Thomas B Smith

University of California, Los Angeles | UCLA · Department of Ecology and Evolutionary Biology

La protección y conservación de las aves terrestres migratorias neártico-neotropicales es una responsabilidad compartida por varios países del hemisferio occidental. Sin embargo, la colaboración transfronteriza entre múltiples organizaciones, misiones e idiomas puede ser un desafío. El Instituto de Poblaciones de Aves, la Universidad Estatal de Col...

Three‐dimensional (3D) vegetation structure influences animal movements and, consequently, ecosystem functions. Animals disperse the seeds of 60%–90% of trees in tropical rainforests, which are among the most structurally complex ecosystems on Earth. Here, we investigated how 3D rainforest structure influences the movements of large, frugivorous bi...

Animals disperse seeds in various ways that affect seed deposition sites and seed survival, ultimately shaping plant species distribution, community composition, and ecosystem structure. Some animal species can disperse seeds through multiple pathways (e.g., defecation, regurgitation, epizoochory), each likely producing distinct seed dispersal outc...

The extraction of crude oil and gold has substantially increased heavy metal contamination in the environment, yet the study of wildlife exposure and biological response to this pollution remains nascent even in the most biodiverse places in the world. We present a survey of heavy metal exposure in the feathers of wedge‐billed woodcreepers ( Glypho...

Tracking climatic conditions throughout the year is often assumed to be an adaptive behaviour underlying seasonal migration patterns in animal populations. We investigate this hypothesis using genetic markers data to map migratory connectivity for 27 genetically distinct bird populations from 7 species. We found that the variation in seasonal clima...

Species evolve from populations with ancestor-descendant relationships in a bifurcating process shaped by geography, gene flow, genetic drift, and natural selection leading to local adaptation to prevailing environmental and ecological conditions. Building on this foundational understanding, we explored local adaptation in chimpanzees ( Pan troglod...

Central African rainforests are predicted to be disproportionately affected by future climate change. How species will cope with these changes is unclear, but rapid environmental changes will likely impose strong selection pressures. Here we examined environmental drivers of genomic variation in the central African puddle frog ( Phrynobatrachus aur...

accurate mapping and monitoring of tropical forests aboveground biomass (aGB) is crucial to design effective carbon emission reduction strategies and improving our understanding of Earth's carbon cycle. However, existing large-scale maps of tropical forest aGB generated through combinations of Earth Observation (EO) and forest inventory data show m...

The Yellow Warbler (Setophaga petechia) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from...

The Yellow Warbler ( Setophaga petechia ) is a small songbird in the New World Warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler fr...

With new motivation to increase the proportion of energy demands met by zero-carbon sources, there is a greater focus on efforts to assess and mitigate the impacts of renewable energy development on sensitive ecosystems and wildlife, of which birds are of particular interest. One challenge for researchers, due in part to a lack of appropriate tools...

The white-bellied pangolin ( Phataginus tricuspis ) is the world’s most trafficked mammal and is at risk of extinction. Reducing the illegal wildlife trade requires an understanding of its origins. Using a genomic approach for tracing confiscations and analyzing 111 samples collected from known geographic localities in Africa and 643 seized scales...

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to exa...

Renewable energy production and development will drastically affect how we meet global energy demands, while simultaneously reducing the impact of climate change. Although the possible effects of renewable energy production (mainly from solar- and wind-energy facilities) on wildlife have been explored, knowledge gaps still exist, and collecting dat...

Understanding the geographic linkages among populations across the annual cycle is an essential component for understanding the ecology and evolution of migratory species and for facilitating their effective conservation. While genetic markers have been widely applied to describe migratory connections, the rapid development of new sequencing method...

To cope with climate change, species may shift their distributions or adapt in situ to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher (Empidonax traillii extimus) through whole-genome compar...

We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n...

Habitat-specific thermal responses are well documented in various organisms and likely determine the vulnerability of populations to climate change. However, the underlying roles of genetics and plasticity that shape such habitat-specific patterns are rarely investigated together. Here we examined the thermal plasticity of the butterfly Bicyclus do...

Technological advances in migratory tracking tools have revealed a remarkable diversity in migratory patterns. One such pattern is leapfrog migration, where individuals that breed further north migrate to locations further south. Here, we analyzed migration patterns in the Painted Bunting (Passerina ciris) using a genetic-based approach. We started...

Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood....

The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored black...

The tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored black...

Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotyp...

Birds exhibit a remarkable array of seasonal migrations. Despite much research describing migratory behaviour, the underlying forces driving how a species’ breeding and wintering populations redistribute each year, that is, migratory connectivity, remain largely unknown. Here, we test the hypothesis that birds migrate in a way that minimises energy...

Identifying population genetic structure is useful for inferring evolutionary process and comparing the resulting structure with subspecies boundaries can aid in species management. The American Kestrel (Falco sparverius) is a widespread and highly diverse species with 17 total subspecies, only 2 of which are found north of U.S./Mexico border (F. s...

This practical guide is an annex to the paper: PICT: A low-cost, modular, open-source camera trap system to study plant-insect interactions. Methods in Ecology and Evolution (Droissart V., Azandi L., Onguene E.R., Savignac M., Smith T.B., Deblauwe V. 2021). https://doi.org/10.1111/2041-210X.13618 PICT (Plant-insect Interactions Camera Trap) is an...

Understanding how risk factors affect populations across their annual cycle is a major challenge for conserving migratory birds. For example, disease outbreaks may happen on the breeding grounds, the wintering grounds, or during migration, and are expected to accelerate under climate change. The ability to identify the geographic origins of impacte...

Global loss of biodiversity has placed new urgency on the need to understand factors regulating species response to rapid environmental change. While specialists are often less resilient to rapid environmental change than generalists, species‐level analyses may obscure the extent of specialization when locally adapted populations vary in climate to...

Commercial camera traps (CTs) commonly used in wildlife studies have several technical limitations that restrict their scope of application. They are not easily customizable, unit prices sharply increase with image quality and importantly, they are not designed to record the activity of ectotherms such as insects. Those developed for the study of p...

For migratory species, seasonal movements complicate local climate adaptation, as it is unclear whether individuals track climate niches across the annual cycle. In the migratory songbird yellow warbler (Setophaga petechia), we find a correlation between individual‐level wintering and breeding precipitation, but not temperature. Birds wintering in...

Preserving biodiversity under rapidly changing climate conditions is challenging. One approach for estimating impacts and their magnitude is to model current relationships between genomic and environmental data and then to forecast those relationships under future climate scenarios. In this way understanding future genomic and environmental relatio...

One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple sub-species. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains ze...

Habitat loss and alteration has driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The t...

Predicting species' capacity to respond to climate change is an essential first step in developing effective conservation strategies. However, conservation prioritization schemes rarely take evolutionary potential into account. Ecotones provide important opportunities for diversifying selection and may thus constitute reservoirs of standing variati...

Migratory animals are declining worldwide and coordinated conservation efforts are needed to reverse current trends. We devised a novel genoscape‐network model that combines genetic analyses with species distribution modeling and demographic data to overcome challenges with conceptualizing alternative risk factors in migratory species across their...

Adaptation across climate gradients can provide the raw material needed for evolutionary response to climate change. In migratory species, studies of local climate adaptation are made challenging by seasonal movement, where it is unclear to what extent individuals track their local climate niches across the annual cycle. In the migratory songbird y...

As of June 16, 2019, an Ebola virus disease (EVD) outbreak has led to 2136 reported cases in the northeastern region of the Democratic Republic of the Congo (DRC). As this outbreak continues to threaten the lives and livelihoods of people already suffering from civil strife and armed conflict, relatively simple mathematical models and their short-t...

Highly pathogenic avian influenza virus (HPAI H5N1) has caused drastic economic losses in the poultry sector in Egypt, as well as many human deaths, predominantly among women and children. As primary caretakers of a growing poultry industry, women represent a potentially powerful front line for efforts to control and mitigate influenza outbreaks. T...

Pyrenestes finches are unique among birds in showing a non-sex-determined polymorphism in bill size and are considered a textbook example of disruptive selection. Morphs breed randomly with respect to bill size, and differ in diet and feeding performance relative to seed hardness. Previous breeding experiments are consistent with the polymorphism b...

Fitzpatrick et al discuss issues that they had with analyses and interpretation in our recent manuscript on genomic correlates of climate in yellow warblers. We provide evidence that our findings would not change with different analysis and maintain that our study represents a promising direction for integrating the potential for climate adaptation...

Through the rise of global commodity chains, consumer demand in China and the USA has given rise to the extraction of natural resources in the Congo Basin. The Chinese market for high‐valued animal products such as elephant ivory and pangolin scales has encouraged poaching, exploitation and trafficking of these goods in Africa. Chinese demand for o...

Few regions have been more severely impacted by climate change in the USA than the Desert Southwest. Here, we use ecological genomics to assess the potential for adaptation to rising global temperatures in a widespread songbird, the willow flycatcher (Empidonax traillii), and find the endangered desert southwestern subspecies (E. t. extimus) most v...

Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000...

Plant and animal diversity generally increases with increasing environmental heterogeneity. Here, we test whether this relationship also holds for bacterial communities in soil. Specifically, we investigate whether invasive annual grasslands have reduced soil heterogeneity and, thereby, decreased bacterial alpha- and beta-diversity. Soils were samp...

Yellow warblers already in decline As the climate changes, species' ability to adapt to changing conditions may relate directly to their future persistence. Determining whether and when this will happen is challenging, however, because it is difficult to tease apart the causes of decline or maintenance. Bay et al. looked at the relationship between...

Recent outbreaks of Ebola virus disease and Zika virus disease highlight the need for disseminating accurate predictions of emerging zoonotic viruses to national governments for disease surveillance and response. Although there are published maps for many emerging zoonotic viruses, it is unknown if there is agreement among different models or if th...

The burden of arboviruses in the Americas is high and may result in long-term sequelae with infants disabled by Zika virus infection (ZIKV) and arthritis caused by infection with Chikungunya virus (CHIKV). We aimed to identify environmental drivers of arbovirus epidemics to predict where the next epidemics will occur and prioritize municipalities f...

Incidence of lab-confirmed ZIKV and CHIKV cases. (DOCX)

Timing of temperature and lab-confirmed cases of ZIKV (LABFLA dataset) January 2015-July 2016. (DOCX)