Paul A. Hohenlohe’s research while affiliated with University of Idaho and other places

Heat stress can increase disease risk in fishes by reducing immune function. Interactions between redband trout ( Oncorhynchus mykiss gairdneri ) and Flavobacterium columnare , a causative agent of columnaris disease, provide an opportunity to investigate the effects of temperature on immune function and disease resistance during periods of thermal stress. We conducted three trials to characterise differences in immune function and mortality between redband trout held at 18°C and 21°C following challenge with F . columnare . In trial 1, cumulative per cent mortality (CPM) was low and not statistically different between 18°C and 21°C. In trials 2 and 2, we administered higher challenge doses and observed increased CPM overall and significantly greater CPM at 21°C than 18°C. Redband trout upregulated il‐8 , tnf‐α , igm and igt following infection by F . columnare , suggesting that all of these genes may be involved in immune responses to F . columnare infection. We found no differences in the strength of the immune responses between fish held at 21°C versus 18°C. This indicated that 21°C did not elicit sufficient thermal stress to impair immune function and that increased CPM at 21°C versus 18°C was due to enhanced F . columnare virulence.

Shifts in life history traits, such as timing of reproduction, can help mediate population declines following perturbations, and early reproduction should be favoured when adult survival is impacted more than juvenile survival. In Tasmanian devils, following the emergence of a fatal transmissible cancer, females started to breed precocially (i.e., at age one instead of typically age two) and the same time as populations started to decline following disease emergence. Here, we focus on a diseased site (Freycinet Peninsula, Tasmania, Australia) with 18 years of continuous mark-recapture data to test: (1) whether rates of precocial breeding in females continued to increase after the initial rise after the emergence of the disease, (2) whether there was a relationship between body size and breeding success for either one-year-olds or adult females (i.e., at least two-years-old), and (3) whether there was inbreeding depression in breeding success for either age category. We show that rates of precocial breeding did not continue to rise, and that the proportion of precocially breeding females has plateaued at around 50%. We also show that there was no effect of body size on the probability of breeding for either one-year-old or for adult females. Finally, we show that there was no evidence for inbreeding depression in breeding success for either age class. We discuss possible constraints that may have inhibited further rise in rates of precocial breeding in the context of limitations to growth in the offspring of precocially breeding (and therefore smaller) females.

Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself.

Global biodiversity is under accelerating threats, and species are succumbing to extinction before being described. Madagascar’s biota represents an extreme example of this scenario, with the added complication that much of its endemic biodiversity is cryptic. Here we illustrate best practices for clarifying cryptic diversification processes by presenting an integrative framework that leverages multiple lines of evidence and taxon-informed cut-offs for species delimitation, while placing special emphasis on identifying patterns of isolation by distance. We systematically apply this framework to an entire taxonomically controversial primate clade, the mouse lemurs (genus Microcebus, family Cheirogaleidae). We demonstrate that species diversity has been overestimated primarily due to the interpretation of geographic variation as speciation, potentially biasing inference of the underlying processes of evolutionary diversification. Following a revised classification, we find that crypsis within the genus is best explained by a model of morphological stasis imposed by stabilizing selection and a neutral process of niche diversification. Finally, by clarifying species limits and defining evolutionarily significant units, we provide new conservation priorities, bridging fundamental and applied objectives in a generalizable framework.

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's ( Rhinella marina ) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north‐central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic‐environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post‐introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories.

Minimally invasive samples are often the best option for collecting genetic material from species of conservation concern, but they perform poorly in many genomic sequencing methods due to their tendency to yield low DNA quality and quantity. Genotyping‐in‐thousands by sequencing (GT‐seq) is a powerful amplicon sequencing method that can genotype large numbers of variable‐quality samples at a standardized set of single nucleotide polymorphism (SNP) loci. Here, we develop, optimize, and validate a GT‐seq panel for the federally threatened northern Idaho ground squirrel (Urocitellus brunneus) to provide a standardized approach for future genetic monitoring and assessment of recovery goals using minimally invasive samples. The optimized panel consists of 224 neutral and 81 putatively adaptive SNPs. DNA collected from buccal swabs from 2016 to 2020 had 73% genotyping success, while samples collected from hair from 2002 to 2006 had little to no DNA remaining and did not genotype successfully. We evaluated our GT‐seq panel by measuring genotype discordance rates compared to RADseq and whole‐genome sequencing. GT‐seq and other sequencing methods had similar population diversity and FST estimates, but GT‐seq consistently called more heterozygotes than expected, resulting in negative FIS values at the population level. Genetic ancestry assignment was consistent when estimated with different sequencing methods and numbers of loci. Our GT‐seq panel is an effective and efficient genotyping tool that will aid in the monitoring and recovery of this threatened species, and our results provide insights for applying GT‐seq for minimally invasive DNA sampling techniques in other rare animals.

Emerging infectious diseases (EIDs) cause catastrophic declines in wildlife populations, but 2 also generate selective pressures that may result in rapid evolutionary responses. One such EID 3 is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal, 4 which likely causes strong selection for traits that reduce susceptibility to the disease, but 5 population decline has also left Tasmanian devils vulnerable to inbreeding depression. We 6 analysed 22 years of data from an ongoing study of a population of Tasmanian devils on 7 Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on 8 body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) 9 estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether 10 size traits or susceptibility to DFTD were under inbreeding depression. We found a positive 11 phenotypic relationship between head width and susceptibility to DFTD, but this was not 12 underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship 13 between body weight and susceptibility to DFTD, and there was evidence for a negative genetic 14 correlation between susceptibility to DFTD and body weight. There was additive genetic 15 variance in susceptibility to DFTD, head width and body weight, but there was no evidence for 16 inbreeding depression in any of these traits. These results suggest Tasmanian devils have the 17 potential to respond adaptively to DFTD, although the realised evolutionary response will 18 critically depend on the evolution of DFTD itself.

Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles. We investigate the computational feasibility of ABC to perform statistical inference and study the quality of estimates on the position of loci under selection and the strength of selection. To expand the parameter space of positions under selection, we enhance the model by implementing an outlier scan on summarized observed data. We evaluate the usefulness of summary statistics well-known to capture the strength of selection, and assess their informativeness under divergent selection. We also evaluate the effect of genetic drift with respect to an idealized deterministic model with single-locus selection. We discuss the role of the recombination rate as a confounding factor in estimating the strength of divergent selection, and emphasize its importance in break down of linkage disequilibrium (LD). We answer the question for which part of the parameter space of the model we recover strong signal for estimating the selection, and determine whether population differentiation-based summary statistics or LD–based summary statistics perform well in estimating selection.