W. Chris Funk

Colorado State University | CSU · Department of Biology

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...

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...

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...

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 m...

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...

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...

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...

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...

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...

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...

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...

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...

1. 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 underly such life history shifts in wild populations. Single Nucleotide Polymorphisms (SNPs) and Copy Num...

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...

Parasite success is typically dependent upon 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 an...

1. Morphological variation is often maintained by complex and interrelated factors, complicating the identification of underlying drivers. Comprehensive understanding of the evolution of morphological traits thus requires the use of integrative methods that can simultaneously investigate potentially interacting drivers. 2. Tadpole oral morphology...

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...

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...

Urban expansion can fundamentally alter wildlife movement and gene flow, but how urbanization alters pathogen spread is poorly understood. Here, we combine high resolution host and viral genomic data with landscape variables to examine the context of viral spread in puma ( Puma concolor ) from two contrasting regions: one bounded by the wildland ur...

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effectiv...

Population genomics provides a powerful and growing set of approaches for wildlife biology, revealing new insights into demographic history, population structure, adaptation, and the consequences of genetic diversity. Given the multiple threats faced by global biodiversity, it is critical for researchers to advance efforts to manage and conserve wi...

A fundamental gap in climate change vulnerability research is an understanding of the relative thermal sensitivity of ectotherms. Aquatic insects are vital to stream ecosystem function and biodiversity but insufficiently studied with respect to their thermal physiology. With global temperatures rising at an unprecedented rate, it is imperative that...

Urban development has major impacts on connectivity among wildlife populations and is thus likely an important factor shaping pathogen transmission in wildlife. However, most investigations of wildlife diseases in urban areas focus on prevalence and infection risk rather than potential effects of urbanisation on transmission itself. Feline immunode...

Genetic diversity is critically important for all species-domesticated and wild- to adapt to environmental change, and for ecosystem resilience to extreme events. International agreements such as the Convention on Biological Diversity (CBD) have committed to conserve and sustainably and equitably use all levels of biodiversity-genes, species and ec...

The 196 parties to the Convention on Biological Diversity (CBD) will soon agree to a post-2020 global framework for conserving the three elements of biodiversity (genetic, species, and ecosystem diversity) while ensuring sustainable development and benefit sharing. As the most significant global conservation policy mechanism, the new CBD framework...

The ABCD conference format (All continents, Balanced gender, low Carbon transport, Diverse backgrounds) mixes live-streamed and pre-recorded talks with in-person ones to reflect a diverse range of viewpoints and reduce the environmental footprint of meetings while also lowering barriers to inclusiveness.

Species are a fundamental unit of biodiversity that are delimited via genetic data and coalescent-based methods with increasing frequency. Despite the widespread use of coalescent-based species delimitation, we do not fully understand the sensitivity of these methods to potential sources of bias and violations of their underlying assumptions. One i...

The ABCD conference format (All continents, Balanced gender, low Carbon transport, Diverse backgrounds) mixes live-streamed and pre-recorded talks with in-person ones to reflect a diverse range of viewpoints and reduce the environmental footprint of meetings while also lowering barriers to inclusiveness.