Geographical and socioeconomic disparities in post-transcatheter aortic valve replacement pacemaker placement.

INTRODUCTION: Pacemaker (PPM) implantation is indicated for conduction abnormalities which can develop post-transcatheter aortic valve replacement (TAVR). However, whether post-TAVR PPM risk is associated with the geographical location of the hospital and socioeconomic status of the patient is not well established. Our goal was to explore geographical and socioeconomic disparities in post-TAVR PPM implantation. METHODS: A retrospective cohort analysis was conducted using the National Inpatient Sample 2016-2020 with respective ICD-10 codes for TAVR and PPM implantation. A weighted multivariate logistic regression model was used to analyze prognostic outcomes. RESULTS: The number of patients hospitalized for undergoing TAVR was 296,740, out of which 28,265 patients had PPM implantation (prevalence 9.5 %). Patients' demographics including sex, ethnicity, household income, and insurance were not associated with risk of post-TAVR PPM except age (OR 1.01, CI 1.07-12.5, p < 0.001). Compared to rural hospitals, urban non-teaching hospitals were associated with a higher risk of post-TAVR PPM (OR 2.09, 1.3-3.43, p = 0.003). Compared to New England hospitals (ME, NH, VT, MA, RI, CT), middle Atlantic hospitals (NY, NJ, PA) were associated with highest post-TAVR PPM risk (OR 1.54, CI 1.2-1.98, p < 0.001), followed by Pacific (AK, WA, OR, CA, HI), mountain (ID, MT, WY, NV, UT, CO, AZ, NM) and east north central US. CONCLUSION: Patients' demographics including sex, ethnicity, household income, and insurance were not associated with the risk of post-TAVR PPM except for age. Compared to New England hospitals, Middle Atlantic hospitals were associated with the highest post-TAVR PPM risk followed by Pacific, Mountain, and East North Central US. Prospective studies with data on TAVR wait times, expertise of the interventional staff, and post-TAVR management and discharge planning are required to further explore the observed regional distribution of TAVR outcomes.

Hurricanes pose a substantial risk to New England forest carbon stocks.

Nature-based climate solutions (NCS) are championed as a primary tool to mitigate climate change, especially in forested regions capable of storing and sequestering vast amounts of carbon. New England is one of the most heavily forested regions in the United States (>75% forested by land area), and forest carbon is a significant component of climate mitigation policies. Large infrequent disturbances, such as hurricanes, are a major source of uncertainty and risk for policies relying on forest carbon for climate mitigation, especially as climate change is projected to alter the intensity and extent of hurricanes. To date, most research into disturbance impacts on forest carbon stocks has focused on fire. Here, we show that a single hurricane in the region can down between 121 and 250 MMTCO2e or 4.6%-9.4% of the total aboveground forest carbon, much greater than the carbon sequestered annually by New England's forests (16 MMTCO2e year-1). However, emissions from hurricanes are not instantaneous; it takes approximately 19 years for downed carbon to become a net emission and 100 years for 90% of the downed carbon to be emitted. Reconstructing hurricanes with the HURRECON and EXPOS models across a range of historical and projected wind speeds, we find that an 8% and 16% increase in hurricane wind speeds leads to a 10.7- and 24.8-fold increase in the extent of high-severity damaged areas (widespread tree mortality). Increased wind speed also leads to unprecedented geographical shifts in damage, both inland and northward, into heavily forested regions traditionally less affected by hurricanes. Given that a single hurricane can emit the equivalent of 10+ years of carbon sequestered by forests in New England, the status of these forests as a durable carbon sink is uncertain. Understanding the risks to forest carbon stocks from disturbances is necessary for decision-makers relying on forests as a NCS.

Ecotoxicology of Trace Elements in European Oyster (Ostrea edulis), Seawater, and Sedimentsacross Boston Harbor, Massachusetts,USA.

European oyster (Ostrea edulis) can be used for biological monitoring of water and sediment quality and serve as a conduit of trace elements to humans via consumption. Trace element concentrations in seawater, sediment, O. edulis edible tissues and shells from Boston Harbor were studied and found to be elevated relative to comparative studies in native ecosystems in the Adriatic Sea and Bay of Biscay. Average edible oyster tissues concentrations (mg/kg) were: arsenic 6, cadmium 1.7, cobalt 3.1, chromium 1.9, copper 153, mercury 0.265, nickel 1.8, lead 3.3, and zinc 2390. Arsenic was elevated in seawater and oyster shells. Mercury was elevated in sediments and oyster tissues. Lead was elevated in suspended sediments. Total Hazard Quotient (THQ) was < 1 but when summed across trace elements, THQ was nominally > 1 for all sites. Further study is warranted to determine mechanisms and spatial extent of bioaccumulation.

Eelgrass (Zostera marina L.) populations are threatened by high sea-surface temperatures and impaired waters on Nantucket Island, USA.

Eelgrass (Zostera marina L.) is a key foundation species that provides multiple ecosystem services to shallow coastal and estuarine systems in the Northern Hemisphere. It is estimated that, over the last century, up to 50 % of all Z. marina habitat has been lost along the east coast of the USA due to factors including light reduction, eutrophication, and physical disturbance. Warming sea surface temperatures are also believed to be exacerbating losses and the future of this ecosystem is unclear. Here, we assess Z. marina meadows on Nantucket, an island system located 50 km off-shore of Massachusetts, by using common indicators of seagrass plant health and environmental quality. Our results show that Z. marina meadows on Nantucket Island are thermally stressed and light-limited during parts of their peak growing season. This suggests that sea-surface temperatures are a pivotal factor, along with cultural eutrophication, in observed large-scale losses of Z. marina and that further degradation could be expected in the future as the climate continues to warm. Methods from this study may be used by managers as a guide to assess seagrass ecosystem status in degrading systems.

Radical shift in the genetic composition of New England chicory populations.

Human activities have been altering the flora and fauna across the planet. Distributions and the diversity of species, and the phenotypes of individuals in those species are changing. New England with its rapidly changing human demographics is an ideal place to investigate these temporal changes in the habitat. The flora of New England consists of both native and nonnative species. Non-indigenous plant species have been introduced since the first Europeans arrived in North America in the 15th century. Cichorium intybus (chicory), native to Eurasia, was first recorded in North America in 1774. Subsequently, chicory spread and became naturalized throughout much of the continent.In this study, we used chloroplast DNA sequences and 12 microsatellite nuclear markers to assess the temporal genetic changes in New England populations of chicory. We analysed 84 herbarium specimens and 18 contemporary extant populations (228 individuals in total).Three chloroplast DNA haplotypes were detected and all were present in New England prior to 1890; however, Hap3 was rare prior to the 1950s. The nuclear DNA markers showed a major shift in the genetic diversity and composition, with all historical herbarium collections belonging to a single genetic cluster and 16 out of 18 contemporary chicory populations belonging to different genetic clusters. This change occurred regionally and also on a local scale with contemporary populations being very different from herbarium specimens collected previously in the corresponding localities. Synthesis. Our results indicate that the genetic diversity and structure of Cichorium intybus populations have changed substantially since the founding populations in New England. These changes may have contributed to the success of this nonnative species and helped to fuel its rapid expansion and adaptation to the changing landscapes in both New England and the rest of North America.

Mechanical power and 30-day mortality in mechanically ventilated, critically ill patients with and without Coronavirus Disease-2019: a hospital registry study.

BACKGROUND: Previous studies linked a high intensity of ventilation, measured as mechanical power, to mortality in patients suffering from "classic" ARDS. By contrast, mechanically ventilated patients with a diagnosis of COVID-19 may present with intact pulmonary mechanics while undergoing mechanical ventilation for longer periods of time. We investigated whether an association between higher mechanical power and mortality is modified by a diagnosis of COVID-19. METHODS: This retrospective study included critically ill, adult patients who were mechanically ventilated for at least 24 h between March 2020 and December 2021 at a tertiary healthcare facility in Boston, Massachusetts. The primary exposure was median mechanical power during the first 24 h of mechanical ventilation, calculated using a previously validated formula. The primary outcome was 30-day mortality. As co-primary analysis, we investigated whether a diagnosis of COVID-19 modified the primary association. We further investigated the association between mechanical power and days being alive and ventilator free and effect modification of this by a diagnosis of COVID-19. Multivariable logistic regression, effect modification and negative binomial regression analyses adjusted for baseline patient characteristics, severity of disease and in-hospital factors, were applied. RESULTS: 1,737 mechanically ventilated patients were included, 411 (23.7%) suffered from COVID-19. 509 (29.3%) died within 30 days. The median mechanical power during the first 24 h of ventilation was 19.3 [14.6-24.0] J/min in patients with and 13.2 [10.2-18.0] J/min in patients without COVID-19. A higher mechanical power was associated with 30-day mortality (ORadj 1.26 per 1-SD, 7.1J/min increase; 95% CI 1.09-1.46; p = 0.002). Effect modification and interaction analysis did not support that this association was modified by a diagnosis of COVID-19 (95% CI, 0.81-1.38; p-for-interaction = 0.68). A higher mechanical power was associated with a lower number of days alive and ventilator free until day 28 (IRRadj 0.83 per 7.1 J/min increase; 95% CI 0.75-0.91; p < 0.001, adjusted risk difference - 2.7 days per 7.1J/min increase; 95% CI - 4.1 to - 1.3). CONCLUSION: A higher mechanical power is associated with elevated 30-day mortality. While patients with COVID-19 received mechanical ventilation with higher mechanical power, this association was independent of a concomitant diagnosis of COVID-19.

Biopsychosocial contexts of timely and adequate prenatal care utilization among women with criminal legal involvement and opioid use disorder.

OBJECTIVE: Pregnant women with criminal legal involvement and opioid use disorder (CL-OUD) living in non-urban regions may be at risk for complex biomedical, psychological, and social barriers to prenatal care and healthy pregnancy. Yet, limited research has explored prenatal care utilization patterns among this subpopulation. This study describes the biopsychosocial factors of pregnant women with a history of criminal legal involvement and opioid use disorder (CL-OUD) associated with timely prenatal care initiation and adequate prenatal care utilization (APNCU). METHODS: Analyses were conducted on a subsample of medical record data from an observational comparative effectiveness study of medication treatment models for pregnant women with diagnosed opioid use disorder (OUD) who received prenatal care in Northern New England between 2015 and 2022. The subsample included women aged ≥ 16 years with documented criminal legal involvement. Analyses included χ2, Fisher exact tests, and multiple logistic regression to assess differences in timely prenatal care and APNCU associated with biopsychosocial factors selected by backwards stepwise regression. RESULTS: Among 317 women with CL-OUD, 203 (64.0%) received timely prenatal care and 174 (54.9%) received adequate care. Timely prenatal care was associated with having two or three prior pregnancies (aOR 2.37, 95% CI 1.07-5.20), receiving buprenorphine at care initiation (aOR 1.85, 95% CI 1.01-3.41), having stable housing (aOR 2.49, 95% CI 1.41-4.41), and being mandated to court diversion (aOR 4.06, 95% CI 1.54-10.7) or community supervision (aOR 2.05, 95% CI 1.16-3.63). APNCU was associated with having a pregnancy-related medical condition (aOR 2.17, 95% CI 1.27-3.71), receiving MOUD throughout the entire prenatal care period (aOR 3.40, 95% CI 1.45-7.94), having a higher number of psychiatric diagnoses (aOR 1.35, 95% CI 1.07-1.70), attending a rurally-located prenatal care practice (aOR 2.14, 95% CI 1.22-3.76), having stable housing (aOR 1.94, 95% CI 1.06-3.54), and being mandated to court diversion (aOR 3.11, 95% CI 1.19-8.15). CONCLUSION: While not causal, results suggest that timely and adequate prenatal care among women with CL-OUD may be supported by OUD treatment, comorbid indications for care, stable access to social resources, and maintained residence in the community (i.e., community-based alternatives to incarceration).

Highly Pathogenic Avian Influenza A(H5N1) Virus Outbreak in New England Seals, United States.

We report the spillover of highly pathogenic avian influenza A(H5N1) into marine mammals in the northeastern United States, coincident with H5N1 in sympatric wild birds. Our data indicate monitoring both wild coastal birds and marine mammals will be critical to determine pandemic potential of influenza A viruses.

"I've been to more of my friends' funerals than I've been to my friends' weddings": Witnessing and responding to overdose in rural Northern New England.

PURPOSE: Overdose is a leading cause of death among people who use drugs (PWUDs), but policies to reduce fatal overdose have had mixed results. Summaries of naloxone access and Good Samaritan Laws (GSLs) in prior studies provide limited information about local context. Witnessing overdoses may also be an important consideration in providing services to PWUDs, as it contributes to post traumatic stress disorder (PTSD) symptoms, which complicate substance use disorder treatment. METHODS: We aim to estimate the prevalence and correlates of witnessing and responding to an overdose, while exploring overdose context among rural PWUD. The Drug Injection Surveillance and Care Enhancement for Rural Northern New England (DISCERNNE) mixed-methods study characterized substance use and risk behaviors in 11 rural Massachusetts, Vermont, and New Hampshire counties between 2018 and 2019. PWUD completed surveys (n = 589) and in-depth interviews (n = 22). FINDINGS: Among the survey participants, 84% had ever witnessed an overdose, which was associated with probable PTSD symptoms. Overall, 51% had ever called 911 for an overdose, though some experienced criminal legal system consequences despite GSL. Although naloxone access varied, 43% had ever used naloxone to reverse an overdose. CONCLUSIONS: PWUD in Northern New England commonly witnessed an overdose, which they experienced as traumatic. Participants were willing to respond to overdoses, but faced barriers to effective overdose response, including limited naloxone access and criminal legal system consequences. Equipping PWUDs with effective overdose response tools (education and naloxone) and enacting policies that further protect PWUDs from criminal legal system consequences could reduce overdose mortality.

The New England Neurosurgical Society: growth and evolution over 70 years.

The New England Neurosurgical Society (NENS) was founded in 1951 under the leadership of its first President (Dr. William Beecher Scoville) and Secretary-Treasurer (Dr. Henry Thomas Ballantine). The purpose of creating the NENS was to unite local neurosurgeons in the New England area; it was one of the first regional neurosurgical societies in America. Although regional neurosurgical societies are important supplements to national organizations, they have often been overshadowed in the available literature. Now in its 70th year, the NENS continues to serve as a platform to represent the needs of New England neurosurgeons, foster connections and networks with colleagues, and provide research and educational opportunities for trainees. Additionally, regional societies enable discussion of issues uniquely relevant to the region, improve referral patterns, and allow for easier attendance with geographic proximity. In this paper, the authors describe the history of the NENS and provide a roadmap for its future. The first section portrays the founders who led the first meetings and establishment of the NENS. The second section describes the early years of the NENS and profiles key leaders. The third section discusses subsequent neurosurgeons who steered the NENS and partnerships with other societies. In the fourth section, the modern era of the NENS and its current activities are highlighted.

Gathered from the Vine: A Survey of Seven Grapevine Viruses Within New England Vineyards.

Vineyards in the Southeastern New England American Viticultural Area were surveyed for the incidence of seven major viruses: grapevine leafroll-associated viruses (GLRaV-1, GLRaV-2, GLRaV-3, and GLRaV-4), grapevine fanleaf virus (GFLV), tomato ringspot virus (ToRSV), and tobacco ringspot virus (TRSV). Viruses were detected by DAS-ELISA and confirmed by RT-PCR and Sanger sequencing. Multiple viruses were present in 19 out of the 25 vineyards surveyed between 2018 and 2020. GLRaV-3 (27.59%) was the most prevalent virus followed by GLRaV-4 (14.90%), GLRaV-1 (13.52%), GLRaV-2 (11.03%), ToRSV (6.34%), GFLV (5.24%), and TRSV (2.62%). Furthermore, phylogenetic analyses of the viral partial genome sequences acquired in this study revealed that the grapevine viruses present in this area are diverse, indicating that they may have been introduced from different sources. Our findings stress the need for improving the sanitary status of planting materials to avoid the introduction and dissemination of viruses to vineyards in this important wine-producing region of New England.

Coastal Recreation in Southern New England: Results from a Regional Survey.

This paper presents a summary of coastal recreation of New England residents from a survey conducted in the summer of 2018. The management of New England's coasts benefits from understanding the value of coastal recreation and the factors influencing recreational behavior. To address this need, the survey collected the geographic location and trip details for both day and overnight visits to any type of location on the New England coast for a range of water recreation activities, providing a comprehensive view of coastal recreation in the region. This paper summarizes participation in various types of water recreation activities, including beachgoing, swimming, fishing, wildlife viewing, boating, and other coastal recreation activities. We quantify demand for coastal recreation using participation and effort models that disaggregate the dimensions of recreational behavior over space and census demographics. This provides insights on the scale and location of beneficiaries of this important human use of the natural environment. We found that 71% of people in the surveyed region participate in coastal recreation and engage in a wide range of coastal recreation activities at varied locations from open-ocean-facing coastal beaches to sheltered, estuarine ways to water. On average, people in the region take 37 trips to recreate on the coast of New England in a year, spending 167 hours per year visiting recreation sites and 66 hours traveling. This adds up to nearly 170.5 million trips from our sample region, 772.4 million hours of recreation time, and 304.6 million hours of travel time. Distance to the coast, demographics, and recreational activities affect how often people go and how much time they spend on coastal recreation.

Separating Proactive Conservation from Species Listing Decisions.

Proactive Conservation is a paradigm of natural resource management in the United States that encourages voluntary, collaborative efforts to restore species before they need to be protected through government regulations. This paradigm is widely used to conserve at-risk species today, and when used in conjunction with the Policy for Evaluation of Conservation Efforts (PECE), it allows for successful conservation actions to preclude listing of species under the Endangered Species Act (ESA). Despite the popularity of this paradigm, and recent flagship examples of its use (e.g., greater sage grouse, Centrocercus urophasianus), critical assessments of the outcomes of Proactive Conservation are lacking from the standpoint of species status and recovery metrics. Here, we provide such an evaluation, using the New England cottontail (Sylvilagus transitionalis), heralded as a success of Proactive Conservation efforts in the northeastern United States, as a case study. We review the history and current status of the species, based on the state of the science, in the context of the Conservation Initiative, and the 2015 PECE decision not to the list the species under the ESA. In addition to the impacts of the PECE decision on the New England cottontail conservation specifically, our review also evaluates the benefits and limits of the Proactive Conservation paradigm more broadly, and we make recommendations for its role in relation to ESA implementation for the future of at-risk species management. We find that the status and assurances for recovery under the PECE policy, presented at the time of the New England cottontail listing decision, were overly optimistic, and the status of the species has worsened in subsequent years. We suggest that use of PECE to avoid listing may occur because of the perception of the ESA as a punitive law and a misconception that it is a failure, although very few listed species have gone extinct. Redefining recovery to decouple it from delisting and instead link it to probability of persistence under recommended conservation measures would remove some of the stigma of listing, and it would strengthen the role of Species Status Assessments in endangered species conservation.

COVID-19's Perceived Impact on Primary Care in New England: A Qualitative Study.

BACKGROUND: COVID-19 impacted primary care delivery, as clinicians and practices implemented changes to respond to the pandemic while safely caring for patients. This study aimed to understand clinicians' perceptions of the positive and negative impacts of COVID-19 on primary care in New England. METHODS: This qualitative interview study was conducted from October through December 2020. Participants included 22 physicians and 2 nurse practitioners practicing primary care in New England. Data were thematically coded and analyzed deductively and inductively using content analysis. RESULTS: Through qualitative content analysis, 4 areas were identified in which clinicians perceived that COVID-19 impacted primary care: 1) bureaucracy, 2) leadership, 3) telemedicine and patient care, and 4) clinician work-life. Our findings suggest that the positive impacts of COVID-19 included changes in primary care delivery, new leadership opportunities for clinicians, flexible access to care for patients via telemedicine, and a better work-life balance for clinicians. Respondents identified negative impacts related to sustaining pandemic-inspired changes, the inability for some populations to access care via telemedicine, and the rapid implementation of telemedicine causing frustration for clinicians. CONCLUSIONS: Understanding clinician perspectives on how primary care transformed to respond to COVID-19 helps to identify beneficial pandemic-related changes that should be sustained and ideas for improvement that will support patient care and clinician engagement.

Frequency and Geographic Distribution of Borrelia miyamotoi, Borrelia burgdorferi, and Babesia microti Infections in New England Residents.

BACKGROUND: Borrelia miyamotoi is a relapsing fever spirochete that relatively recently has been reported to infect humans. It causes an acute undifferentiated febrile illness that can include meningoencephalitis and relapsing fever. Like Borrelia burgdorferi, it is transmitted by Ixodes scapularis ticks in the northeastern United States and by Ixodes pacificus ticks in the western United States. Despite reports of clinical cases from North America, Europe, and Asia, the prevalence, geographic range, and pattern of expansion of human B. miyamotoi infection are uncertain. To better understand these characteristics of B. miyamotoi in relation to other tickborne infections, we carried out a cross-sectional seroprevalence study across New England that surveyed B. miyamotoi, B. burgdorferi, and Babesia microti infections. METHODS: We measured specific antibodies against B. miyamotoi, B. burgdorferi, and B. microti among individuals living in 5 New England states in 2018. RESULTS: Analysis of 1153 serum samples collected at 11 catchment sites showed that the average seroprevalence for B. miyamotoi was 2.8% (range, 0.6%-5.2%), which was less than that of B. burgdorferi (11.0%; range, 6.8%-15.6%) and B. microti (10.0%; range, 6.5%-13.6%). Antibody screening within county residence in New England showed varying levels of seroprevalence for these pathogens but did not reveal a vectoral geographical pattern of distribution. CONCLUSIONS: Human infections caused by B. miyamotoi, B. burgdorferi, and B. microti are widespread with varying prevalence throughout New England.

Spectacles of Settler Colonial Memory: Archaeological Findings from an Early Twentieth-Century "First" Settlement Pageant and Other Commemorative Terrain in New England.

In 1923, rural New England mill town Dover, New Hampshire, staged a Tercentenary pageant of extraordinary proportions to celebrate its "first" settlement. This public spectacle memorialized a specific, and deeply exclusionary, narrative of English settler colonialism, shaped by social anxieties of the post-First World War United States. Recent archaeological research has found possible remnants from this spectacle on a seventeenth-century site. In disturbing this site, the Tercentenary pageant appears to have disregarded actual significant material traces from the very era it aimed to memorialize--traces that offer distinct, fuller understandings of deeply nuanced Native-settler interactions in the Piscataqua River region. Dover's pageant is situated in a regional analysis of Native and Euro-colonial commemorative place-making of the early twentieth century, exploring how different communities pursued multivocal, monovocal, or other approaches in their performative engagements with the seventeenth century.

Inorganic and methylated mercury dynamics in estuarine water of a salt marsh in Massachusetts, USA.

Salt marsh estuaries serve as sources and sinks for nutrients and elements to and from estuarine water, which enhances and alleviates watershed fluxes to the coastal ocean. We assessed sources and sinks of mercury in the intertidal Plum Island Sound estuary in Massachusetts, the largest salt marsh estuary of New England, using 25-km spatial water sampling transects. Across all seasons, dissolved (FHg) and total (THg) mercury concentrations in estuarine water were highest and strongly enhanced in upper marshes (1.31 ± 0.20 ng L-1 and 6.56 ± 3.70 ng L-1, respectively), compared to riverine Hg concentrations (0.86 ± 0.17 ng L-1 and 0.88 ± 0.34 ng L-1, respectively). Mercury concentrations declined from upper to lower marshes and were lowest in ocean water (0.38 ± 0.10 ng L-1 and 0.56 ± 0.25 ng L-1, respectively). Conservative mixing models using river and ocean water as endmembers indicated that internal estuarine Hg sources strongly enhanced estuarine water Hg concentrations. For FHg, internal estuarine Hg contributions were estimated at 26 g yr-1 which enhanced Hg loads from riverine sources to the ocean by 44%. For THg, internal sources amounted to 251 g yr-1 and exceeded riverine sources six-fold. Proposed sources for internal estuarine mercury contributions include atmospheric deposition to the large estuarine surface area and sediment re-mobilization, although sediment Hg concentrations were low (average 23 ± 2 µg kg-1) typical of uncontaminated sediments. Soil mercury concentrations under vegetation, however, were ten times higher (average 200 ± 225 µg kg-1) than in intertidal sediments suggesting that high soil Hg accumulation might drive lateral export of Hg to the ocean. Spatial transects of methylated Hg (MeHg) showed no concentration enhancements in estuarine water and no indication of internal MeHg sources or formation. Initial mass balance considerations suggest that atmospheric deposition may either be in similar magnitude, or possibly exceed lateral tidal export which would be consistent with strong Hg accumulation observed in salt marsh soils sequestering Hg from current and past atmospheric deposition.

Location and Species Matters: Variable Influence of the Environment on the Gene Flow of Imperiled, Native and Invasive Cottontails.

The environment plays an important role in the movement of individuals and their associated genes among populations, which facilitates gene flow. Gene flow can help maintain the genetic diversity both within and between populations and counter the negative impact of genetic drift, which can decrease the fitness of individuals. Sympatric species can have different habitat preferences, and thus can exhibit different patterns of genetic variability and population structure. The specialist-generalist variation hypothesis (SGVH) predicts that specialists will have lower genetic diversity, lower effective population sizes (Ne), and less gene flow among populations. In this study, we used spatially explicit, individual-based comparative approaches to test SGVH predictions in two sympatric cottontail species and identify environmental variables that influence their gene flow. New England cottontail (Sylvilagus transitionalis) is the only native cottontail in the Northeast US, an early successional habitat specialist, and a species of conservation concern. Eastern cottontail (S. floridanus) is an invasive species in the Northeast US and a habitat generalist. We characterized each species' genomic variation by developing double-digest Restriction-site Associated DNA sequence single nucleotide polymorphism markers, quantified their habitat with Geographic Information System environmental variables, and conducted our analyses at multiple scales. Surprisingly, both species had similar levels of genetic diversity and eastern cottontail's Ne was only higher than New England cottontail in one of three subregions. At a regional level, the population clusters of New England cottontail were more distinct than eastern cottontail, but the subregional levels showed more geographic areas of restricted gene flow for eastern cottontail than New England cottontail. In general, the environmental variables had the predicted effect on each species' gene flow. However, the most important environmental variable varied by subregion and species, which shows that location and species matter. Our results provide partial support for the SGVH and the identification of environmental variables that facilitate or impede gene flow can be used to help inform management decisions to conserve New England cottontail.

Identifying the minimum amplicon sequence depth to adequately predict classes in eDNA-based marine biomonitoring using supervised machine learning.

Environmental DNA metabarcoding is a powerful approach for use in biomonitoring and impact assessments. Amplicon-based eDNA sequence data are characteristically highly divergent in sequencing depth (total reads per sample) as influenced inter alia by the number of samples simultaneously analyzed per sequencing run. The random forest (RF) machine learning algorithm has been successfully employed to accurately classify unknown samples into monitoring categories. To employ RF to eDNA data, and avoid sequencing-depth artifacts, sequence data across samples are normalized using rarefaction, a process that inherently loses information. The aim of this study was to inform future sampling designs in terms of the relationship between sampling depth and RF accuracy. We analyzed three published and one new bacterial amplicon datasets, using a RF, based initially on the maximal rarefied data available (minimum mean of > 30,000 reads across all datasets) to give our baseline performance. We then evaluated the RF classification success based on increasingly rarefied datasets. We found that extreme to moderate rarefaction (50-5000 sequences per sample) was sufficient to achieve prediction performance commensurate to the full data, depending on the classification task. We did not find that the number of classification classes, data balance across classes, or the total number of sequences or samples, were associated with predictive accuracy. We identified the ability of the training data to adequately characterize the classes being mapped as the most important criterion and discuss how this finding can inform future sampling design for eDNA based biomonitoring to reduce costs and computation time.