Population Trajectories Research Articles

Environmental factors influence cross-talk between a heat shock protein and an oxidative stress protein modification in the lizard Gallotia galloti.

Better understanding how organisms respond to their abiotic environment, especially at the biochemical level, is critical in predicting population trajectories under climate change. In this study, we measured constitutive stress biomarkers and protein post-translational modifications associated with oxidative stress in Gallotia galloti, an insular lizard species inhabiting highly heterogeneous environments on Tenerife. Tenerife is a small volcanic island in a relatively isolated archipelago off the West coast of Africa. We found that expression of GRP94, a molecular chaperone protein, and levels of protein carbonylation, a marker of cellular stress, change across different environments, depending on solar radiation-related variables and topology. Here, we report in a wild animal population, cross-talk between the baseline levels of the heat shock protein-like GRP94 and oxidative damage (protein carbonylation), which are influenced by a range of available temperatures, quantified through modelled operative temperature. This suggests a dynamic trade-off between cellular homeostasis and oxidative damage in lizards adapted to this thermally and topologically heterogeneous environment.

Dynamic Morphological Growth Trajectory of Crouzon Population: A Geometric Morphometric Analysis.

This study is to visualize the morphological growth trajectory of the Crouzon population and provide a more comprehensive and perceptual understanding of pathologic aggregation in terms of maxillofacial and soft tissue surfaces. Twenty-two patients with Crouzon syndrome were included in this retrospective surgery. Preoperative computed tomography was segmented into maxillofacial and soft tissue surface morphologies. Fifty-two anatomical landmarks and a standardized template were used to extract the morphological phenotypes and transform them into spatial coordinates. Geometric morphometrics (GM) were applied to visualize the growth trajectory and estimate the morphological variation of the Crouzon population. Cephalometric analysis was conducted to validate the growth trajectory in a clinical aspect. It was found that both maxillofacial and soft tissue surface morphologies were strongly covaried with age. Morphological development of the Crouzon population was characterized by (1) maxillary retrusion and clockwise rotation, (2) mandibular counterclockwise rotation, (3) facial width narrowing and aggregated concave face, and (4) sunken nasal bone. Pathologic maxillary retrusion continuously existed from infancy to adulthood, and rapid aggravation took place at 3 to 6 years old. In conclusion, this study is the first to visualize the dynamic growth trajectories on both maxillofacial and soft tissue surface morphologies. More attention and monitoring of breathing, snoring, intelligence, and global development should be cast on Crouzon patients between 3 and 6 years old in family care. If any functional abnormalities occur during this period, professional consultations and evaluations should be conducted timely to avoid pathologic aggravation. Consistency between GMs and cephalometry validates the reliability of GM potentials in the clinical field, allowing a promising and revolutionary methodology for dynamically and qualitatively analyzing pathologic changes in some rare congenital diseases.

Regime shift in the interaction between domestic livestock and the deer-tiger food chain

The effects of grazing on wildlife have received considerable attention. Depending on factors such as its intensity and duration, grazing can impact higher-level species along the food chain through competition for available resources with wild herbivores. However, relatively few studies have investigated whether there are tipping points at which grazing intensity begins to seriously impact wildlife. In particular, studies that assess the impact of overgrazing on food chains that include carnivores remain scarce. We developed a time dynamic, age-structured model for the wild ungulates-Amur tiger trophic chain, including cattle grazing as a disturbance. We explored 1) the impact of cattle grazing intensity on the long-term behaviour of the wildlife population; 2) the effect of demographic parameters on wildlife population viability; and 3) the temporal dynamic impact of periods of heavy grazing on the population trajectory. Our results showed that increasing cattle density reaches a tipping point, triggering a rapid and significant shift in wildlife population size. Below the tipping point, wildlife can coexist with grazing livestock; when cattle density exceeds the tipping point, wild ungulate and tiger populations move towards extinction. In the case of heavy grazing, the dynamics of the wild ungulate population was more affected by its intensity, and the dynamics of the Amur tiger population was more affected by its duration. Our model and results suggest that theoretically wildlife conservation and cattle production can coexist but that serious regime shifts in wildlife populations may occur if grazing intensity exceeds a tipping point. These findings provide new insights useful for developing policies related to balancing livestock and wildlife conservation.

Demographic and evolutionary consequences of hunting of wild birds.

Hunting has a long tradition in human evolutionary history and remains a common leisure activity or an important source of food. Herein, we first briefly review the literature on the demographic consequences of hunting and associated analytical methods. We then address the question of potential selective hunting and its possible genetic/evolutionary consequences. Birds have historically been popular models for demographic studies, and the huge amount of census and ringing data accumulated over the last century has paved the way for research about the demographic effects of harvesting. By contrast, the literature on the evolutionary consequences of harvesting is dominated by studies on mammals (especially ungulates) and fish. In these taxa, individuals selected for harvest often have particular traits such as large body size or extravagant secondary sexual characters (e.g. antlers, horns, etc.). Our review shows that targeting individuals according to such genetically heritable traits can exert strong selective pressures and alter the evolutionary trajectory of populations for these or correlated traits. Studies focusing on the evolutionary consequences of hunting in birds are extremely rare, likely because birds within populations appear much more similar, and do not display individual differences to the same extent as many mammals and fishes. Nevertheless, even without conscious choice by hunters, there remains the potential for selection through hunting in birds, for example by genetically inherited traits such as personality or pace-of-life. We emphasise that because so many bird species experience high hunting pressure, the possible selective effect of harvest in birds and its evolutionary consequences deserves far more attention, and that hunting may be one major driver of bird evolutionary trajectories that should be carefully considered in wildlife management schemes.

C4 photosynthesis provided an immediate demographic advantage to populations of the grass Alloteropsis semialata.

C4 photosynthesis is a key innovation in land plant evolution, but its immediate effects on population demography are unclear. We explore the early impact of the C4 trait on the trajectories of C4 and non-C4 populations of the grass Alloteropsis semialata. We combine niche models projected into paleoclimate layers for the last 5 million years with demographic models based on genomic data. The initial split between C4 and non-C4 populations was followed by a larger expansion of the ancestral C4 population, and further diversification led to the unparalleled expansion of descendant C4 populations. Overall, C4 populations spread over three continents and achieved the highest population growth, in agreement with a broader climatic niche that rendered a large potential range over time. The C4 populations that remained in the region of origin, however, experienced lower population growth, rather consistent with local geographic constraints. Moreover, the posterior transfer of some C4-related characters to non-C4 counterparts might have facilitated the recent expansion of non-C4 populations in the region of origin. Altogether, our findings support that C4 photosynthesis provided an immediate demographic advantage to A. semialata populations, but its effect might be masked by geographic contingencies.

Preconception weight suppression predicts eating disorder symptoms in pregnancy.

Disordered eating is common in pregnancy and associated with adverse health outcomes. Weight suppression (WS), the discrepancy between highest lifetime and current weight, is a robust predictor of loss of control (LOC) and binge eating and weight gain trajectories in clinical populations. This study explored the role of preconception WS as a predictor of disordered eating and weight gain in pregnancy. Pregnant individuals (n=137) reported their highest, preconception, and current weights to calculate preconception WS, actual gestational weight gain (GWG), and deviations from recommended weight gain trajectories in pregnancy. Participants also completed the Prenatal Eating Behaviours Screening (PEBS) tool, a validated measure of disordered eating specifically in pregnancy. Preconception WS was a significant predictor of PEBS total scores [F(5, 122)=2.70, p=0.02, R2=0.10] and significantly and positively correlated with individual item scores quantifying restrictive eating behaviours. Preconception WS was not predictive of deviations from recommended GWG trajectories or LOC or binge eating frequency and did not interact with pre-pregnancy body mass index or GWG to predict eating disorder symptom severity. Preconception WS was predictive of disordered eating, and specifically restrictive eating behaviours in pregnancy, and should be assessed as part of screening for eating disorder risk in pregnant individuals.

Reconstructing mountain goat history in the Olympic Mountains, USA

AbstractBetween 1925 and 1930, 11 or 12 non‐native mountain goats (Oreamnos americanus) were translocated from Alaska and British Columbia to the foothills of the Olympic Range. By 1970, descendants of these goats had colonized the entire range and concerns about the management of this introduced species developed as damage to alpine soil and vegetation occurred. A series of removals reduced the population from 1175 in 1983 to 389 by 1990, eventually growing to 584 in 2016. We used demographic and genetic data to parameterize a population genetics individual‐based simulation model of the Olympic Range mountain goats. We calibrated the model to replicate the population trajectory for Olympic mountain goats from establishment in the 1920s through the 1983 first census. As expected, modeled population dynamics from 1928 to 1983 mimicked parameter initialization from expanding populations. However, simulated heterozygosity did not align with observations, suggesting a process not accounted for within the simulation model, such as a bottleneck or founder effect. Sensitivity analyses showed changes in annual reproductive rate, juvenile mortality, and adult female mortality influencing population trajectories, but variation in male mortality revealed no changes. Evaluating the population dynamics of the model after removals showed that approximately 80% of the total animals removed during the 1980s needed to be female in order for the observed population estimates to occur. This model has the potential to be used more widely with established or introduced mountain goat populations, as well as to provide an approach for studying other introduced species and their population dynamics.

Influence of interactive effects on long-term population trajectories in multispecies reintroductions.

Reintroduced populations are typically considered to progress through establishment, growth, and regulatory phases. However, most reintroduction programs do not monitor intensively enough to test this conceptual model. We studied population indices derived from track activity of 4 threatened species (greater bilby [Macrotis lagotis], burrowing bettong [Bettongia lesueur], greater stick-nest rat [Leporillus conditor], and Shark Bay bandicoot [Perameles bougainville]) over 23years after multiple reintroductions of each species in arid Australia. We compared population trajectories among species and investigated the effect of time and environmental variables. All species bred immediately after release, and the growth phase lasted 3-16years, varying markedly among but not within species. The end of the growth phase was characterized by an obvious peak in population density followed by either a catastrophic decline and sustained low density (bettongs), a slow decline to extirpation after 20years (stick-nest rat), or a slight decline followed by irregular fluctuations (bilby and bandicoot). Minor fluctuations were related to environmental variables, including 12-month cumulative rainfall and lagged summer maximum temperatures. Three of the 4 species did not reach a regulation phase, even after 23years, possibly due to interspecific competition and trophic cascades triggered by predator removal and multispecies reintroductions. Bilbies and bandicoots exhibited a second growth phase 18years after reintroduction, likely caused by high rainfall and increased resources following the population crash of overabundant bettongs. Our results suggest that assemblages within multispecies reintroductions demonstrate high variability in population trajectories due to interactive effects. Intensive monitoring to assess population viability may require decades, particularly where multiple species are reintroduced, release sites are confined, and the climate is unpredictable. Intensive monitoring also allows for adaptive management to prevent precipitous population declines. Practitioners should not assume reintroduced species pass through predictable postrelease population phases or that viability is assured after a certain period.

DNA hypomethylation ameliorates erosive inflammatory arthritis by modulating interferon regulatory factor-8

Epigenetic regulation plays a crucial role in the pathogenesis of autoimmune diseases such as inflammatory arthritis. DNA hypomethylating agents, such as decitabine (DAC), have been shown to dampen inflammation and restore immune homeostasis. In the present study, we demonstrate that DAC elicits potent anti-inflammatory effects and attenuates disease symptoms in several animal models of arthritis. Transcriptomic and epigenomic profiling show that DAC-mediated hypomethylation regulates a wide range of cell types in arthritis, altering the differentiation trajectories of anti-inflammatory macrophage populations, regulatory T cells, and tissue-protective synovial fibroblasts (SFs). Mechanistically, DAC-mediated demethylation of intragenic 5'-Cytosine phosphate Guanine-3' (CpG) islands of the transcription factor Irf8 (interferon regulatory factor 8) induced its re-expression and promoted its repressor activity. As a result, DAC restored joint homeostasis by resetting the transcriptomic signature of negative regulators of inflammation in synovial macrophages (MerTK, Trem2, and Cx3cr1), TREGs (Foxp3), and SFs (Pdpn and Fapα). In conclusion, we found that Irf8 is necessary for the inhibitory effect of DAC in murine arthritis and that direct expression of Irf8 is sufficient to significantly mitigate arthritis.

Balancing between predation risk and food by boreal breeding ducks.

Wetlands belong to the globally most threatened habitats, and organisms depending on them are of conservation concern. Wetland destruction and quality loss may affect negatively also boreal breeding ducks in which habitat selection often needs balancing between important determinants of habitat suitability. In Finland duck population trajectories are habitat-specific, while the reasons behind are poorly understood. In this research, we studied the balance of nest predation risk and invertebrate food abundance in boreal breeding ducks in Finland at 45 lakes and ponds in 2017 and 2018. We surveyed duck pairs and broods from these and 18 additional water bodies. We evaluated nest predation by monitoring artificial nests with camera traps over a 7-day exposure period and sampled invertebrates from water bodies using emergence and activity traps. Camera trap results indicate that predation risk was higher in the water bodies surrounded by agricultural land than in forestland. Ponds (seasonal, beaver, and man-made) had lower nest predation risk, and they were also more invertebrate-rich than permanent lakes. In addition, artificial nests further away from water bodies had higher survival than shoreline nests. Habitat use of duck pairs was not associated with invertebrate food, but duck broods preferred habitats rich in food. High nest predation pressure in shorelines of especially agricultural landscapes may contribute to the declining population trends of ducks in Finland. Controlling predators could be an important conservation action to improve duck breeding success. This research underlines the benefits of the availability of different water body types for breeding ducks. There is an urgent need to pay attention to protecting seasonal ponds, while the lack of flooded waters may be mitigated by favouring beavers or creating man-made ponds.

Diving into archival data: The hidden decline of the giant grouper (Epinephelus lanceolatus) in Queensland, Australia

AbstractThe giant grouper (Epinephelus lanceolatus) is the largest reef fish in the Indo‐Pacific (~2.5 m TL, >400 kg), and it is highly susceptible to overfishing. Despite regional protections and documented population declines, the species is listed by IUCN as Data Deficient due to minimal long‐term population data and a paucity of life history information. This study used historical fishing records derived from newspaper articles, fishing magazines, grey literature and naturalists' descriptions to collate life history information and reconstruct giant grouper population trends from 1854 to 1958 in Queensland, Australia. Historical recreational catch trends of four biologically distinct grouper size classes demonstrated that over 92 years, fishing disproportionately affected two size classes: immature (fish below reproductive size) and mature individuals. Changes in the probability of capturing a grouper within a recreational fishery were examined as a proxy of relative abundance. The probability of catching a giant grouper within a popular recreational fishery significantly declined from 81% in 1860 to 2% in 1958. Further analysis based on a non‐probabilistic method of giant grouper sighting records showed fluctuations in the giant grouper population trajectory, from a steady decline during the early 20th century to an increase during WWII (1939–1945) followed by a reduction in the last half of the 20th century. This study highlights the importance of archival sources to uncover population trends of rare species by combining quantitative assessments and biological inferences to determine the timing and occurrence of population declines and recoveries and inform how vulnerable fish species respond to the cumulative effects of fishing over time.

Evidence of active oviposition avoidance to systemically applied imidacloprid in the Colorado potato beetle.

Agricultural pests can develop behavioral resistance to insecticides by choosing to feed or oviposit on insecticide-free hosts. As young larvae have relatively low mobility, oviposition preferences from female adults may play a critical role in shaping the evolutionary trajectory of pest populations. While oviposition avoidance of insecticide-treated hosts was found in different agriculture pests, it remains unclear whether female adults actively choose to occupy insecticide-free hosts. To address this question, we investigated feeding and oviposition preferences between imidacloprid-treated and imidacloprid-free plants in the Colorado potato beetle, Leptinotarsa decemlineata Say, a major potato pest. We performed behavioral choice assays on two strains that differed in both fecundity and insecticide resistance. We found that one strain preferred to feed on the insecticide-free plants and that this preference is not innate. Meanwhile, the other strain chose plants for feeding and oviposition randomly. Further analyses of the moving patterns of the beetles suggested that the oviposition preference in the first strain is likely due to active learning.

Trajectory inference across multiple conditions with condiments

In single-cell RNA sequencing (scRNA-Seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolution. In such dynamic biological systems, cellular states form a continuum, e.g., for the differentiation of stem cells into mature cell types. This process is often represented via a trajectory in a reduced-dimensional representation of the scRNA-Seq dataset. While many methods have been suggested for trajectory inference, it is often unclear how to handle multiple biological groups or conditions, e.g., inferring and comparing the differentiation trajectories of wild-type and knock-out stem cell populations. In this manuscript, we present condiments, a method for the inference and downstream interpretation of cell trajectories across multiple conditions. Our framework allows the interpretation of differences between conditions at the trajectory, cell population, and gene expression levels. We start by integrating datasets from multiple conditions into a single trajectory. By comparing the cell’s conditions along the trajectory’s path, we can detect large-scale changes, indicative of differential progression or fate selection. We also demonstrate how to detect subtler changes by finding genes that exhibit different behaviors between these conditions along a differentiation path.

Threats to the persistence of sugar pine (Pinus lambertiana) in the western USA

This study assesses how numerous stressors shape the vital rates (survival, growth, and fecundity) of sugar pine across the vast majority of its range. Sugar pine (Pinus lambertiana Dougl.) is the largest Pinus species, an important timber species, and a component of several dry conifer forest types of western North America, in particular the extensive Sierra Nevada mixed conifer forest. The species faces several challenges in the Anthropocene, including a disrupted fire regime, an invasive pathogen, forest structure changes, and drought with ensuing bark beetle epidemics. Managers are concerned about the conservation outlook for sugar pine, but it is unclear where and how to best invest conservation resources. Using data from the US Forest Service’s Forest Inventory and Analysis program, we estimate the parameters for the vital rate functions and use these to construct an integral projection model which predicts the effects of various stressors on the asymptotic population growth rate. The asymptotic population growth rate is near or slightly below one even under reference conditions, and the actual abundance (in terms of both stem density and basal area) slightly declined over the duration of the study (2001–2019). The analysis reveals that wildfire, white pine blister rust, and forest density are key drivers of the demographic rates of sugar pine across its range. Drought and site dryness had lesser, but still meaningful, effects. Fire has strong negative effects on survival, resulting in a strongly negative population trajectory on burned sites. Conversely, lower than average forest density (plot-level basal area) results in a positive population growth rate via beneficial effects on individual growth. These results highlight the value of fire hazard mitigation, particularly where it also reduces forest density, in the conservation of this important species.

Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae).

While haplotype-specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed-haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame-shifting variants as the most deleterious type, followed by mutations in the 5'-UTR, 3'-UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high-impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter-haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype-resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.

Incorporating life history diversity in an integrated population model to inform viability analysis

Life history diversity can significantly affect population dynamics and effects of management actions. For instance, variation in individual responses to environmental variability can reduce extirpation risk to populations, as the portfolio effect dampens temporal variability in abundance. Moreover, differences in habitat use may cause individuals to respond differently to habitat management and climate variability. To explore the role of life history diversity in population trajectories, population models need to incorporate within-population variation. Integrated population modeling (IPM) is a population modeling approach that offers several advantages for sharing information and propagating uncertainty across datasets. In this study, we developed an IPM for an endangered population of Chinook salmon ( Oncorhynchus tshawytscha) in the Wenatchee River, Washington, USA, that accounts for diversity in juvenile life histories, spawning location, and return age. Our analysis revealed that diversity in the age of juvenile emigration from natal streams had a portfolio effect, resulting in a 20% reduction in year-to-year variability in adult abundance in population projections. Our population viability analysis suggests that management interventions may be necessary to meet recovery goals, and our model should be useful for simulating the outcomes of proposed actions.

Urban tolerance does not protect against population decline in North American birds.

Population declines of organisms are widespread and severe, but some species' populations have remained stable, or even increased. The reasons some species are less vulnerable to population decline than others are not well understood. Species that tolerate urban environments often have a broader environmental tolerance, which, along with their ability to tolerate one of the most human-modified habitats (i.e. cities), might allow them to persist in the face of diverse anthropogenic challenges. Here, we examined the relationship between urban tolerance and annual population trajectories for 397 North American bird species. Surprisingly, we found that urban tolerance was unrelated to species' population trajectories. The lack of a relationship between urban tolerance and population trajectories may reflect other factors driving population declines independent of urban tolerance, challenges that are amplified in cities (e.g. climate warming, disease), and other human impacts (e.g. conservation efforts, broad-scale land-use changes) that have benefitted some urban-avoidant species. Overall, our results illustrate that urban tolerance does not protect species against population decline.

Psychosocial distress patterns among key populations living with HIV in Nigeria

Abstract Background: The human immunodeficiency virus (HIV) continues to pose a substantial public health challenge in Nigeria, particularly affecting key populations due to various factors such as diminished risk perception, engaging in risky sexual and behavioral practices, stigma, discrimination, and legal barriers. Recognizing and addressing the mental health and psychosocial needs (MHPN) of HIV-positive key populations are essential for implementing tailored interventions and ensuring comprehensive care, aligning with the Joint United Nations Program on HIV and AIDS (UNAIDS) goal of ending acquired immune deficiency syndrome (AIDS) by 2030. Materials and Methods: This retrospective observational study was conducted among key populations (KPs) living with HIV who were enrolled in care at 17 one-stop shop (OSS) facilities operated by Heartland Alliance LTD/GTE across six states in Nigeria. The assessment tool used was the HALG Mental Health Screening Form III (MHSF-III). The study population consisted of diverse KPs enrolled in OSS facilities across six Nigerian states. Data analysis was performed using IBM-SPSS version 28. Results: The study revealed varying levels of MHPN among HIV-positive vital populations, with sex partners (8.9%), prisoners (7.1%), and female sex workers (6.1%) showing the highest prevalence. Among participants aged below 20, the need was most pronounced (10.7%). Female participants had increased odds (AOR = 2.072) of experiencing MHPN, as did individuals with sexual partners (AOR = 1.591), a history of drug/alcohol use (AOR = 10.458), and exposure to gender-based violence (AOR = 7.733). All respondents received brief interventions, with 69.3% being referred for further psychosocial support and 47.6% ultimately receiving specialized mental health intervention. The majority of participants preferred in-person counseling (72.7%) and a single session (74.0%), and most displayed mild confirmation outcomes (86.8%). Conclusion: The results highlight the importance of tackling the mental health obstacles encountered by these vulnerable groups to prevent HIV transmission and ensure comprehensive care. To enhance the well-being of these populations in Nigeria, policymakers and healthcare providers should prioritize integrated care and support services. Lastly, future research in this domain should concentrate on conducting long-term studies to monitor the mental health trajectories of HIV-positive key populations thoroughly.

Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations.

As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression. However, the rescued populations were more similar to the migrant source population (average FST range 0.05-0.10) compared to the historical recipient population (average FST range 0.23-0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.

Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird.

Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.