological divergence in alpine lineages, with convergent shifts in body shape and thermal tolerance breadth. This provides strong evidence that the climate-driven species pump can generate ecological novelty, though it is argued that spatial scale may be a key determinant of broader patterns of macroevolution in alpine communities.

Calochortus gunnisonii furthers evidence for the complex genetic legacy of historical climate change in the southern Rocky Mountains

PREMISE OF THE STUDY

Climate cycles of the Quaternary have impacted plants at a global scale, leaving behind a complex genetic legacy. Species of the northern Rocky Mountains of North America were exposed to more uniform glacial patterns than the central and southern ranges, where synergistic relationships between temperature and precipitation caused differences in the timing and extent of glacier onset. We examined the genetic impacts of climate oscillations on Calochortus gunnisonii (Liliaceae) in the central and southern Rocky Mountains.

METHODS

Populations were sampled from disjunct mountain ranges across the basins of Wyoming and northern and central Colorado. Allelic data from nuclear microsatellites and plastid sequences (trnV-ndhC, petA-psbJ, and rpl16) were used to examine patterns of genetic structure between and among populations along the southern Rocky Mountain corridor.

KEY RESULTS

We infer considerable population structure concordant with mountain range of origin. Clustering analysis supports separate north and south genetic clusters on either side of major basins in Wyoming, suggesting that populations were maintained in two distinct refugia. Additionally, populations within the Sierra Madre Range of southern Wyoming show localized, divergent genetic signal indicative of a third potential glacial refugium. By contrast, recent genetic admixture is observed in the Laramie, Medicine Bow, and Front ranges, where population expansion from glacial refugia has likely occurred.

CONCLUSIONS

We conclude that during climate cycles of the Quaternary, C. gunnisonii experienced periods of population expansion and reduction, habitat fragmentation, isolation in three or more refugia, and admixture mirroring genetic impacts of other southern Rocky Mountains organisms.

Retreat to refugia: Severe habitat contraction projected for endemic alpine plants of the Olympic Peninsula

PREMISE OF THE STUDY

The unique geography of the Olympic Peninsula in Washington State, USA has promoted a flora with exceptional endemism that may face high rates of extinction due to climate change. The Olympic Mountains provide an unparalleled opportunity to test predicted responses in topographically complex environments and inform conservation plans for threatened alpine taxa.

METHODS

We estimated the potential impact of climate change for five endemic alpine plants of the Olympic Peninsula. We used Principal Components Analysis (PCA) to visualize changes in climate niche-space in the alpine zone and the exposure of the endemics to changing conditions. We then constructed climate and topographic-based Species Distribution Models (SDMs) to estimate changes in the distribution of habitat for each taxon.

KEY RESULTS

The Olympic alpine zone will experience novel environmental conditions in the future, with a pronounced decrease in winter snow and an increase in growing-season moisture stress. When topography was taken into account, the losses were more dramatic than the impact of climate alone. Indeed, 85-99% of the suitable habitat will be lost for each of the five focal taxa by 2080, with thermal refugia remaining only on the highest peaks of the eastern Olympics.

CONCLUSIONS

The Olympic alpine endemics are stranded on ever-shrinking habitat islands. Within a few, isolated thermal refugia, the distribution of micro-topography may be a critical factor in determining long-term survival. The Olympic Mountains and their alpine taxa are a model system for endemics worldwide, illustrating the biogeographic characteristics that underpin vulnerability to climate change.

Why georeferencing matters: Introducing a practical protocol to prepare species occurrence records for spatial analysis

Species Distribution Models (SDMs) are widely used to understand environmental controls on species' ranges and to forecast species range shifts in response to climatic changes. The quality of input data is crucial determinant of the model's accuracy. While museum records can be useful sources of presence data for many species, they do not always include accurate geographic coordinates. Therefore, actual locations must be verified through the process of georeferencing. We present a practical, standardized manual georeferencing method (the Spatial Analysis Georeferencing Accuracy (SAGA) protocol) to classify the spatial resolution of museum records specifically for building improved SDMs. We used the high-elevation plant Saxifraga austromontana Wiegand (Saxifragaceae) as a case study to test the effect of using this protocol when developing an SDM. In MAXENT, we generated and compared SDMs using a comprehensive occurrence dataset that had undergone three different levels of georeferencing: (1) trained using all publicly available herbarium records of the species, minus outliers (2) trained using herbarium records claimed to be previously georeferenced, and (3) trained using herbarium records that we have manually georeferenced to a ≤ 1-km resolution using the SAGA protocol. Model predictions of suitable habitat for S. austromontana differed greatly depending on georeferencing level. The SDMs fitted with presence locations georeferenced using SAGA outperformed all others. Differences among models were exacerbated for future distribution predictions. Under rapid climate change, accurately forecasting the response of species becomes increasingly important. Failure to georeference location data and cull inaccurate samples leads to erroneous model output, limiting the utility of spatial analyses. We present a simple, standardized georeferencing method to be adopted by curators, ecologists, and modelers to improve the geographic accuracy of museum records and SDM predictions.