Biology subjects

McMahon, S. M.

Publications and source records attributed to McMahon, S. M..

7 recordsLinked to original sources

bioRxiv2023

Major axes of variation in tree demography across global forests

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatial-temporal patterns in tree population dynamics. While historical research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach is to group mechanisms according to their shared effects on the variability of tree vital rates and to quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions, categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6,500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28-33% of demographic variance alone, and in interaction with space 14-17%, totalling 40-43%. The average variability among species declined with species richness across forests, indicating that diverse forests featured smaller interspecific differences in vital rates supporting the theory that the range of vital rates is similar across global forests. Decomposing the variance in vital rates into the proposed OPs showed that taxonomy is crucial to predicting and understanding tree demography on large forest plots. A focus on how variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.

ecology↗

bioRxiv2022

Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech.

Transcriptomics provides a versatile tool for ecological monitoring. Here, through genome-guided profiling of transcripts mapping to 33,042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck due to post-Columbian deforestation, the SNP-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our expression analyses during spring-summer and summer-fall transitions for two consecutive years involved 4197 differentially expressed protein coding genes. Using Populus orthologs we reconstructed a protein-protein interactome representing leaf physiological states of trees during the seasonal transitions. Gene set enrichment analysis revealed GO terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of GO terms that could be putatively attributed to late spring phenological shifts. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture diverse ranges of responses including air quality, chronic disease, as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms maintaining the survival of long living trees such as the American beech (Fagus grandifolia).

ecology↗

bioRxiv2022

Topographically driven microclimatic gradients shape patterns of forest structure, diversity, and composition at a forest-grassland transition zone

O_LIGlobally, forests provide important ecosystem services, but anthropogenic change may shift the boundaries of forested biomes, because small-scale environmental changes govern biome transitions. This is especially true in semi-arid forests, where minor topographic and microclimatic changes influence forest functioning and transitions to open biomes such as grasslands. However, we lack quantitative descriptions of topographically driven microclimate variation and how it shapes forest structure, diversity, and composition in these transition zones. C_LIO_LILeveraging a 20.2-ha forest inventory plot (Niobrara plot) at a semi-arid forest-grassland transition zone in the Niobrara River valley (Nebraska, USA), we paired data on abundances and distributions of seedlings, saplings, and adults of woody species with topographic and microclimate data to test the hypothesis that if topographic variation causes variation in microclimate that affects forest function, then forest structure, diversity, and composition should vary significantly with topography and microclimate. C_LIO_LIMicroclimatic variation within the Niobrara plot strongly corresponded with topography, creating a sharp water availability and exposure gradient from the river floodplain to the forest-grassland transition zone. The magnitude of microclimate variation corresponded to that of regional macroclimate variation. Mean soil moisture was 10.2% lower along the higher-elevation transition zone than in the canyon bottoms, corresponding to variation across approximately 2.5 degrees of longitude. Mean air temperature increased by 2.2 {degrees}C from the canyon bottoms to upper canyon, corresponding to variation across approximately 3 degrees of latitude. C_LIO_LIForest structure, diversity, and composition correlated strongly with topographic and microclimatic gradients. More complex forest structure and higher species richness of adults and saplings occurred in moister, less exposed habitats with steeper slopes and lower elevations, whereas seedling stem density and richness were higher in higher-light, moister habitats at lower elevations. Species occupied well-defined topographic niches, promoting high beta diversity along topographic and microclimatic gradients and high species turnover from the floodplain to the transition zone. C_LIO_LISynthesis: Microclimatic and topographic variation drive patterns of structure, diversity, and composition in the forests at this forest-grassland transition zone. As the macroclimate becomes warmer and drier, topographically mediated microclimatic refuges supporting diverse, structurally complex forested ecosystems may shrink in semi-arid regions. C_LI

ecology↗

bioRxiv2021

Strategies of tolerance reflected in two North American maple genomes

Maples (the genus Acer) represent important and beloved forest, urban, and ornamental trees distributed throughout the Northern hemisphere. They exist in a diverse array of native ranges and distributions, across spectrums of tolerance or decline, and have varying levels of susceptibility to biotic and abiotic stress. Among Acer species, several stand out in their importance to economic interest. Here we report the first two chromosome-scale genomes for North American species, Acer negundo and Acer saccharum. Both assembled genomes contain scaffolds corresponding to 13 chromosomes, with A. negundo at a length of 442 Mb, N50 of 32 Mb and 30,491 genes, and A. saccharum at 626 Mb, N50 of 46 Mb, and 40,074 genes. No recent whole genome duplications were detected, though A. saccharum has local gene duplication and more recent bursts of transposable elements, as well as a large-scale translocation between two chromosomes. Genomic comparison revealed that A. negundo has a smaller genome with recent gene family evolution that is predominantly contracted and expansions that are potentially related to invasive tendencies and tolerance to abiotic stress. Examination of expression from RNA-Seq obtained from A. saccharum grown in long-term aluminum and calcium soil treatments at the Hubbard Brook Experimental Forest, provided insights into genes involved in aluminum stress response at the systemic level, as well as signs of compromised processes upon calcium deficiency, a condition contributing to maple decline. Significance statementThe first chromosome-scale assemblies for North American members of the Acer genus, sugar maple (Acer saccharum) and boxelder (Acer negundo), as well as transcriptomic evaluation of abiotic stress response in A. saccharum. This integrated study describes in-depth aspects contributing to each species approach to tolerance and applies current knowledge in many areas of plant genome biology with Acer physiology to help convey the genomic complexities underlying tolerance in broadleaf tree species.

genomics↗

bioRxiv2021

Comparative Transcriptomics of Tropical Woody Plants Supports Fast and Furious Strategy along the Leaf Economics Spectrum in Lianas.

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, include upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-mediated stress response as well as lignin and suberin synthesis. All together, these genes are known to be significant in shaping plant morphologies through responses such as gravitropism, phyllotaxy and shade avoidance.

plant biology↗

bioRxiv2021

Tropical tree growth sensitivity to climate is driven by species intrinsic growth rate and leaf traits

A better understanding of how climate affects growth in tree species is essential for improved predictions of forest dynamics under climate change. Long-term climate averages (mean climate) and short-term deviations from these averages (anomalies) both influence tree growth, but the rarity of long-term data integrating climatic gradients with tree censuses has so far limited our understanding of their respective role, especially in tropical systems. Here, we combined 49 years of growth data for 509 tree species across 23 tropical rainforest plots along a climatic gradient to examine how tree growth responds to both climate means and anomalies, and how species functional traits mediate these tree growth responses to climate. We showed that short-term, anomalous increases in atmospheric evaporative demand and solar radiation consistently reduced tree growth. Drier forests and fast-growing species were more sensitive to water stress anomalies. In addition, species traits related to water use and photosynthesis partly explained differences in growth sensitivity to both long-term and short-term climate variations. Our study demonstrates that both climate means and anomalies shape tree growth in tropical forests, and that species traits can be leveraged to understand these demographic responses to climate change, offering a promising way forward to forecast tropical forest dynamics under different climate trajectories.

ecology↗

bioRxiv2018

Comparative metabolomics of forest communities: Species differences in foliar chemistry are greater in the tropics.

Interspecific variation in the secondary metabolites of plants constrains host specificity of insect herbivores and microbial pathogens. The intensity and specificity of these plant-pest interactions is widely believed to increase towards the Equator, leading to the prediction that secondary metabolites should differ more among co-occurring plant species in tropical communities than in temperate communities. To evaluate this prediction, we quantified metabolomic similarity for 203 tree species that represent >89% of all individuals in large forest plots in Maryland and Panama. We constructed molecular networks based on mass spectrometry of all 203 species, quantified metabolomic similarity for all pairwise combinations of species, and evaluated how pairwise metabolomic similarity varies phylogenetically. Leaf metabolomes exhibited clear phylogenetic signal for the temperate plot, with high similarity among congeneric species. In contrast, leaf metabolomes lacked phylogenetic signal for the tropical plot, with low similarity among congeners. Our results suggest that species differences in secondary chemistry comprise important axes of niche differentiation among tropical trees, especially within species-rich genera, and that the contribution of species differences in secondary chemistry to niche differences increases towards the equator in forest tree communities.

ecology↗