W. Chris Funk

• PhD, University of Montana
• Professor at Colorado State University

The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may...

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysi...

Genetic rescue, an increase in population growth owing to the infusion of new alleles, can aid the persistence of small populations, but its use as a management tool is limited by a lack of empirical data geared towards predicting effects of gene flow on local adaptation and demography. Experimental translocations provide an ideal opportunity to mo...

Evolutionary theory predicts that divergent selection pressures across elevational gradients could cause adaptive divergence and reproductive isolation in the process of ecological speciation. Although there is substantial evidence for adaptive divergence across elevation, there is less evidence that this restricts gene flow. Previous work in the b...

Genomic data have the potential to revolutionize the delineation of conservation units (CUs) by allowing the detection of adaptive genetic variation, which is otherwise difficult for rare, endangered species. In contrast to previous recommendations, we propose that the use of neutral versus adaptive markers should not be viewed as alternatives. Rat...

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We fi...

Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied at the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play a crucial role in determining vulnerability. Genomic data can inform intrasp...

Biologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding of these effects in the wild is incomplete, in part due to the rarity of sufficient genetic and demographic data needed to measure their impact. The genomics revolution is promising a potential solut...

National, subnational, and supranational entities are creating biodiversity strategy and action plans (BSAPs) to develop concrete commitments and actions to curb biodiversity loss, meet international obligations, and achieve a society in harmony with nature. In light of policymakers' increasing recognition of genetic diversity in species and ecosys...

Temporally variable climates are expected to drive the evolution of thermal physiological traits that enable performance across a wider range of temperatures (i.e. climate variability hypothesis, CVH). Spatial thermal variability, however, may mediate this relationship by providing ectotherms with the opportunity to behaviourally select preferred t...

Genetic diversity is essential for maintaining healthy populations and ecosystems. Several approaches have recently been developed to evaluate population genetic trends without necessarily collecting new genetic data. Such “genetic diversity indicators” enable rapid, large-scale evaluation across dozens to thousands of species. Empirical genetic st...

The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Methods that estimate Ne are important in population and conservation genetic studies as they quantify the risk of a population being inbred or lacking genetic diversity. Yet there are very few m...

Under the recently adopted Kunming‐Montreal Global Biodiversity Framework, 196 Parties committed to reporting the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct po...

Inferring the environmental selection pressures responsible for phenotypic variation is a challenge in adaptation studies as traits often have multiple functions and are shaped by complex selection regimes. We provide indirect evidence that morphology of the multifunctional avian bill is primarily shaped by climate and thermoregulatory ability in M...

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextu...

Testing for intraspecific variation for host tolerance or resistance in wild populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test the importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) against Batrachochytrium de...

Globally, national, subnational, and supranational entities are creating Biodiversity Strategy and Action Plans, to develop concrete commitments and actions to curb biodiversity loss, meet international obligations and achieve a society in harmony with nature. In light of policy makers' increasing recognition of genetic diversity in helping species...

Measuring genetic diversity of wild species using DNA-based data remains resource intensive and time consuming for nearly all species. However, genetic assessments are needed for global conservation commitments, including the Convention on Biological Diversity, and for governments and managers to evaluate conservation progress, as well as prioritiz...

Temperature is arguably one of the most critical environmental factors impacting organisms at molecular, organismal, and ecological levels. Temperature variation across elevation may cause divergent selection in physiological critical thermal limits (CTMAX and CTMIN). Generally, high elevation populations are predicted to withstand lower environmen...

Hunting can fundamentally alter wildlife population dynamics, but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here we present a study that leverages a unique landscape-scale experiment coupled with pathogen transmission tracing, network simulation and phylodynamics to provide insights into how huntin...

Hunting mortality can affect population abundance, demography, patterns of dispersal and philopatry, breeding, and genetic diversity. We investigated the effects of hunting on the reproduction and genetic diversity in a puma population in western Colorado, USA. We genotyped over 11,000 single nucleotide polymorphisms (SNPs), using double‐digest, re...

Adaptive plasticity in thermal tolerance traits may buffer organisms against changing temperatures, making such responses of particular interest in the face of global climate change. Although population variation is integral to the evolvability of this trait, many studies inferring proxies of physiological vulnerability from thermal tolerance trait...

Wildlife diseases are a major global threat to biodiversity. Boreal toads (Anaxyrus [Bufo] boreas) are a state‐endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). We perfor...

Due to the ubiquity of disease in natural systems, hosts have evolved strategies of disease resistance and tolerance to defend themselves from further harm once infected. Resistance strategies directly limit pathogen growth, typically leading to lower infection burdens in the host. A tolerance approach limits the fitness consequences caused by the...

In ecology and evolution, genetic and genomic data are commonly collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, such data are typically used only once by the data-generating authors. The repurposing of genetic and genomic datasets remains uncommon because it is often difficult, if not impossible...

The genetic effective size (Ne) is arguably one of the most important characteristics of a population as it impacts the rate of loss of genetic diversity. Genetic estimators of (Ne) increasingly popular tools in population and conservation genetic studies. Yet there are very few methods that can estimate the Ne from data from a single population an...

Striking examples of local adaptation at fine geographic scales are increasingly being documented in natural populations. However, the relative contributions made by natural selection, phenotype-dependent dispersal (when individuals disperse with respect to a habitat preference), and mate preference in generating and maintaining microgeographic ada...

Estimates of organismal thermal tolerance are frequently used to assess physiological risk from warming, yet the assumption that these estimates are predictive of mortality has been called into question. We tested this assumption in the cold-water-specialist frog, Ascaphus montanus. For seven populations, we used dynamic experimental assays to meas...

1. Critical thermal limits represent an important component of an organism's capacity to cope with future temperature changes. Understanding the drivers of variation in these traits may uncover patterns in physiological vulnerability to climate change. Local temperature extremes have emerged as a major driver of thermal limits, although their effec...

Wildlife diseases are a major global threat to biodiversity. Boreal toads (Anaxyrus [Bufo] boreas) are a state-endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). We perfor...

Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patte...

Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity’s (CBD) draft post-2020 global biodiversity framework...

Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and...

Genetic diversity among and within populations of all species is necessary for people and the planet to survive in a changing world. Over the past three years, the conservation of genetic diversity has received increased ambition and specificity in commitments under the draft Convention on Biological Diversity's (CBD) post 2020 Global Biodiversity...

Aim Island biotas provide opportunities to study colonization and adaptation to novel environments. Islands, especially near‐shore islands, may have a long record of human habitation such that some lineages result from human‐assisted introductions. Here, we combine phylogenetic analyses with fossil data and historical specimen records to reconstruc...

Understanding the causes of population variation in host response to disease, and the mechanisms of persistence, can serve as vital information for species conservation. One such mechanism of population persistence that has gained support is the demographic process of compensatory recruitment. Host populations may persist by increasing recruitment...

Identifying drivers of transmission—especially of emerging pathogens—is a formidable challenge for proactive disease management efforts. While close social interactions can be associated with microbial sharing between individuals, and thereby imply dynamics important for transmission, such associations can be obscured by the influences of factors s...

Extinction‐risk assessments play a major role in prioritizing conservation action at national and international levels. However, quantifying extinction risk is challenging, especially when including the full suite of adaptive responses to environmental change. In particular, evolutionary potential (EP) – the capacity to evolve genetically based cha...

Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We...

Captive breeding represents the last chance of survival for many species faced with imminent extinction in the wild. Captive breeding should be used sparingly because it is sometimes ineffective, and it can harm wild populations both indirectly and directly if not done correctly. There are a variety of crucial genetic issues to be considered in the...

Population genetic models become much more complex when two or more loci are considered simultaneously. Random association of the alleles (and genotypes) at two loci is called gametic equilibrium. Linkage is the primary factor that can cause the alleles at two loci to be in nonrandom association within a population. This is called gametic disequili...

Natural selection is the differential contribution of genotypes to the next generation due to differences in survival and reproduction. Understanding the effects of natural selection on allele frequencies involves using a variety of mathematical models along with the fitness of different genotypes. Finesses are not constant. For example, fitness so...

All populations are finite in size so that genetic drift will occur in all natural and managed populations. Genetic drift causes both changes in allele frequencies and the loss of genetic variation. Loss of heterozygosity and loss of alleles are t^ghe two primary measures of the loss of genetic variation in populations. Matings between related indi...

Invasive species have significant effects on biodiversity. Genetics provides insights important for eradication and control crucial for conservation. Invasive species can be successful despite bottlenecks because of increased genetic diversity following hybridization or multiple introductions, rapid evolutionary change, lack of natural enemies, or...

Genetic analysis allows genetic identification of individuals, populations, and species for a range of conservation purposes, including wildlife trafficking, detecting invasive species, determining relatedness in captive breeding, and identifying community composition. Genomics provides increased power for genetic identification at individual, popu...

Genetics is the study of the inheritance of differences among individuals. Genomic approaches now make it possible to better understand the genetic basis and adaptive significance of phenotypic differences among individuals. Population-level differences in disease resistance will have important implications for population persistence in the face of...

Genetic factors affect the extinction probability of populations in a variety of ways. Inbreeding depression can reduce fecundity and survival, and thereby decrease population growth rate and increase extinction probability. Multiple studies have shown that inbreeding depression can negatively impact populations in the wild. Loss of genetic variati...

We discuss the roles of gene flow, genetic drift, and selection in determining the distribution of genetic variation in complex, real-world landscapes. A metapopulation is a group of populations that experience some degree of gene flow among them. Metapopulation structure can have complex effects on patterns of genetic variation within and among po...

We introduce the Hardy–Weinberg principle, which is the fundamental model of population genetics. The use of mathematical models is essential to understand the effects of Mendelian inheritance and the evolution of allele frequencies in natural populations. The Hardy–Weinberg model assumes random mating, infinite population size, no natural selectio...

Populations may respond to environmental changes through phenotypic plasticity, adaptation, or migration, or suffer demographic declines if they are unable to respond. Climate change is already causing shifts in species ranges, changes in phenotypes, and altered interspecific interactions. The capacity for a population to adapt to new conditions is...

Hybridization occurs between species or populations, and can arise from either natural or anthropogenic causes. Hybridization is important in natural evolutionary processes, but can be a harmful force reducing species identity and reproductive success. Hybridization can increase fitness through heterosis, or reduce fitness through outbreeding depre...

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are...

The Coalition for Conservation Genetics (CCG) brings together four eminent organizations with the shared goal of improving the integration of genetic information into conservation policy and practice. We provide a historical context of conservation genetics as a field and reflect on current barriers to conserving genetic diversity, highlighting the...

We investigated the potential mechanisms driving habitat‐linked genetic divergence within a bird species endemic to a single 250‐km² island. The island scrub‐jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine–oak ecotones on Santa Cruz Island, California (USA), similar to adaptive differences described in...

Populations may respond to environmental changes through phenotypic plasticity, adaptation, migration, or suffer demographic declines if they are unable to respond. Climate change is already causing shifts in species ranges, changes in phenotypes, and altered life history traits and interspecific interactions. The capacity for a population to adapt...

Sequencing all or part of the genome of individuals from different populations allows for many analyses of genetic variation that are not possible with a small number of unlinked markers. Genomic datasets may include sequences of anonymous regions scattered throughout the genome, sequences of targeted regions such as exomes, whole genome sequences,...

In this chapter, we discuss the importance of and methods for delineating conservation units, including species and intraspecific units (e.g., evolutionarily significant units and management units). It is essential to conserve all levels of biodiversity, including genes, populations, species, and ecosystems, for effective biodiversity conservation....

There is mounting evidence that human exploitation of wild populations can lead to genetic changes that greatly increase the complexity of managing sustainable populations. Harvest can reduce the effective population size and cause loss of genetic variation by reducing population size directly and by reducing the number of migrants into local popul...

Most phenotypic traits are the product of many genes as well as environmental effects, and the resulting phenotypic variation is quantitative rather than qualitative. The extent to which traits are under genetic control is termed heritability, and can be estimated by analyzing the phenotypic similarity of related individuals. Quantitative genetic a...

Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or comme...

Mutations are errors in the transmission of genetic information from parents to progeny, and an understanding of mutation assists in interpreting patterns of genetic variation to inform conservation. Mutation is the source of all variation, and can be neutral, beneficial, or detrimental. Mutation rates vary across the nuclear genome, and are genera...

Natural populations of most species are subdivided or “structured” into partially isolated local random mating populations that are called “demes.” The subdivision of a species into subpopulations means that genetic variation exists at two levels: (1) genetic variation within local populations and (2) genetic diversity between local populations. Th...

We expect heterozygosity to be lost at a rate of 1/2 N per generation in an ideal population because of genetic drift where N is the census population size. The effective size of a population is the size of the ideal (Wright–Fisher) population that will result in the same amount of genetic drift as in the actual population being considered. Heteroz...

Genetics plays an increasing role in monitoring demographic and genetic changes in populations over time. One of the most powerful advances in genetic monitoring is the development of techniques to detect trace amounts of DNA in noninvasive samples (e.g., feathers, skin, etc.) and environmental DNA (eDNA) from elusive and rare species in water and...

Genetic variation among individuals within populations and among populations can be assessed at the chromosomal, protein, or DNA sequence level. The best tool or approach depends on the question being asked. Variation in the number or structure of chromosomes can result in reproductive incompatibilities and reduced fitness that influences the succe...

Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genomics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or comme...

Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulation and phylodynamics to provide insights into how...

Theory suggests that the evolution of dispersal is balanced by its fitness costs and benefits, yet empirical evidence is sparse due to the difficulties of measuring dispersal and fitness in natural populations. Here, we use spatially explicit data from a multi‐generational capture–mark–recapture study of two populations of Trinidadian guppies (Poec...

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functi...

Phenotypic and genetic divergence are shaped by the homogenizing effects of gene flow and the differentiating processes of genetic drift and local adaptation. Herein, we examined the mechanisms that underlie phenotypic (size and color) and genetic divergence in 35 populations (535 individuals) of the poison frog Epipedobates anthonyi along four ele...

Disentangling the effects of neutral and adaptive processes in maintaining phenotypic variation across environmental gradients is challenging in natural populations. Song sparrows (Melospiza melodia) on the California Channel Islands occupy a pronounced east‐west climate gradient within a small spatial scale, providing a unique opportunity to exami...

Island populations are at higher risk of extinction than mainland populations. Therefore, understanding the factors that facilitate connectivity is particularly pressing for the conservation of island taxa. Sceloporus occidentalis becki, the Island Fence Lizard, is an endemic taxon restricted to the Northern Channel Islands, part of a nearshore arc...

Inferring the environmental selection pressures responsible for phenotypic variation is a challenge in adaptation studies as traits often have multiple functions and are shaped by complex selection regimes. We provide experimental evidence that morphology of the multifunctional avian bill is related to climate, not foraging efficiency, in song spar...

A long‐standing question in evolutionary biology is the extent to which adaptation to novel stressors can buffer populations from extinction. This question is arguably one of the most important questions for evolutionary biologists to answer in this age of rapid global change. Knowledge of how best to manage genetic variation in organisms faced wit...

Frameworks exclusively considering functional diversity are gaining popularity, as they complement and extend the information provided by taxonomic diversity metrics, particularly in response to disturbance. Taxonomic diversity should be included in functional diversity frameworks to uncover the functional mechanisms causing species loss following...

A correction to this paper has been published: https://doi.org/10.1007/s10592-021-01376-9

Large body size is an important determinant of individual fitness in many animal species, especially in island systems where habitat saturation may result in strong intraspecific competition for mates and breeding territories. Here we show that large body size is associated with benefits to yearling breeding and extra-pair mating in the Island Scru...

International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve, and sustainably and equitably use, biodiversity. The CBD is a vital instrument for global conservation because it guides 195 countries and the European Union in setting priorities and allocating resources, and requires regular reporting on prog...

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on the conservation of genome-wide genetic variation, and that this approach should be replaced with another that foc...

Temperature is a critical driver of ectotherm life‐history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life‐history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number...

Parasite success typically depends on a close relationship with one or more hosts; therefore, attributes of parasitic infection have the potential to provide indirect details of host natural history and are biologically relevant to animal conservation. Characterization of parasite infections has been useful in delineating host populations and has s...

Hunting can fundamentally alter wildlife population dynamics, but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here we present a study that leverages a unique landscape-scale experiment coupled with pathogen transmission tracing, network simulation and phylodynamics to provide insights into how huntin...

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been d...

A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, m...

Structured demographic models are among the most common and useful tools in population biology. However, the introduction of integral projection models (IPMs) has caused a profound shift in the way many demographic models are conceptualized. Some researchers have argued that IPMs, by explicitly representing demographic processes as continuous funct...

Morphological variation is often maintained by complex and interrelated factors, complicating the identification of underlying drivers. Tadpole oral morphology is one such trait that may be driven by the independent and interacting effects of the environment and variation in developmental processes. Although many studies have investigated tadpole o...

Identifying drivers of transmission prior to an epidemic - especially of an emerging pathogen - is a formidable challenge for proactive disease management efforts. We tested a novel approach in the Florida panther, hypothesizing that apathogenic feline immunodeficiency virus (FIV) transmission could predict transmission dynamics for pathogenic feli...