Biology subjects

Doughty, C. E.

Publications and source records attributed to Doughty, C. E..

3 recordsLinked to original sources

bioRxiv2024

Disentangling the effect of heritability and plasticity on Populus fremontii leaf reflectance across a temperature gradient

Globally, vegetation biodiversity is expected to decline as the rate of plant adaptation struggles to keep pace with rising temperatures. To support conservation efforts through remote sensing, we disentangled the nested effects of genetic and environmental influences on reflectance spectra, leveraging spectroscopy to assess plant adaptations to temperature. Specifically, we quantified the relative effect of plasticity and heritability on Populus fremontii (Fremont cottonwood) leaf reflectance using clonal replicates propagated from 16 populations and grown across three common gardens spanning a mean annual temperature gradient representing the thermal range of P. fremontii. We used variance partitioning to decompose phenotypic variation expressed in the leaf spectra into genotypic and environmental components to estimate broad-sense heritability. Heritability was strongly expressed in the spectral red edge ([~]680-750nm) and shortwave infrared ([~]1400-3000nm), though the heritability peak in the red edge was sensitive to extreme temperatures. By comparing distances of group centroids in principal component space, we determined that P. fremontii intraspecific spectral variation was shaped by the interaction between common garden site conditions and source population. Support vector machine models indicated pronounced environmental influence on spectral variation, as P. fremontii source population and garden location were classified at 71.8% and 92.6% accuracy, respectively. These findings emphasize the utility of reflectance data in separating genetic and environmental influences on plant phenotypes, offering a pathway to scale these insights across broader landscapes and aid in the conservation and management of vulnerable ecosystems in a warming climate.

ecology↗

bioRxiv2023

The impact of late Pleistocene mammal extinctions on pathogen richness in extant hosts.

Many species of large mammals were driven to extinction during the late Pleistocene and early Holocene (approx. 10,000 - 50,000 years ago), with cascading effects on the physical structure of ecosystems and the dispersal of seeds, nutrients, and microbes. However, it remains uncertain whether the parasites associated with these extinct hosts also disappeared or persisted in surviving (extant) mammals. We hypothesize that if some parasites endured, extant mammals sharing their ranges with phylogenetically similar extinct mammals would have a greater pathogen richness than expected based on current levels of host diversity. We find that the inclusion of variables related to these extinctions account for an additional 5% of deviance when modelling per-host viral and bacterial richness, compared to models run without these variables. Partial dependence plots show a positive correlation between the number of extinct mammals lost and per-host viral and bacterial richness (p < 0.001 and p = 0.03, respectively). Additionally, decreasing phylogenetic distance between the extinct and extant species is associated with an increasing viral richness (p < 0.001). We discuss four mechanisms that may be driving these patterns and highlight future research to distinguish between them. Next, we use the models and IUCN range maps to identify geographic regions where viral and bacterial richness differs due to the inclusion of extinction variables. Notably, the richness of both pathogen types is increased in South America (viruses: +6.8%; bacteria: +3.1%) and decreased in Africa (viruses: -2.6%; bacteria: -13.6%), two continents known to have high and low levels of historical mammal extinctions, respectively. Viral richness is also elevated in North America (+8.6%), Europe (+5.1%), Oceania (+3.3%), and Asia (+2.3%). These results support the inclusion of extinction variables in future models of pathogen richness and may allow for improved targeting of future surveillance efforts.

paleontology↗

bioRxiv2022

Metagenomic analysis of coprolites from three Late Pleistocene megaherbivores from the Southwestern United States.

1.BackgroundDetermining the life-history traits of extinct species is often difficult from skeletal remains alone, limiting the accuracy of studies modeling past ecosystems. However, the analysis of the degraded endogenous bacterial DNA present in paleontological fecal matter (coprolites) may enable the characterization of specific traits such as the hosts digestive physiology and diet. An issue when evaluating the microbial composition of coprolites is the degree to which the microbiome is representative of the hosts original gut community versus the changes that occur in the weeks following deposition due to desiccation. Analyses of paleontological microorganisms are also relevant in the light of recent studies linking the Late Pleistocene and Early Holocene extinctions with modern-day zoonotic pathogen outbreaks. MethodsShotgun sequencing was performed on ancient DNA (aDNA) extracted from coprolites of the Columbian mammoth (Mammuthus Columbi), Shasta ground sloth (Nothrotheriops shastensis) and paleontological bison (Bison sp.) collected from caves on the Colorado Plateau, Southwestern USA. The novel metagenomic classifier MTSv, parameterized for studies of aDNA, was used to assign bacterial taxa to sequencing reads. The resulting bacterial community of coprolites was then compared to those from modern fecal specimens of the African savannah elephant (Loxodonta africana), the brown-throated sloth (Bradypus variegatus) and the modern bison (Bison bison). Both paleontological and modern bison fecal bacterial communities were also compared to those of progressively dried cattle feces to determine whether endogenous DNA from coprolites had a microbiome signal skewed towards aerobic microorganisms typical of desiccated fecal matter. ResultsThe diversity of phyla identified from coprolites was lower than modern specimens. The relative abundance of Actinobacteria was increased in coprolites compared to modern specimens, with fewer Bacteroidetes and Euryarchaeota. Firmicutes had a reduced relative abundance in the mammoth and bison coprolites, compared to the African savanna elephants and modern bison. There was a significant separation of samples in NMDS plots based on their classification as either paleontological or modern, and to a lesser extent, based on the host species. Increasingly dried cattle feces formed a continuum between the modern and paleontological bison samples. ConclusionOur results reveal that any coprolite metagenomes should always be compared to desiccated modern fecal samples from closely related hosts fed a comparable diet to determine the degree to which the coprolite metagenome is a result of desiccation versus true dissimilarities between the modern and paleontological hosts. Also, a large-scale desiccation study including a variety of modern species may shed light on life-history traits of extinct species without close extant relatives, by establishing the proximity of coprolite metagenomes with those from dried modern samples.

paleontology↗