Fluctuating selection and the determinants of genetic variation.

Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.

Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.

Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.

Genetic adaptations to SIV across chimpanzee populations.

Central and eastern chimpanzees are infected with Simian Immunodeficiency Virus (SIV) in the wild, typically without developing acute immunodeficiency. Yet the recent zoonotic transmission of chimpanzee SIV to humans, which were naïve to the virus, gave rise to the Human Immunodeficiency Virus (HIV), which causes AIDS and is responsible for one of the deadliest pandemics in human history. Chimpanzees have likely been infected with SIV for tens of thousands of years and have likely evolved to reduce its pathogenicity, becoming semi-natural hosts that largely tolerate the virus. In support of this view, central and eastern chimpanzees show evidence of positive selection in genes involved in SIV/HIV cell entry and immune response to SIV, respectively. We hypothesise that the population first infected by SIV would have experienced the strongest selective pressure to control the lethal potential of zoonotic SIV, and that population genetics will reveal those first critical adaptations. With that aim we used population genetics to investigate signatures of positive selection in the common ancestor of central-eastern chimpanzees. The genes with signatures of positive selection in the ancestral population are significantly enriched in SIV-related genes, especially those involved in the immune response to SIV and those encoding for host genes that physically interact with SIV/HIV (VIPs). This supports a scenario where SIV first infected the central-eastern ancestor and where this population was under strong pressure to adapt to zoonotic SIV. Interestingly, integrating these genes with candidates of positive selection in the two infected subspecies reveals novel patterns of adaptation to SIV. Specifically, we observe evidence of positive selection in numerous steps of the biological pathway responsible for T-helper cell differentiation, including CD4 and multiple genes that SIV/HIV use to infect and control host cells. This pathway is active only in CD4+ cells which SIV/HIV infects, and it plays a crucial role in shaping the immune response so it can efficiently control the virus. Our results confirm the importance of SIV as a selective factor, identify specific genetic changes that may have allowed our closest living relatives to reduce SIV's pathogenicity, and demonstrate the potential of population genomics to reveal the evolutionary mechanisms used by naïve hosts to reduce the pathogenicity of zoonotic pathogens.

Mitochondrial TXNRD2 and ME3 Genetic Risk Scores Are Associated with Specific Primary Open-Angle Glaucoma Phenotypes.

PURPOSE: Genetic variants in regions that include the mitochondrial genes thioredoxin reductase 2 (TXNRD2) and malic enzyme 3 (ME3) are associated with primary open-angle glaucoma (POAG) in genome-wide association studies (GWASs). To assess their clinical impact, we investigated whether TXNRD2 and ME3 genetic risk scores (GRSs) are associated with specific glaucoma phenotypes. DESIGN: Cross-sectional study. PARTICIPANTS: A total of 2617 patients with POAG and 2634 control participants from the National Eye Institute Glaucoma Human Genetics Collaboration Hereditable Overall Operational Database (NEIGHBORHOOD) consortium. METHODS: All POAG-associated single nucleotide polymorphisms (SNPs) in the TXNRD2 and ME3 loci were identified using GWAS data (P < 0.05). Of these, 20 TXNRD2 and 24 ME3 SNPs were selected after adjusting for linkage disequilibrium. The correlation between SNP effect size and gene expression levels was investigated using the Gene-Tissue Expression database. Genetic risk scores were constructed for each individual using the unweighted sum of TXNRD2, ME3, and TXNRD2 + ME3 combined risk alleles. Age- and sex-adjusted odds ratios (ORs) for POAG diagnosis were calculated per decile for each GRS. Additionally, the clinical features of patients with POAG in the top 1%, 5%, and 10% of each GRS were compared with those in the bottom 1%, 5%, and 10%, respectively. MAIN OUTCOME MEASURES: Primary open-angle glaucoma OR per GRS decile, maximum treated intraocular pressure (IOP), and prevalence of paracentral visual field loss among patients with POAG with high versus low GRSs. RESULTS: A larger SNP effect size strongly correlated with higher TXNRD2 and lower ME3 expression levels (r = 0.95 and r = -0.97, respectively; P < 0.05 for both). Individuals in decile 10 of the TXNRD2 + ME3 GRS had the highest odds of POAG diagnosis (OR, 1.79 compared with decile 1; 95% confidence interval, 1.39-2.30; P < 0.001). Patients with POAG in the top 1% of the TXNRD2 GRS showed higher mean maximum treated IOP compared with the bottom 1% (19.9 mmHg vs. 15.6 mmHg; adjusted P = 0.03). Patients with POAG in the top 1% of the ME3 and TXNRD2 + ME3 GRS showed a higher prevalence of paracentral field loss than the bottom 1% (72.7% vs. 14.3% for ME3 GRS and 88.9% vs. 33.3% for TXNRD2+ME3 GRS; adjusted P = 0.03 for both). CONCLUSIONS: Patients with POAG with higher TXNRD2 and ME3 GRSs showed higher treated IOP and a greater prevalence of paracentral field loss. Functional studies exploring how these variants impact mitochondrial function in patients with glaucoma are warranted. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

High Polygenic Risk Is Associated with Earlier Initiation and Escalation of Treatment in Early Primary Open-Angle Glaucoma.

PURPOSE: To assess the association between a glaucoma polygenic risk score (PRS) and treatment outcomes in primary open-angle glaucoma. DESIGN: Prospective, observational cohort study. PARTICIPANTS: Participants from the Progression Risk of Glaucoma: Relevant SNPs with Significant Association Study were divided into a cohort with suspect glaucoma who were treatment naive at enrollment and one with early manifest and suspect glaucoma receiving treatment at enrollment. METHODS: A per-allele weighted glaucoma PRS was calculated for 1107 participants. Multivariable mixed-effects Cox proportional regression analysis assessed the association between PRS and time to commencement of intraocular pressure (IOP)-lowering therapy in 416 patients with suspect glaucoma who were treatment naive at study enrollment. Secondary analysis evaluated the association between PRS and escalation of IOP-lowering therapy among 691 patients with suspect and early manifest glaucoma who were receiving IOP-lowering therapy at enrollment. MAIN OUTCOME MEASURES: Commencement or escalation of IOP-lowering therapy. RESULTS: A higher PRS was associated with a greater risk of commencing IOP-lowering therapy within 5 years (hazard ratio [HR], 1.45 per 1 standard deviation [/SD]; 95% confidence interval [CI], 1.27-1.62; P < 0.001). Participants in the upper population-based quintile showed a 3.3 times greater risk of commencing therapy by 5 years than those in the lowest quintile (HR, 3.30; 95% CI, 1.63-6,70; P < 0.001) and a 5.4 times greater risk of commencing IOP-lowering therapy by 2 years than the those in the lowest quintile (HR, 5.45; 95% CI, 2.08-14.25; P < 0.001). A higher PRS was associated with a greater risk of treatment escalation among patients receiving treatment at enrollment (HR, 1.19/SD; 95% CI, 1.09-1.31; P < 0.001). In combined analysis of all participants, participants in the top population-based quintile were at 2.3 times greater risk of requiring initiation or escalation of IOP-lowering therapy than those in the lowest quintile (HR, 2.33; 95% CI, 1.75-3.01; P < 0.001). CONCLUSIONS: This study demonstrated novel associations between glaucoma polygenic risk and risk of commencement or escalation of IOP-lowering therapy, building on previous work highlighting the potential clinical usefulness of genetic risk stratification in glaucoma. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

Tree and shrub expansion at treeline drive contrasting responses in a subarctic passerine community.

Inferences about the mechanisms of distributional change are often made from simple assessments of variation in the geographical positions of populations. However, direct assessments of species' responses to local habitat change may be necessary for proper understanding of the drivers of distributional dynamics. Amplified climate warming is inducing cascading impacts in boreal-tundra regions including the expansion of conifers and deciduous shrubs (shrubs). In Denali National Park (Denali), Alaska, passerine birds are exhibiting rapid upslope shifts in distribution but the relative roles of conifer and shrub (woody vegetation) expansion in driving these shifts are unknown. Without directly assessing passerine-vegetation dynamics, the assumption has been that the observed upslope shifts are indicative of shrub-adapted passerines tracking the upslope expansion of shrubs. Here, we jointly investigate the processes of conifer and shrub expansion and their relationship to changes in passerine abundance in Denali. We used a remotely sensed vegetation cover timeseries (1985-2020) to assess the topographic and edaphic correlates of conifer and shrub expansion. We then assessed the impacts of changes in shrub and conifer cover on the relative abundance of 12 passerine species (1995-2020). Shrub and conifer colonization rates were highest at intermediate elevations near treeline. However, forest- and shrub-adapted passerines differed in terms of the location in which their response was concentrated relative to treeline. The population growth rates of forest-adapted passerines exhibited stronger effects of woody vegetation expansion at sites that were initially above treeline (IAT). In contrast, the population growth rates of shrub-adapted passerines exhibited the negative effects of conifer expansion together with the positive effects of shrub expansion at initially below treeline sites. However, they showed a weak response to woody vegetation expansion at sites that were IAT. Below treeline conifer infilling appears to be pushing the elevational distributions of shrub-adapted passerines upslope rather than these species following the pull of modest shrub expansion above treeline, as previously assumed. Overall, our findings illustrate the need for explicitly accommodating heterogeneity in habitat change at small spatial scales to properly view the distributional response, particularly when habitat change is concentrated at ecotones.

Genetic Risk Assessment of Degenerative Eye Disease (GRADE): study protocol of a prospective assessment of polygenic risk scores to predict diagnosis of glaucoma and age-related macular degeneration.

BACKGROUND: Glaucoma and age-related macular degeneration (AMD) account for a substantial portion of global blindness. Both conditions are highly heritable, with recognised monogenic and polygenic inheritance patterns. Current screening guidelines lack decisive recommendations. Polygenic risk scores (PRS) allow for cost-effective broad population risk stratification for these conditions. The predictive potential of PRS could facilitate earlier diagnosis and treatment, and prevent unnecessary vision loss. METHODS: The Genetic Risk Assessment of Degenerative Eye disease (GRADE) study is a prospective study designed to generate high-quality evidence about the feasibility of PRS to stratify individuals from the general population, enabling identification of those at highest risk of developing glaucoma or AMD. The targeted recruitment is 1000 individuals aged over 50 years, from which blood or saliva samples will be used for genotyping and an individual PRS for glaucoma and AMD will be derived. Individuals with PRS values in the bottom decile (n = 100), top decile (n = 100) and middle 80% (n = 100) for both glaucoma and AMD will undergo a detailed eye examination for glaucoma and/or AMD. DISCUSSION: The primary objective will be to compare the prevalence of glaucoma and AMD cases between low, intermediate, and high PRS risk groups. We expect to find a higher prevalence of both diseases in the high PRS risk group, as compared to the middle and low risk groups. This prospective study will assess the clinical validity of a PRS for glaucoma and AMD in the general Australian population. Positive findings will support the implementation of PRS into clinical practice.

The impact of genetic adaptation on chimpanzee subspecies differentiation.

Chimpanzees, humans' closest relatives, are in danger of extinction. Aside from direct human impacts such as hunting and habitat destruction, a key threat is transmissible disease. As humans continue to encroach upon their habitats, which shrink in size and grow in density, the risk of inter-population and cross-species viral transmission increases, a point dramatically made in the reverse with the global HIV/AIDS pandemic. Inhabiting central Africa, the four subspecies of chimpanzees differ in demographic history and geographical range, and are likely differentially adapted to their particular local environments. To quantitatively explore genetic adaptation, we investigated the genic enrichment for SNPs highly differentiated between chimpanzee subspecies. Previous analyses of such patterns in human populations exhibited limited evidence of adaptation. In contrast, chimpanzees show evidence of recent positive selection, with differences among subspecies. Specifically, we observe strong evidence of recent selection in eastern chimpanzees, with highly differentiated SNPs being uniquely enriched in genic sites in a way that is expected under recent adaptation but not under neutral evolution or background selection. These sites are enriched for genes involved in immune responses to pathogens, and for genes inferred to differentiate the immune response to infection by simian immunodeficiency virus (SIV) in natural vs. non-natural host species. Conversely, central chimpanzees exhibit an enrichment of signatures of positive selection only at cytokine receptors, due to selective sweeps in CCR3, CCR9 and CXCR6 -paralogs of CCR5 and CXCR4, the two major receptors utilized by HIV to enter human cells. Thus, our results suggest that positive selection has contributed to the genetic and phenotypic differentiation of chimpanzee subspecies, and that viruses likely play a predominate role in this differentiation, with SIV being a likely selective agent. Interestingly, our results suggest that SIV has elicited distinctive adaptive responses in these two chimpanzee subspecies.

Climate and weather have differential effects in a high latitude passerine community.

Climatic factors act on populations at multiple timescales leading to the separation of long-term climate and shorter-term weather effects. We used passerine counts from 1995 to 2019 in subarctic Alaska (Denali National Park, USA) to assess the impacts of the prior breeding season's weather on breeding season abundance and the impacts of climate measured through shifts in elevational distribution. Weather and climate appear to have had opposing effects on the abundance of some shrub-associated species as evidenced by a positive response to nesting phase temperature over a 1-year lag and a negative response to warming-induced shifts in shrub-dominated habitats over the long term. The latter response was indicated by declines in abundance which occurred in some part through portions of these populations shifting upslope of our fixed sampling frame. Overall, the abundance of species was related to one or more of the lagged effects of weather and the effects of weather alone drove nearly twofold variation in annual abundance in most species. The effect of nesting phase temperature was a strong positive predictor at both community and individual species levels, whereas arrival phase temperature had weak support at both levels. The effects of total precipitation during the nesting phase and snowmelt timing shared mixed support at community and species levels, but generally indicated higher abundance following seasons that were drier and had earlier snowmelt. Together, our findings of opposing effects of climatic variables at different timescales have implications for understanding the mechanisms of population and distributional change in passerines in the subarctic.

Human local adaptation of the TRPM8 cold receptor along a latitudinal cline.

Ambient temperature is a critical environmental factor for all living organisms. It was likely an important selective force as modern humans recently colonized temperate and cold Eurasian environments. Nevertheless, as of yet we have limited evidence of local adaptation to ambient temperature in populations from those environments. To shed light on this question, we exploit the fact that humans are a cosmopolitan species that inhabit territories under a wide range of temperatures. Focusing on cold perception-which is central to thermoregulation and survival in cold environments-we show evidence of recent local adaptation on TRPM8. This gene encodes for a cation channel that is, to date, the only temperature receptor known to mediate an endogenous response to moderate cold. The upstream variant rs10166942 shows extreme population differentiation, with frequencies that range from 5% in Nigeria to 88% in Finland (placing this SNP in the 0.02% tail of the FST empirical distribution). When all populations are jointly analyzed, allele frequencies correlate with latitude and temperature beyond what can be explained by shared ancestry and population substructure. Using a Bayesian approach, we infer that the allele originated and evolved neutrally in Africa, while positive selection raised its frequency to different degrees in Eurasian populations, resulting in allele frequencies that follow a latitudinal cline. We infer strong positive selection, in agreement with ancient DNA showing high frequency of the allele in Europe 3,000 to 8,000 years ago. rs10166942 is important phenotypically because its ancestral allele is protective of migraine. This debilitating disorder varies in prevalence across human populations, with highest prevalence in individuals of European descent-precisely the population with the highest frequency of rs10166942 derived allele. We thus hypothesize that local adaptation on previously neutral standing variation may have contributed to the genetic differences that exist in the prevalence of migraine among human populations today.

Direct and indirect effects of temperature and prey abundance on bald eagle reproductive dynamics.

Understanding the mechanisms by which populations are regulated is critical for predicting the effects of large-scale perturbations. While discrete mortality events provide clear evidence of direct impacts, indirect pathways are more difficult to assess but may play important roles in population and ecosystem dynamics. Here, we use multi-state occupancy models to analyze a long-term dataset on nesting bald eagles in south-central Alaska with the goal of identifying both direct and indirect mechanisms influencing reproductive output in this apex predator. We found that the probabilities of both nest occupancy and success were higher in the portion of the study area where water turbidity was low, supporting the hypothesis that access to aquatic prey is a critical factor limiting the reproductive output of eagles in this system. As expected, nest success was also positively related to salmon abundance; however, the negative effect of spring warmth suggested that access to salmon resources is indirectly diminished in warm springs as a consequence of increased glacial melt. Together, these findings reveal complex interrelationships between a critical prey resource and large-scale weather and climate processes which likely alter the accessibility of resources rather than directly affecting resource abundance. While important for understanding bald eagle reproductive dynamics in this system specifically, our results have broader implications that suggest complex interrelationships among system components.

Weather-driven change in primary productivity explains variation in the amplitude of two herbivore population cycles in a boreal system.

Vertebrate populations throughout the circumpolar north often exhibit cyclic dynamics, and predation is generally considered to be a primary driver of these cycles in a variety of herbivore species. However, weather and climate play a role in entraining cycles over broad landscapes and may alter cyclic dynamics, although the mechanism by which these processes operate is uncertain. Experimental and observational work has suggested that weather influences primary productivity over multi-year time periods, suggesting a pathway through which weather and climate may influence cyclic herbivore dynamics. Using long-term monitoring data, we investigated the relationships among multi-year weather conditions, measures of primary productivity, and the abundance of two cyclic herbivore species: snowshoe hare and northern red-backed vole. We found that precipitation (rain and snow) and growing season temperatures were strongly associated with variation in primary productivity over multi-year time horizons. In turn, fourfold variation in the amplitude of both the hare and vole cycles observed in our study area corresponded to long-term changes in primary productivity. The congruence of our results for these two species suggests a general mechanism by which weather and climate might influence cyclic herbivore population dynamics. Our findings also suggested that the association between climate warming and the disappearance of cycles might be initiated by changes in primary productivity. This work provides an explanation for observed influences of weather and climate on primary productivity and population cycles and will help our collective understanding of how future climate warming may influence these ecological phenomena in the future.

Total Mercury and Methylmercury Response in Water, Sediment, and Biota to Destratification of the Great Salt Lake, Utah, United States.

Measurements of chemical and physical parameters made before and after sealing of culverts in the railroad causeway spanning the Great Salt Lake in late 2013 documented dramatic alterations in the system in response to the elimination of flow between the Great Salt Lake's north and south arms. The flow of denser, more-saline water through the culverts from the north arm (Gunnison Bay) to the south arm (Gilbert Bay) previously drove the perennial stratification of the south arm and the existence of oxic shallow brine and anoxic deep brine layers. Closure of the causeway culverts occurred concurrently with a multiyear drought that resulted in a decrease in the lake elevation and a concomitant increase in top-down erosion of the upper surface of the deep brine layer by wind-forced mixing. The combination of these events resulted in the replacement of the formerly stratified water column in the south arm with one that was vertically homogeneous and oxic. Total mercury concentrations in the deep waters of the south arm decreased by approximately 81% and methylmercury concentrations in deep waters decreased by roughly 86% due to destratification. Methylmercury concentrations decreased by 77% in underlying surficial sediment, whereas there was no change observed in total mercury. The dramatic mercury loss from deep waters and methylmercury loss from underlying sediment in response to causeway sealing provides new understanding of the potential role of the deep brine layer in the accumulation and persistence of methylmercury in the Great Salt Lake. Additional mercury measurements in biota appear to contradict the previously implied connection between elevated methylmercury concentrations in the deep brine layer and elevated mercury in avian species reported prior to causeway sealing.

Trophic dynamics of shrinking Subarctic lakes: naturally eutrophic waters impart resilience to rising nutrient and major ion concentrations.

Shrinking lakes were recently observed for several Arctic and Subarctic regions due to increased evaporation and permafrost degradation. Along with lake drawdown, these processes often boost aquatic chemical concentrations, potentially impacting trophic dynamics. In particular, elevated chemical levels may impact primary productivity, which may in turn influence populations of primary and secondary consumers. We examined trophic dynamics of 18 shrinking lakes of the Yukon Flats, Alaska, that had experienced pronounced increases in nutrient (>200 % total nitrogen, >100 % total phosphorus) and ion concentrations (>100 % for four major ions combined) from 1985-1989 to 2010-2012, versus 37 stable lakes with relatively little chemical change over the same period. We found that phytoplankton stocks, as indexed by chlorophyll concentrations, remained unchanged in both shrinking and stable lakes from the 1980s to 2010s. Moving up the trophic ladder, we found significant changes in invertebrate abundance across decades, including decreased abundance of five of six groups examined. However, these decadal losses in invertebrate abundance were not limited to shrinking lakes, occurring in lakes with stable surface areas as well. At the top of the food web, we observed that probabilities of lake occupancy for ten waterbird species, including adults and chicks, remained unchanged from the period 1985-1989 to 2010-2012. Overall, our study lakes displayed a high degree of resilience to multi-trophic cascades caused by rising chemical concentrations. This resilience was likely due to their naturally high fertility, such that further nutrient inputs had little impact on waters already near peak production.

Gene duplication in the major insecticide target site, Rdl, in Drosophila melanogaster.

The Resistance to Dieldrin gene, Rdl, encodes a GABA-gated chloride channel subunit that is targeted by cyclodiene and phenylpyrazole insecticides. The gene was first characterized in Drosophila melanogaster by genetic mapping of resistance to the cyclodiene dieldrin. The 4,000-fold resistance observed was due to a single amino acid replacement, Ala(301) to Ser. The equivalent change was subsequently identified in Rdl orthologs of a large range of resistant insect species. Here, we report identification of a duplication at the Rdl locus in D. melanogaster. The 113-kb duplication contains one WT copy of Rdl and a second copy with two point mutations: an Ala(301) to Ser resistance mutation and Met(360) to Ile replacement. Individuals with this duplication exhibit intermediate dieldrin resistance compared with single copy Ser(301) homozygotes, reduced temperature sensitivity, and altered RNA editing associated with the resistant allele. Ectopic recombination between Roo transposable elements is involved in generating this genomic rearrangement. The duplication phenotypes were confirmed by construction of a transgenic, artificial duplication integrating the 55.7-kb Rdl locus with a Ser(301) change into an Ala(301) background. Gene duplications can contribute significantly to the evolution of insecticide resistance, most commonly by increasing the amount of gene product produced. Here however, duplication of the Rdl target site creates permanent heterozygosity, providing unique potential for adaptive mutations to accrue in one copy, without abolishing the endogenous role of an essential gene.

Estimating demographic parameters using a combination of known-fate and open N-mixture models.

Accurate estimates of demographic parameters are required to infer appropriate ecological relationships and inform management actions. Known-fate data from marked individuals are commonly used to estimate survival rates, whereas N-mixture models use count data from unmarked individuals to estimate multiple demographic parameters. However, a joint approach combining the strengths of both analytical tools has not been developed. Here we develop an integrated model combining known-fate and open N-mixture models, allowing the estimation of detection probability, recruitment, and the joint estimation of survival. We demonstrate our approach through both simulations and an applied example using four years of known-fate and pack count data for wolves (Canis lupus). Simulation results indicated that the integrated model reliably recovered parameters with no evidence of bias, and survival estimates were more precise under the joint model. Results from the applied example indicated that the marked sample of wolves was biased toward individuals with higher apparent survival rates than the unmarked pack mates, suggesting that joint estimates may be more representative of the overall population. Our integrated model is a practical approach for reducing bias while increasing precision and the amount of information gained from mark-resight data sets. We provide implementations in both the BUGS language and an R package.

Climate sensitivity of reproduction in a mast-seeding boreal conifer across its distributional range from lowland to treeline forests.

Mast-seeding conifers such as Picea glauca exhibit synchronous production of large seed crops over wide areas, suggesting climate factors as possible triggers for episodic high seed production. Rapidly changing climatic conditions may thus alter the tempo and spatial pattern of masting of dominant species with potentially far-reaching ecological consequences. Understanding the future reproductive dynamics of ecosystems including boreal forests, which may be dominated by mast-seeding species, requires identifying the specific cues that drive variation in reproductive output across landscape gradients and among years. Here we used annual data collected at three sites spanning an elevation gradient in interior Alaska, USA between 1986 and 2011 to produce the first quantitative models for climate controls over both seedfall and seed viability in P. glauca, a dominant boreal conifer. We identified positive associations between seedfall and increased summer precipitation and decreased summer warmth in all years except for the year prior to seedfall. Seed viability showed a contrasting response, with positive correlations to summer warmth in all years analyzed except for one, and an especially positive response to warm and wet conditions in the seedfall year. Finally, we found substantial reductions in reproductive potential of P. glauca at high elevation due to significantly reduced seed viability there. Our results indicate that major variation in the reproductive potential of this species may occur in different landscape positions in response to warming, with decreasing reproductive success in areas prone to drought stress contrasted with increasing success in higher elevation areas currently limited by cool summer temperatures.

Population genetic simulation: Benchmarking frameworks for non-standard models of natural selection.

Population genetic simulation has emerged as a common tool for investigating increasingly complex evolutionary and demographic models. Software capable of handling high-level model complexity has recently been developed, and the advancement of tree sequence recording now allows simulations to merge the efficiency and genealogical insight of coalescent simulations with the flexibility of forward simulations. However, frameworks utilizing these features have not yet been compared and benchmarked. Here, we evaluate various simulation workflows using the coalescent simulator msprime and the forward simulator SLiM, to assess resource efficiency and determine an optimal simulation framework. Three aspects were evaluated: (1) the burn-in, to establish an equilibrium level of neutral diversity in the population; (2) the forward simulation, in which temporally fluctuating selection is acting; and (3) the final computation of summary statistics. We provide typical memory and computation time requirements for each step. We find that the fastest framework, a combination of coalescent and forward simulation with tree sequence recording, increases simulation speed by over twenty times compared to classical forward simulations without tree sequence recording, although it does require six times more memory. Overall, using efficient simulation workflows can lead to a substantial improvement when modelling complex evolutionary scenarios-although the optimal framework ultimately depends on the available computational resources.

Local genetic adaptation to habitat in wild chimpanzees.

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.

Pseudo-fivefold diffraction symmetries in tetrahedral packing.

We review the way in which atomic tetrahedra composed of metallic elements pack naturally into fused icosahedra. Orthorhombic, hexagonal, and cubic intermetallic crystals based on this packing are all shown to be united in having pseudo-fivefold rotational diffraction symmetry. A unified geometric model involving the 600-cell is presented: the model accounts for the observed pseudo-fivefold symmetries among the different Bravais lattice types. The model accounts for vertex-, edge-, polygon-, and cell-centered fused-icosahedral clusters. Vertex-centered and edge-centered types correspond to the well-known pseudo-fivefold symmetries in Ih and D5h quasicrystalline approximants. The concept of a tetrahedrally-packed reciprocal space cluster is introduced, the vectors between sites in this cluster corresponding to the principal diffraction peaks of fused-icosahedrally-packed crystals. This reciprocal-space cluster is a direct result of the pseudosymmetry and, just as the real-space clusters, can be rationalized by the 600-cell. The reciprocal space cluster provides insights for the Jones model of metal stability. For tetrahedrally-packed crystals, Jones zone faces prove to be pseudosymmetric with one another. Lower and upper electron per atom bounds calculated for this pseudosymmetry-based Jones model are shown to accord with the observed electron counts for a variety of Group 10-12 tetrahedrally-packed structures, among which are the four known Cu/Cd intermetallic compounds: CdCu2, Cd3Cu4, Cu5Cd8, and Cu3Cd10. The rationale behind the Jones lower and upper bounds is reviewed. The crystal structure of Zn11Au15Cd23, an example of a 1:1 MacKay cubic quasicrystalline approximant based solely on Groups 10-12 elements is presented. This compound crystallizes in Im3 (space group no. 204) with a = 13.842(2) Å. The structure was solved with R1 = 3.53 %, I > 2σ; = 5.33 %, all data with 1282/0/38 data/restraints/parameters.