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DOE OSTI2025

Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism over multiple spatiotemporal scales

Abstract Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in Drosophila melanogaster as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field. We show that D. melanogaster pigmentation evolves as a highly parallel and deterministic response to shared environmental variation across latitude and season in natural North American populations. We then experimentally evolved replicate, genetically diverse fly populations in field mesocosms to remove any confounding effects of demography and/or cryptic structure that may drive patterns in wild populations; we show that pigmentation rapidly responds, in parallel, in fewer than 15 generations. Thus, pigmentation evolves concordantly in response to spatial and temporal climatic axes. We next examined whether phenotypic differentiation was associated with allele frequency change at loci with established links to genetic variance in pigmentation in natural populations. We found that across all spatial and temporal scales, phenotypic patterns were associated with variation at pigmentation-related loci, and the sets of genes we identified at each scale were largely nonoverlapping. Therefore, our findings suggest that parallel phenotypic evolution is associated with distinct components of the polygenic architecture shifting across each environmental axis to produce redundant adaptive patterns.

Evolutionary Biology↗

DOE OSTI2022

The primordial matter power spectrum on sub-galactic scales

The primordial matter power spectrum quantifies fluctuations in the distribution of dark matter immediately following inflation. Over cosmic time, overdense regions of the primordial density field grow and collapse into dark matter haloes, whose abundance and density profiles retain memory of the initial conditions. By analysing the image magnifications in 11 strongly lensed and quadruply imaged quasars, we infer the abundance and concentrations of low-mass haloes, and cast the measurement in terms of the amplitude of the primordial matter power spectrum. We anchor the power spectrum on large scales, isolating the effect of small-scale deviations from the Lambda cold dark matter (ΛCDM) prediction. Assuming an analytic model for the power spectrum and accounting for several sources of potential systematic uncertainty, including three different models for the halo mass function, we obtain correlated inferences of $\log _{10}\left(P / P_{\Lambda \rm {CDM}}\right)$, the power spectrum amplitude relative to the predictions of the concordance cosmological model, of $0.0_{-0.4}^{+0.5}$, $0.1_{-0.6}^{+0.7}$, and $0.2_{-0.9}^{+1.0}$ at k = 10, 25, and 50 $\rm {Mpc^{-1}}$ at $68 {{\ \rm per\ cent}}$ confidence, consistent with CDM and single-field slow-roll inflation.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Revisit NGC 5466 tidal stream with Gaia , SDSS/SEGUE, and LAMOST

ABSTRACT By mining the data from Gaia Early Data Release 3, Sloan Digital Sky Survey/Sloan Extension for Galactic Understanding and Exploration Data Release 16, and Large Sky Area Multi-Object Fiber Spectroscopic Telescope Data Release 8, 11 member stars of the NGC 5466 tidal stream are detected and 7 of them are newly identified. To reject contaminators, a variety of cuts are applied in sky position, colour–magnitude diagram, metallicity, proper motion, and radial velocity. We compare our data to a mock stream generated by modelling the cluster’s disruption under a smooth Galactic potential plus the Large Magellanic Cloud (LMC). The concordant trends in phase space between the model and observations imply that the stream might have been perturbed by the LMC. The two most distant stars among the 11 detected members trace the stream’s length to 60° of sky, supporting and extending the previous length of 45°. Given that NGC 5466 is so distant and potentially has a longer tail than previously thought, we expect that the NGC 5466 tidal stream could be a useful tool in constraining the Milky Way gravitational field.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2024

Matter power spectra in modified gravity: a comparative study of approximations and N -body simulations

ABSTRACT Testing gravity and the concordance model of cosmology, $\Lambda$CDM, at large scales is a key goal of this decade’s largest galaxy surveys. Here we present a comparative study of dark matter power spectrum predictions from different numerical codes in the context of three popular theories of gravity that induce scale-independent modifications to the linear growth of structure: nDGP, Cubic Galileon, and K-mouflage. In particular, we compare the predictions from N-body simulations solving the full scalar field equation, two N-body codes with approximate time integration schemes, a parametrized modified N-body implementation, and the analytic halo model reaction approach. We find the modification to the $\Lambda$CDM spectrum is in 2 per cent agreement at $z\le 1$ and $k\le 1~h\,{\rm Mpc}^{-1}$ over all gravitational models and codes, in accordance with many previous studies, indicating these modelling approaches are robust enough to be used in forthcoming survey analyses under appropriate scale cuts. We further make public the new code implementations presented, specifically the halo model reaction K-mouflage implementation and the relativistic Cubic Galileon implementation.

Bose, B. (ORCID:0000000319658614)↗

DOE OSTI2022

Structural basis for topological regulation of Tn3 resolvase

Site-specific DNA recombinases play a variety of biological roles, often related to the dissemination of antibiotic resistance, and are also useful synthetic biology tools. The simplest site-specific recombination systems will recombine any two cognate sites regardless of context. Other systems have evolved elaborate mechanisms, often sensing DNA topology, to ensure that only one of multiple possible recombination products is produced. The closely related resolvases from the Tn3 and γδ transposons have historically served as paradigms for the regulation of recombinase activity by DNA topology. However, despite many proposals, models of the multi-subunit protein–DNA complex (termed the synaptosome) that enforces this regulation have been unsatisfying due to a lack of experimental constraints and incomplete concordance with experimental data. Here, we present new structural and biochemical data that lead to a new, detailed model of the Tn3 synaptosome, and discuss how it harnesses DNA topology to regulate the enzymatic activity of the recombinase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.

Ahrendt, Steven R. [USDOE Joint Genome Institute (↗

DOE OSTI2026

SPT-3G D1: Axion early dark energy with CMB experiments and DESI observations

We present the most up-to-date constraints on axion early dark energy (AEDE) from cosmic microwave background (CMB) and baryon acoustic oscillation (BAO) measurements. In particular, we assess the impact of data from ground-based CMB experiments, the South Pole Telescope (SPT) and the Atacama Cosmology Telescope (ACT)—both with and without Planck—on constraints on AEDE. We also highlight the impact that BAO information from the Dark Energy Spectroscopic Instrument (DESI) has on these constraints. From CMB data alone, we do not find statistically significant evidence for the presence of AEDE, and we find only moderate reduction in the Hubble tension. From the latest SPT data alone, we find the maximal fractional contribution of AEDE to the cosmic energy budget is f EDE < 0.12 at 95% confidence level (CL), and the Hubble tension between the SPT and Supernovae, H0, for the Equation of State of Dark Energy (SH0ES) results is reduced to the 2.3 σ level. When combining the latest SPT, ACT, and Planck datasets, we find f EDE < 0.070 at 95% CL and the Hubble tension at the 3.6 σ level. In contrast, adding DESI data to the CMB datasets results in mild preference for AEDE and, in some cases, non-negligible reduction in the Hubble tension. From SPT + DESI , we find f EDE = 0.08 1 - 0.052 + 0.037 at 68% CL, and the Hubble tension reduces to 1.5 σ . From the combination of DESI with all three CMB experiments, we get f EDE = 0.05 5 - 0.047 + 0.024 at 68% CL and a weak preference for AEDE over Λ CDM . This data combination, in turn, reduces the Hubble tension to 2.6 σ . We highlight that this shift in parameters when adding the DESI dataset is a manifestation of the discrepancy currently present between DESI and CMB experiments in the concordance model Λ CDM .

Khalife, A. R. [Paris, Inst. Astrophys.] (ORCID:00↗

DOE OSTI2020

Hubble constant difference between CMB lensing and BAO measurements

We apply a tension metric QUDM, the update difference in mean parameters, to understand the source of the difference in the measured Hubble constant H0 inferred with cosmic microwave background lensing measurements from the Planck satellite (H 0 = $67.9$ $^{+1.1}_{–1.3}$ km/s/Mpc) and from the South Pole Telescope (H 0 = $72.0$ $^{+2.1}_{–2.5}$ km/s/Mpc) when both are combined with baryon acoustic oscillation (BAO) measurements with priors on the baryon density (BBN). Q UDM isolates the relevant parameter directions for tension or concordance where the two data sets are both informative, and aids in the identification of subsets of data that source the observed tension. With Q UDM , we uncover that the difference in H 0 is driven by the tension between Planck lensing and BAO+BBN, at probability-to-exceed of 6.6%. Most of this mild tension comes from the galaxy BAO measurements parallel to the line of sight in the redshift range 0.2 < z < 0.75. Here, the redshift dependence of the parallel BAOs pulls both the matter density Ω m and H 0 high in Λ CDM, but these parameter anomalies are usually hidden when the BAO measurements are combined with other cosmological data sets with much stronger Ω m constraints.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

No H 0 assistance from assisted quintessence

Early dark energy, as a proposed solution to the Hubble tension, faces an additional “why now” problem. Why should dark energy emerge just prior to recombination, billions of years before the onset of cosmic acceleration? Assisted quintessence explains this connection by positing that multiple scaling fields build up over time to drive the present-day cosmic acceleration. In this framework, early dark energy is inevitable. Yet, we show that scaling also leads to the demise of the scenario: the same feature that solves the coincidence problem then spoils a concordance of the Hubble constant inferred from the cosmic microwave background with that from the local distance ladder. In conclusion, the failure of the model offers a novel lesson on the ability of new physics to resolve the Hubble tension.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Constraints on dark matter to dark radiation conversion in the late universe with DES-Y1 and external data

We study a phenomenological class of models where dark matter converts to dark radiation in the low redshift epoch. This class of models, dubbed DMDR, characterizes the evolution of comoving dark-matter density with two extra parameters, and may be able to help alleviate the observed discrepancies between early and late-time probes of the Universe. We investigate how the conversion affects key cosmological observables such as the cosmic microwave background (CMB) temperature and matter power spectra. Combining 3x2pt data from Year 1 of the Dark Energy Survey, Planck-2018 CMB temperature and polarization data, supernovae (SN) Type Ia data from Pantheon, and baryon acoustic oscillation (BAO) data from BOSS DR12, MGS and 6dFGS, we place new constraints on the amount of dark matter that has converted to dark radiation and the rate of this conversion. The fraction of the dark matter that has converted since the beginning of the Universe in units of the current amount of dark matter, ζ, is constrained at 68% confidence level to be <0.32 for DES-Y1 3x2pt data, <0.030 for CMB+SN+BAO data, and <0.037 for the combined dataset. The probability that the DES and CMB+SN+BAO datasets are concordant increases from 4% for the ΛCDM model to 8% (less tension) for DMDR. The tension in S8=σ8Ωm/0.3 between DES-Y1 3x2pt and CMB+SN+BAO is slightly reduced from 2.3σ to 1.9σ. We find no reduction in the Hubble tension when the combined data is compared to distance-ladder measurements in the DMDR model. The maximum-posterior goodness-of-fit statistics of DMDR and ΛCDM model are comparable, indicating no preference for the DMDR cosmology over ΛCDM.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Beta Decay of Molecular Tritium

The beta decay of tritium in the form of molecular T 2 is the basis of sensitive experiments to measure neutrino mass. The final-state electronic, vibrational, and rotational excitations modify the beta spectrum significantly and are obtained from theory. We further determine measurements of the branching ratios to specific ionization states for the isotopolog HT. Two earlier, concordant measurements gave branching ratios of HT to the bound HHe + ion of 89.5% and 93.2%, in sharp disagreement with the theoretical prediction of 55%–57%, raising concerns about the theory’s reliability in neutrino mass experiments. Our finding, 56.5(6)%, is compatible with the theoretical expectation and disagrees strongly with the previous measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2026

Dark Energy Survey: Implications for cosmological expansion models from the final DES baryon acoustic oscillation and supernova data

The Dark Energy Survey (DES) recently released the final results of its two principal probes of the expansion history: Type Ia supernovae (SNe) and baryonic acoustic oscillations (BAO). In this paper, we explore the cosmological implications of these data in combination with external cosmic microwave background (CMB), big bang nucleosynthesis (BBN), and age-of-the-Universe information. The BAO measurement, which is ∼ 2 σ away from Planck ’s Λ CDM predictions, pushes for low values of Ω m compared to Planck, in contrast to SN which prefers a higher value than Planck. We identify several tensions among datasets in the Λ CDM model that cannot be resolved by including either curvature ( k Λ CDM ) or a constant dark energy equation of state ( w CDM ). By combining BAO + SN + CMB despite these mild tensions, we obtain Ω k = - 5.5 - 4.2 + 4.6 × 10 - 3 in k Λ CDM , and w = - 0.94 8 - 0.027 + 0.028 in w CDM . In w CDM , BAO and SN push again in different directions of parameter space, favoring, respectively, w < - 1 and w > - 1 . If we open the parameter space to w 0 w a CDM [where the equation of state of dark energy varies as w ( a ) = w 0 + ( 1 - a ) w a ], all the datasets are mutually more compatible, and we find concordance in the [ w 0 > - 1 , w a < 0 ] quadrant, with BAO pushing for w a < 0 and SN for [ w 0 > - 1 , w a < 0 ] . For DES BAO and SN in combination with Planck -CMB, we find a 3.2 σ deviation from Λ CDM , with w 0 = - 0.67 3 - 0.097 + 0.098 , w a = - 1.3 7 - 0.50 + 0.51 , a Hubble constant of H 0 = 67.8 1 - 0.86 + 0.96 km s - 1 Mpc - 1 , and an abundance of matter of Ω m = 0.310 9 - 0.0099 + 0.0086 . For the combination of all the background cosmological probes considered (including CMB’s angular acoustic scale θ ⋆ ), we still find a deviation of 2.8 σ from Λ CDM in the w 0 - w a plane. Assuming a minimal neutrino mass, this work provides tentative evidence for non- Λ CDM physics, which is consistent with recent claims in support of evolving dark energy, or a source of unknown systematics.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

Compensatory Guaiacyl Lignin Biosynthesis at the Expense of Syringyl Lignin in 4CL1 -Knockout Poplar -Knockout Poplar

The lignin biosynthetic pathway is highly conserved in angiosperms, yet pathway manipulations give rise to a variety of taxon-specific outcomes. Knockout of lignin-associated 4-coumarate:CoA ligases (4CLs) in herbaceous species mainly reduces guaiacyl (G) lignin and enhances cell wall saccharification. In this work we show that CRISPR-knockout of 4CL1 in poplar (Populus tremula x alba) preferentially reduced syringyl (S) lignin, with negligible effects on biomass recalcitrance. Concordant with reduced S-lignin was downregulation of ferulate 5-hydroxylases (F5Hs). Lignification was largely sustained by 4CL5, a low-affinity paralog of 4CL1 typically with only minor xylem expression or activity. Levels of caffeate, the preferred substrate of 4CL5, increased in line with significant upregulation of caffeoyl shikimate esterase1. Upregulation of caffeoyl-CoA O-methyltransferase1 and downregulation of F5Hs are consistent with preferential funneling of 4CL5 products toward G-lignin biosynthesis at the expense of S-lignin. Thus, transcriptional and metabolic adaptations to 4CL1-knockout appear to have enabled 4CL5 catalysis at a level sufficient to sustain lignification. Finally, genes involved in sulfur assimilation, the glutathione-ascorbate cycle, and various antioxidant systems were upregulated in the mutants, suggesting cascading responses to perturbed thioesterification in lignin biosynthesis.

09 BIOMASS FUELS↗

DOE OSTI2022

Genotype–environment associations across spatial scales reveal the importance of putative adaptive genetic variation in divergence

Abstract Identifying areas of high evolutionary potential is a judicious strategy for developing conservation priorities in the face of environmental change. For wide‐ranging species occupying heterogeneous environments, the evolutionary forces that shape distinct populations can vary spatially. Here, we investigate patterns of genomic variation and genotype–environment associations in the hermit thrush ( Catharus guttatus ), a North American songbird, at broad (across the breeding range) and narrow spatial scales (at a hybrid zone). We begin by building a genoscape or map of genetic variation across the breeding range and find five distinct genetic clusters within the species, with the greatest variation occurring in the western portion of the range. Genotype–environment association analyses indicate higher allelic turnover in the west than in the east, with measures of temperature surfacing as key predictors of putative adaptive genomic variation rangewide. Since broad patterns detected across a species' range represent the aggregate of many locally adapted populations, we investigate whether our broadscale analysis is consistent with a finer scale analysis. We find that top rangewide temperature‐associated loci vary in their clinal patterns (e.g., steep clines vs. fixed allele frequencies) across a hybrid zone in British Columbia, suggesting that the environmental predictors and the associated candidate loci identified in the rangewide analysis are of variable importance in this particular region. However, two candidate loci exhibit strong concordance with the temperature gradient in British Columbia, suggesting a potential role for temperature‐related barriers to gene flow and/or temperature‐driven ecological selection in maintaining putative local adaptation. This study demonstrates how patterns identified at the broad (macrogeographic) scale can be validated by investigating genotype–environment correlations at the local (microgeographic) scale. Furthermore, our results highlight the importance of considering the spatial distribution of putative adaptive variation when assessing population‐level sensitivity to climate change and other stressors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Visual and genetic stock identification of a test fishery to forecast Columbia River spring Chinook salmon stocks 2 weeks into the future

Abstract Modern fisheries management strives to balance opposing goals of protection for weak stocks and opportunity for harvesting healthy stocks. Test fisheries can aid management of anadromous fishes if they can forecast the strength and timing of an annual run with adequate time to allow fisheries planning. Integration of genetic stock identification (GSI) can further maximize utility of test fisheries by resolving run forecasts into weak‐ and healthy‐stock subcomponents. Using 5 years (2017–2022) of test fishery data, our study evaluated accuracy, resolution, and lead time of predictions for stock‐specific run timing and abundance of Columbia River spring Chinook salmon ( Oncorhynchus tshawytscha ). We determined if this test fishery (1) could use visual stock identification (VSI) to forecast at the coarse stock resolution (i.e., classification of “lower” vs. “upriver” stocks) upon which current management is based and (2) could be enhanced with GSI to forecast at higher stock resolution. VSI accurately identified coarse stocks (83.3% GSI concordance), and estimated a proxy for abundance (catch per unit effort, CPUE) of the upriver stock in the test fishery that was correlated ( R 2 = 0.90) with spring Chinook salmon abundance at Bonneville dam (Rkm 235). Salmon travel rates (~8.6 Rkm/day) provided predictions with 2‐week lead time prior to dam passage. Importantly, GSI resolved this predictive ability as finely as the hatchery broodstock level. Lower river stock CPUE in the test fishery was correlated with abundance at Willamette Falls (Rkm 196, R 2 = 0.62), but could not be as finely resolved as achieved for upriver stocks. We described steps to combine VSI and GSI to provide timely in‐season information and with prediction accuracy of ~12.4 mean absolute percentage error and high stock resolution to help plan Columbia River mainstem fisheries.

Hess, Jon E.↗

DOE OSTI2025

Genetic Identification of Lamprey Genera and Anadromous Ecotypes in Watersheds of the Northeastern Pacific Ocean

ABSTRACT Nonparasitic, nonmigratory Western Brook Lamprey (WBL; Lampetra ayresii ), and parasitic, anadromous Western River Lamprey (WRL; L. ayresii ) are sympatric lampreys that likely represent different life history variations of a single species. Novel genetic tools are critical for differentiating WBL and WRL, whose larvae preclude morphological identification (ID) and will enable comprehensive assessment of imperiled native lampreys of the Northeastern Pacific (including WBL, WRL, and Pacific Lamprey, Entosphenus tridentatus ). We developed 47 candidate single nucleotide polymorphism (SNP) markers using whole genome resequencing of WBL ( N = 24) and WRL ( N = 15) from Ksi Ts'oohl Ts'ap Creek (Nass River, British Columbia, Canada) which are likely ecotypes distinguished by few divergent SNPs across multiple chromosomes. We used five novel candidate SNPs to perform genetic ID of WBL and WRL ecotypes in collections of mixed native lampreys from lower Columbia River tributaries ( N = 1474), Ksi Ts'oohl Ts'ap Creek ( N = 352), and ocean phase WRL from the Georgia Basin (Salish Sea, British Columbia, Canada; N = 91). Two previously published SNPs were used to ID genera, Entosphenus versus Lampetra . Morphological ID utilized photographs collected from a subset of genotyped lampreys, and high concordance was demonstrated between ID methods for genera (99%) and Lampetra ecotypes (> 98%). We characterized spatial and temporal composition of lamprey genera and ecotypes surveyed across NE Pacific tributaries under the expectation these compositions would be similar across nearby sites and across years at the same site. Proportions of lamprey genera were highly variable within regions and across years; however, Lampetra ecotypic proportions were spatially and temporally stable. WRL were rare in lower Columbia tributaries (~1% average rate among Lampetra ) and common further north (> 40% of Lampetra ). Genetic ID methods are powerful monitoring tools that create the novel ability to ascertain genera and ecotypes regardless of life stage, while increasing the efficiency of surveys by eliminating time‐intensive morphological data collection.

Silver, G. S. [Columbia River Inter‐Tribal Fish Co↗

DOE OSTI2022

Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism

Abstract Closely related species are expected to have similar functional traits due to shared ancestry and phylogenetic inertia. However, few tests of this hypothesis are available for plant‐associated fungal symbionts. Fungal leaf endophytes occur in all land plants and can protect their host plant from disease by a variety of mechanisms, including by parasitizing pathogens (e.g., mycoparasitism). Here, we tested whether phylogenetic relatedness among species of Cladosporium , a widespread genus that includes mycoparasitic species, predicts the effect of this endophyte on the severity of leaf rust disease. First, we used congruence among different marker sequences (i.e., genealogical concordance phylogenetic species recognition criterion) to delimit species of Cladosporium . Next, in a controlled experiment, we quantified both mycoparasitism and disease modification for the selected Cladosporium species. We identified 17 species of Cladosporium ; all the species reduced rust disease severity in our experiment. Cladosporium phylogeny was a significant predictor of mycoparasitism. However, we did not observe a phylogenetic effect on disease severity overall, indicating that other mechanism/s operating independently of shared ancestry also contributed to endophyte effects on disease severity. Indeed, a second experiment showed that Cladosporium endophyte exudates (no live organism) from divergent species groups equally reduced disease severity. Our results reveal that multiple mechanisms contribute to the protective effects of an endophyte against a plant pathogen, but not all traits underlying these mechanisms are phylogenetically conserved.

Barge, Edward G.↗

DOE OSTI2025

Spatial Replication Is Important for Developing Landscape Genetic Inferences for a Wetland Salamander

Habitat fragmentation is a pressing threat to wildlife populations, and maintenance of gene flow between populations is an essential goal of conservation. Resistance surfaces have emerged as an important tool for modelling connectivity and developing management strategies to mitigate effects of habitat fragmentation. However, recent studies have noted inconsistencies in the factors most strongly associated with connectivity across different landscapes. Thus, replication of genetic-based resistance surface optimisation across landscapes may be necessary for making robust conclusions about the influence of environmental variables. Accordingly, replication represents a substantive challenge and opportunity in the field of landscape genetics. In this study, we conducted replicated landscape genetic analyses across five landscapes in Tennessee and Kentucky for a threatened wetland amphibian, the four-toed salamander (Hemidactylium scutatum). We tested multiple hypotheses of how different landscape features that could directly affect small, desiccation-intolerant amphibians (e.g., canopy cover) influenced gene flow and assessed the appropriate scale at which to model different features. We found some concordance in the landscape features that influenced gene flow (e.g., a common importance of forest cover and topography), but also some differences—potentially owing to the difference in variability of predictors across landscapes. We also found discordance in the scale of effect of different features across landscapes. In conclusion, our work emphasises that flat areas of moist forest not bisected by roads may be important for H. scutatum conservation, and our replicated design allows us to identify relationships that would have been missed if only using one study site.

59 BASIC BIOLOGICAL SCIENCES↗