
Liliana M. DavalosStony Brook University | Stony Brook · Department of Ecology and Evolution
Liliana M. Davalos
Professor
About
291
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Introduction
Additional affiliations
September 2007 - May 2008
August 2005 - October 2006
Sackler Institute for Comparative Genomics
Position
- PostDoc Position
August 2004 - June 2005
Publications
Publications (291)
Are bats really just what they eat? Oh well yes of course, plus a few parts per meal/mil. In this paper we sought to answer how interrelationships among different structures of the head may influence the evolution of a species, and how this can be associated with diet. After sampling a few sensory and mechanical structures from the Noctilionoid sup...
High viral tolerance coupled with an extraordinary regulation of the immune response makes bats a great model to study host-pathogen evolution. Although many immune-related gene gains and losses have been previously reported in bats, important gene families such as antimicrobial peptides (AMPs) remain understudied. We built an exhaustive bioinforma...
To meet the challenge of wintering in place many high-latitude small mammals reduce energy demands through hibernation. In contrast, short-lived Eurasian common shrews, Sorex araneus, remain active and shrink, including energy-intensive organs in winter, regrowing in spring in an evolved strategy called Dehnel's phenomenon. How this size change is...
Compared to their free-ranging counterparts, wild animals in captivity are subject to different conditions with lasting effects on their physiology and behavior. Alterations in gene expression in response to environmental changes occur upstream of physiological and behavioral phenotypes, but there are no experiments analyzing differential gene expr...
Contrasting almost all other mammalian wintering strategies, Eurasian common shrews, Sorex araneus , endure winter by shrinking their brain, skull, and most organs, only to then regrow to breeding size the following spring. How such tiny mammals achieve this unique brain size plasticity while maintaining activity through the winter remains unknown....
Zoonoses are infectious diseases transmitted from animals to humans. Bats have been suggested to harbour more zoonotic viruses than any other mammalian order¹. Infections in bats are largely asymptomatic2,3, indicating limited tissue-damaging inflammation and immunopathology. To investigate the genomic basis of disease resistance, the Bat1K project...
Under an adaptive hypothesis, the reciprocal influence between mutualistic plants and frugivores is expected to result in suites of matching frugivore and plant traits that structure fruit consumption. Recent work has suggested fruit traits can represent adaptations to broad groups of functionally similar frugivores, but the role of frugivore trait...
Compared with their free-ranging counterparts, wild animals in captivity experience different conditions with lasting physiological and behavioural effects. Although shifts in gene expression are expected to occur upstream of these phenotypes, we found no previous gene expression comparisons of captive versus free-ranging mammals. We assessed gene...
Contrasting almost all other mammalian wintering strategies, Eurasian common shrews, Sorex araneus , endure winter by shrinking their brain, skull, and most organs, only to then regrow to breeding size the following spring. How such tiny mammals achieve this unique brain size plasticity while maintaining activity through the winter remains unknown....
Contrasting almost all other mammalian wintering strategies, Eurasian common shrews, Sorex araneus , endure winter by shrinking their brain, skull, and most organs, only to then regrow to breeding size the following spring. How such tiny mammals achieve this unique brain size plasticity while maintaining activity through the winter remains unknown....
First isolated from neotropical fruit bats in Trinidad in 1956, Tacaribe virus (TCRV) has rarely been detected since. We searched for New World arenavirus reads in roughly 5.7 million sequencing runs available on public databases using Serratus. We recovered a complete genome of a divergent TCRV in metatranscriptomic data derived from heart and eye...
Neotropical ecosystems are renowned for numerous examples of adaptive radiation in both plants and animals resulting in high levels of biodiversity and endemism. However, we still lack a comprehensive review of the abiotic and biotic factors that contribute to these adaptive radiations. To fill this gap, we delve into the geological history of the...
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and genetic variation. Mutations generated by APOBEC3 contribute to genetic variation and tumor evolvability. However, the influence of APOBEC3 on the evolvability of the genome and its differential impact on cancer genes versus non-cancer genes remains unclear...
We use generalized joint attribute modeling (GJAM) to estimate how the proclivity to consume different Piper species varies among three syntopic Carollia species my depend on bat traits (e.g., body size and age) or Piper fruit traits. How these ecologically and morphologically similar bats coexist is unclear. Compared to the Piper -specialist Carol...
Under an adaptive hypothesis, the reciprocal influence between mutualistic plants and frugivores is expected to result in dispersal syndromes comprising both frugivore and plant traits that structure fruit consumption. Tests of this adaptive hypothesis, however, focus on traits of either fruits or frugivores but not both and often ignore within-spe...
Sensory organs must develop alongside the skull within which they are largely encased, and this relationship can manifest as the skull constraining the organs, organs constraining the skull, or organs constraining one another in relative size. How this interplay between sensory organs and the developing skull plays out during the evolution of senso...
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus–bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from...
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and, ultimately, genetic variation. Mutations generated by APOBEC3 cytidine deaminases can contribute to genetic variation and the consequences of APOBEC activation differ depending on the stage of cancer, with the most significant impact observed during the ea...
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational ‘hotspots’, can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outb...
APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational 'hotspots,' can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outb...
The common shrew, Sorex araneus, is a small mammal of growing interest in neuroscience research, as it exhibits dramatic and reversible seasonal changes in individual brain size and organization (a process known as Dehnel's phenomenon). Despite decades of studies on this system, the mechanisms behind the structural changes during Dehnel's phenomeno...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion...
How traits affect speciation is a long-standing question in evolution. We investigate whether speciation rates are affected by the traits themselves or by the rates of their evolution, in hummingbirds, a clade with great variation in speciation rates, morphology and ecological niches. Further, we test two opposing hypotheses, postulating that speci...
Horizontal transfer of transposable elements is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of transposable elements at what appears to be a high rate compared to other mammals. We investigated the occurrence of horizontally transferred...
Horizontal transfer of transposable elements is an important mechanism contributing to genetic diversity and innovation. Bats (order Chiroptera) have repeatedly been shown to experience horizontal transfer of transposable elements at what appears to be a high rate compared to other mammals. We investigated the occurrence of horizontally transferred...
Bats carry viruses that can cause severe disease in other mammals. Asymptomatic infections in bats suggest limited tissue-damaging inflammation and immunopathology. To investigate the genomic basis of disease resistance, the Bat1K project generated reference-quality genomes of ten bat species. A systematic analysis showed that signatures of selecti...
Many of Madagascar’s unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We m...
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We find that while mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and...
Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pron...
Madagascar's biota has suffered recent extinctions and many of its unique species are threatened. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. We compiled a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimated natural rates of extinction, coloniza...
While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness‐related resources, and thus the underlying genomic architecture and morphology must cope with...
This Report provides a comprehensive, objective, open, transparent, systematic, and rigorous scientific assessment of the state of the Amazon’s ecosystems, current trends, and their implications for the long-term well-being of the region, as well as opportunities and policy relevant options for conservation and sustainable development.
Relationships among laurasiatherian clades represent one of the most highly disputed
topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the...
Scientists recognize the Caribbean archipelago as a biodiversity hotspot and employ it for their research as a “natural laboratory”. Yet, they do not always appreciate that these ecosystems are in fact palimpsests shaped by multiple human cultures over millennia. Although post-European anthropogenic impacts are well documented, human influx into th...
Human impacts on the Earth’s biosphere are driving the global biodiversity crisis. Governments are preparing to agree on a set of actions intended to halt the loss of biodiversity and put it on a path to recovery by 2050. We provide evidence that the proposed actions can bend the curve for biodiversity, but only if these actions are implemented urg...
EXPERT INPUT TO THE POST-2020 GLOBAL BIODIVERSITY FRAMEWORK:
TRANSFORMATIVE ACTIONS ON ALL DRIVERS OF BIODIVERSITY LOSS ARE
URGENTLY REQUIRED TO ACHIEVE THE GLOBAL GOALS BY 2050
Forests and aquatic ecosystems are the basis for ecosystem services, which play a crucial role in people’s livelihoods, human well-being, and health. Some of the most relevant and challenging current health problems in Amazonia are associated with deforestation and degradation of terrestrial and aquatic ecosystems, including the risk of contracting...
This Report provides a comprehensive, objective, open, transparent, systematic, and rigorous scientific assessment of the state of the Amazon’s ecosystems, current trends, and their implications for the long-term well-being of the region, as well as opportunities and policy relevant options for conservation and sustainable development.
Critical thinking (CT) underpins the analytical and systems-thinking capacities needed for effective conservation in the 21st century but is seldom adequately fostered in most postsecondary courses and programs. Many instructors fear that devoting time to process skills will detract from content gains and struggle to define CT skills in ways releva...
Population growth with weak economic development can promote tropical deforestation, but government infrastructure investment can also open new frontiers and thus increase deforestation. In the Andean region of South America, population growth has been a leading explanation for both deforestation and coca cultivation, but coca generates armed confl...
While evolvability of genes and traits may promote specialization during species diversification, how ecology subsequently restricts such variation remains unclear. Chemosensation requires animals to decipher a complex chemical background to locate fitness-related resources, and thus the underlying genomic architecture and morphology must cope with...
In most vertebrates, the demand for glucose as the primary substrate for cellular respiration is met by the breakdown of complex carbohydrates, or energy is obtained by protein and lipid catabolism. In contrast, a few bat and bird species have convergently evolved to subsist on nectar, a sugar-rich mixture of glucose, fructose, and sucrose.1-4 How...
Despite the widespread notion that animal-mediated seed dispersal led to the evolution of fruit traits that attract mutualistic frugivores, the dispersal syndrome hypothesis remains controversial, particularly for complex traits such as fruit scent. Here, we test this hypothesis in a community of mutualistic, ecologically important neotropical bats...
The United Nations set “The 2030 Agenda for Sustainable Development,” which includes the Sustainable Development Goals (SDGs), a collection of 17 global goals designed to be a “blueprint to achieve a better and more sustainable future for all”. Although only mentioned in one of the seventeen goals (goal 3), we argue that drugs in general, and growi...
Fire plays a dominant role in deforestation, particularly in the tropics, but the relative extent of transformations and influence of fire frequency on eventual forest loss remain unclear. Here, we analyze the frequency of fire and its influence on postfire forest trajectories between 2001 and 2018. We account for ~1.1% of Latin American forests bu...
Mammalian olfactory receptor genes (ORs) are a diverse family of genes encoding proteins that directly interact with environmental chemical cues. ORs evolve via gene duplication in a birth-death fashion, neofunctionalizing and pseudogenizing over time. Olfaction is a primary sense used for food detection in plant-visiting bats, but the relationship...
Los bosques Amazónicos y los ecosistemas acuáticos son la base de varios servicios ecosistémicos, los cuales desempeñan un papel crucial en los medios de vida, bienestar y salud de los seres humanos. Algunos de los problemas de salud más relevantes y desafiantes de la Amazonía están relacionados con la deforestación y la degradación de los ecosiste...
Negative environmental impacts of violent conflict have been observed worldwide. Whether or not active global conflicts are declining in number remains hotly debated, the number of countries entering post-conflict periods is on the rise, and the impact of this transition on land cover changes remains poorly understood. In Colombia, though large-sca...
Comprising more than 1,400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the...
The role of mechanical morphologies in the exploitation of novel niche space is well characterized, however, the role of sensory structures in unlocking new niches is less clear. Here we investigate the relationship between the evolution of sensory structures and diet during the radiation of noctilionoid bats. With a broad range of foraging ecologi...
Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have...
Populations along steep environmental gradients are subject to differentiating selection that can result in local adaptation, despite countervailing gene flow and genetic drift. In montane systems, where species are often restricted to narrow ranges of elevation, it is unclear whether selection is strong enough to influence functional differentiati...
Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sourc...
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent l...
Mammalian olfactory receptors ( OR s) are a diverse family of genes encoding proteins that directly interact with environmental chemical cues. OR s evolve via gene duplication in a birth-death fashion, neofunctionalizing and pseudogenizing over time. Olfaction is a primary sense used for food detection in plant-visiting bats, but the relationship b...
This book discusses in detail the adaptive radiation of American leaf-nosed bats (Phyllostomidae), the most diverse family morphologically, behaviorally, and trophically of all bats. It is divided into five major sections that cover the family’s evolution, classification, and historical biogeography; many aspects of its basic biology; its trophic,...
Diversification and adaptive radiations are tied to evolvability, which in turn is linked to morphological integration. Tightly integrated structures typically evolve in unison, whereas loosely integrated structures evolve separately. Highly integrated structures are therefore thought to constrain evolutionary change by limiting morphological dispa...
Bats possess extraordinary adaptations, including flight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scaffolding protocols¹ to generate, to our knowledge, the first reference-...
Although cases of independent adaptation to the same dietary niche have been documented in mammalian ecology, the molecular correlates of such shifts are seldom known. Here we used genome‐wide analyses of molecular evolution to examine two lineages of bats that, from an insectivorous ancestor, have both independently evolved obligate frugivory: the...
Changes in behaviour may initiate shifts to new adaptive zones, with physical adaptations for novel environments evolving later. While new mutations are commonly considered engines of adaptive change, sensory evolution enabling access to new resources might also arise from standing genetic diversity, and even gene loss. We examine the relative cont...