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Invasive species surveillance programs can utilize environmental DNA sampling and analysis to provide information on the presence of invasive species. Wider utilization of eDNA techniques for invasive species surveillance may be warranted. This paper covers topics directed towards invasive species managers and eDNA practitioners working at the intersection of eDNA techniques and invasive species surveillance. It provides background information on the utility of eDNA for invasive species management and points to various examples of its use across federal and international programs. It provides information on 1) why an invasive species manager should consider using eDNA, 2) deciding if eDNA can help with the manager's surveillance needs, 3) important components to operational implementation, and 4) a high-level overview of the technical steps necessary for eDNA analysis. The goal of this paper is to assist invasive species managers in deciding if, when, and how to use eDNA for surveillance. If eDNA use is elected, the paper provides guidance on steps to ensure a clear understanding of the strengths and limitation of the methods and how results can be best utilized in the context of invasive species surveillance.

Author(s): Read, QD; Zarnetske, PL; Record, S; Dahlin, KM; Costanza, JK; Finley, AO; Gaddis, KD; Grady, JM; Hobi, ML; Latimer, AM; Malone, SL; Ollinger, SV; Pau, S; Wilson, AM | Abstract: Aim: We may be able to buffer biodiversity against the effects of ongoing climate change by prioritizing the protection of habitat with diverse physical features (high geodiversity) associated with ecological and evolutionary mechanisms that maintain high biodiversity. Nonetheless, the relationships between biodiversity and habitat vary with spatial and biological context. In this study, we compare how well habitat geodiversity (spatial variation in abiotic processes and features) and climate explain biodiversity patterns of birds and trees. We also evaluate the consistency of biodiversity–geodiversity relationships across ecoregions. Location: Contiguous USA. Time period: 2007–2016. Taxa studied: Birds and trees. Methods: We quantified geodiversity with remotely sensed data and generated biodiversity maps from the Forest Inventory and Analysis and Breeding Bird Survey datasets. We fitted multivariate regressions to alpha, beta and gamma diversity, accounting for spatial autocorrelation among Nature Conservancy ecoregions and relationships among taxonomic, phylogenetic and functional biodiversity. We fitted models including climate alone (temperature and precipitation), geodiversity alone (topography, soil and geology) and climate plus geodiversity. Results: A combination of geodiversity and climate predictor variables fitted most forms of bird and tree biodiversity with ln10% relative error. Models using geodiversity and climate performed better for local (alpha) and regional (gamma) diversity than for turnover-based (beta) diversity. Among geodiversity predictors, variability of elevation fitted biodiversity best; interestingly, topographically diverse places tended to have higher tree diversity but lower bird diversity. Main conclusions: Although climatic predictors tended to have larger individual effects than geodiversity, adding geodiversity improved climate-only models of biodiversity. Geodiversity was correlated with biodiversity more consistently than with climate across ecoregions, but models tended to have a poor fit in ecoregions held out of the training dataset. Patterns of geodiversity could help to prioritize conservation efforts within ecoregions. However, we need to understand the underlying mechanisms more fully before we can build models transferable across ecoregions.

Two common approaches to conserving biodiversity are conserving the actors (species) and conserving the stage (habitat). Many management efforts focus on conserving the actors, but a major challenge to this strategy is uncertainty surrounding how species’ geographic ranges might shift in response to global change, including climate and land use change. The Nature Conservancy has moved to conserving the stage, with the aim of maintaining the processes that generate and support biodiversity. This strategy requires knowing how biodiversity responds to geodiversity—the abiotic features and processes that define the stage. Here we explore how remote sensing illuminates the relationship between biodiversity and geodiversity. We introduce a variety of geodiversity measures and discuss how they can be combined with biodiversity data. We then explore the relationship between biodiversity and geodiversity with tree biodiversity data from the US Forest Inventory and Analysis Program and geodiversity data from the Shuttle Radar Topography Mission as a case study and proof of concept. We find that whereas beta diversity was not well explained by geodiversity, both alpha and gamma diversities were positively related to geodiversity. We also outline the challenges and opportunities of using remote sensing to understand the relationship between biodiversity and geodiversity.

Author(s): Zarnetske, Phoebe L; Read, Quentin D; Record, Sydne; Gaddis, Keith D; Pau, Stephanie; Hobi, Martina L; Malone, Sparkle L; Costanza, Jennifer; M Dahlin, Kyla; Latimer, Andrew M; Wilson, Adam M; Grady, John M; Ollinger, Scott V; Finley, Andrew O | Abstract: IssueGeodiversity (i.e., the variation in Earth's abiotic processes and features) has strong effects on biodiversity patterns. However, major gaps remain in our understanding of how relationships between biodiversity and geodiversity vary over space and time. Biodiversity data are globally sparse and concentrated in particular regions. In contrast, many forms of geodiversity can be measured continuously across the globe with satellite remote sensing. Satellite remote sensing directly measures environmental variables with grain sizes as small as tens of metres and can therefore elucidate biodiversity-geodiversity relationships across scales.EvidenceWe show how one important geodiversity variable, elevation, relates to alpha, beta and gamma taxonomic diversity of trees across spatial scales. We use elevation from NASA's Shuttle Radar Topography Mission (SRTM) and c.n16,000 Forest Inventory and Analysis plots to quantify spatial scaling relationships between biodiversity and geodiversity with generalized linear models (for alpha and gamma diversity) and beta regression (for beta diversity) across five spatial grains ranging from 5 to 100nkm. We illustrate different relationships depending on the form of diversity; beta and gamma diversity show the strongest relationship with variation in elevation.ConclusionWith the onset of climate change, it is more important than ever to examine geodiversity for its potential to foster biodiversity. Widely available satellite remotely sensed geodiversity data offer an important and expanding suite of measurements for understanding and predicting changes in different forms of biodiversity across scales. Interdisciplinary research teams spanning biodiversity, geoscience and remote sensing are well poised to advance understanding of biodiversity-geodiversity relationships across scales and guide the conservation of nature.

In deserts, many plant species exhibit a patchy spatial distribution within a harsh habitat matrix, where the likelihood of propagule dispersal among patches is uncertain, but may be promoted by landscape corridors or dispersal vectors. We examine the connectivity of a representative desert plant species (Acacia (Senegalia) greggii), and the ability of three major factors (animal dispersal agents, water flow along dry-washes, and climate) to facilitate dispersal within four watersheds in the Mojave National Preserve. We genotyped 323 individuals sampled across 22 one-hectare sites using ten nuclear microsatellite markers. A hierarchical AMOVA revealed no significant differentiation among watersheds (F RT = 0.00, P > 0.10), and very little genetic structure among all sites (F ST = 0.03, P 0.05), a distance measure based on rodent dispersal (P > 0.05), and a distance measure avoiding inhospitable climate (P > 0.05). An AIC comparison of generalized linear models found that within site genetic diversity (H E and allelic richness) and average relatedness were best explained by slope (which increases seed dispersal potential via water flow) and area of the upstream watershed (which determines the number of potential seed donors), rather than plant density or habitat suitability. Together, these findings indicate that dry-washes are key landscape features that enhance dispersal and regional connectivity in this patchy desert plant.

Текст статьи не публикуется в открытом доступе в соответствии с политикой журнала. Global change has become a major ecological concern that has the potential to dramatically alter plant distributions and assemblages worldwide. The specific response of plants to global change will depend on their ability to move, evolve, or adjust through phenotypic plasticity. Advances in biogeographic research are on the verge of a giant leap forward if we can take advantage of emerging tools in genetics and genomics. In this review, we appraise how new, post-Sanger, high-throughput sequencing and associated technologies can be used by next generation biogeographers to assess plant responses to global change. First, we briefly review the recent advances in genome sequencing and available approaches of genomic analysis. Secondly, we discuss the three main plant responses to global change: migration, adaptation, and phenotypic plasticity. This review is intended to spark the interest of biogeographers who do not traditionally use genetics but could benefit from including genetic and genomic tools into their research. Our goal is to illustrate that their use can contribute to new perspective and add an additional level of resolution into future biogeographic research.

Biogeography is a multifaceted field that integrates geography, geology, ecology, and biology to investigate both historical and ecological questions of how spatial and temporal patterns of varying environmental factors impact the distribution of species and their evolutionary history. Genomes contain imprints of these impacts and, when such genomic imprints are rightly deciphered and interpreted, can help us address these questions. In the past 10 years, incredible advances have been made with respect to acquiring and deciphering genome sequences. The advances in genomics and bioinformatics and the decreasing costs of nucleotide sequencing have reduced many of the barriers to using genomics in biogeography. Here, we introduce some of the strategies and approaches from population genomics that can be integrated into biogeography research. First, we introduce the field of biogeography and define the two well-established broad subdisciplines of ecological and historical biogeography along with the traditional methods that they use. Next, we present examples of how population genomics approaches can be used to address biogeographic questions. To illustrate how both ecological and historical biogeography can benefit from adopting a population genomics approach, we outline our own research on mountain hemlock as a case study. We also briefly discuss the application of biogeography in biological conservation. We conclude the chapter by discussing some of the remaining challenges and future research avenues that become possible by integrating population genomics into biogeography research.

PREMISE OF THE STUDY Partitioning of population genetic variation in plants may be affected by numerous factors including life history and dispersal characteristics. In parasitic plants, interactions with host populations may be an additional factor influencing partitioning. To test for hierarchical population genetic patterns related to obligate endoparasitism, we studied three species of Rafflesiaceae, which grow as extremely reduced endophytes infecting Tetrastigma vines in Southeast Asia. METHODS Microsatellite markers were developed and multilocus genotypes were determined for Rafflesia cantleyi, Rafflesia tuan-mudae, and Sapria himalayana and each of their Tetrastigma hosts. Relatedness among parasite individuals was estimated, and AMOVAs were used to determine levels of population genetic subdivision. KEY RESULTS Microsatellite genotypes for 340 paired parasite and host samples revealed that host vines were infected by numerous Rafflesiaceae individuals that may spread for up to 14 m within stem tissues. Surprisingly, Rafflesiaceae parasites within a given host are significantly more closely related to each other than individuals of the same species in other host individuals. The pattern of hierarchical population genetic subdivision we detected across species is likely due to limited seed dispersal with reinfection of natal host vines. CONCLUSIONS These findings demonstrate common population genetic patterns between animal and plant parasites, potentially indicating advantages of close relatives infecting hosts. This study also has important conservation implications for Rafflesiaceae since our data suggest that destruction of a single infected host vine could result in large genetic losses.

Alpine treelines are expected to advance to higher elevations in conjunction with global warming. Nevertheless, the importance of treeline reproductive patterns and seed dispersal within the alpine treeline ecotone remains unresolved. In this study, we address two research questions at mountain hemlock treelines on the Kenai Peninsula, Alaska: (1) What is the primary mode of reproduction and (2) are seeds leading to recruitment derived from within the local treeline populations or are they arriving from more distant seed sources? To answer these questions, we exhaustively sampled mountain hemlock individuals along a single mountain slope, and genotyped single nucleotide polymorphisms using doubledigest restriction site-associated DNA sequencing. First, we assessed mode of reproduction by determining the proportion of sampled individuals with identical multilocus genotypes that are the product of clonal reproduction. Second, we used a categorical parentage analysis to identify parent–offspring pairs, so that the proportion of treeline reproduction events could be spatially quantified and dispersal distance measured. We identified sexual reproduction as the primary mode of reproduction at our study site. Seedling establishment was characterized by extensive seed immigration and gene flow into the ecotone. The average dispersal distance was 73 m with long-distance dispersal identified as dispersal occurring at distances greater than 450 m. We found that production of seeds within the alpine treeline ecotone is not necessarily a requirement for treelines to advance to higher elevations in response to climate change. The extensive seed dispersal and gene flow into the alpine treeline ecotone is likely sufficient to propel the ecotone higher under more favorable climate. peerReviewed

PREMISE OF THE STUDY Untangling alternative historic dispersal pathways in long-lived tree species is critical to better understand how temperate tree species may respond to climatic change. However, disentangling these alternative pathways is often difficult. Emerging genomic technologies and landscape genetics techniques improve our ability to assess these pathways in natural systems. We address the question to what degree have microrefugial patches and long-distance dispersal been responsible for the colonization of mountain hemlock (Tsuga mertensiana) on the Alaskan Kenai Peninsula. METHODS We used double-digest restriction-associated DNA sequencing (ddRADseq) to identify genetic variants across eight mountain hemlock sample sites on the Kenai Peninsula, Alaska. We assessed genetic diversity and linkage disequilibrium using landscape and population genetics approaches. Alternative historic dispersal pathways were assessed using discriminant analysis of principle components and electrical circuit theory. KEY RESULTS A combination of decreasing diversity, high gene flow, and landscape connectivity indicates that mountain hemlock colonization on the Kenai Peninsula is the result of long-distance dispersal. We found that contemporary climate best explained gene flow patterns and that isolation by resistance was a better model explaining genetic variation than isolation by distance. CONCLUSIONS Our findings support the conclusion that mountain hemlock colonization is the result of several long-distance dispersal events following Pleistocene glaciation. The high dispersal capability suggests that mountain hemlock may be able to respond to future climate change and expand its range as new habitat opens along its northern distribution.

[Aim]: Host specificity within plant-feeding insects constitutes a fascinating example of natural selection that promotes inter-specific niche segregation. If specificity is strong, composition of local plant parasitic insect guilds is largely dependent on the presence and prevalence of the preferred hosts. Alternatively, if it is weak or absent, historic and stochastic demographic processes may drive the structuring of insect communities. We assessed whether the species composition of acorn feeding insects (Curculio spp. guilds) and their genetic variation change geographically according to the local host community. [Location]: An 800 km transect across California, USA. [Methods]: We used DNA taxonomy to detect potential Curculio cryptic speciation and assessed intra-specific genetic structure among sampling sites. We monitored larval performance on different hosts, by measuring the weight of each larva upon emerging from the acorn. Our phylogenetic and spatial analyses disentangled host specificity and geographical effects on Curculio community composition and genetic structure. [Results]: DNA taxonomy revealed no specialized cryptic species. Californian Curculio spp. were sister taxa that did not segregate among Quercus species or, at a deeper taxonomic level, between red and white oaks. Curculio species turnover and intra-specific genetic differentiation increased with geographical distance among localities irrespective of local oak species composition. Moreover, larval performance did not differ among oak species or acorn sizes when controlling for the effect of the locality. [Main conclusions]: Historical processes have contributed to the structuring of acorn weevil communities across California. Trophic niche overlapped among species, indicating that ecologically similar species can co-exist. Acorn crop inter-annual variability and unpredictability in mixed oak forests may have selected against narrow specialization, and facilitated co-existence by means of an inter-specific time partitioning of the resources. Wide-scale geographical records of parasitic insects and their host plants are necessary to understand the processes underlying species diversity., This work was financed by the projects: CONSOLIDER-MONTES CSD2008-00040 MICINN, PII1C09-0256-9052JCCM and ESF, AGL2014-54739-R (MINECO), PPII-2014-01-PJCCM ESF and CGL2008-00095 ⁄ BOS (MICINN). A.M.was funded by a Juan de la Cierva contract and R.B. by acontract of the Atracción de Talento Investigador Programme (Gobierno de Extremadura TA13032). J.O. wasfunded by Severo Ochoa (SEV-2012-0262) and Ramón y Cajal (RYC-2013-12501) research fellowships.

PREMISE OF THE STUDY: Geography and climate shape the distribution of organisms, their genotypes, and their phenotypes. To understand historical and future evolutionary and ecological responses to climate, we compared the association of geography and climate of three oak species (Quercus engelmannii, Quercus berberidifolia, and Quercus cornelius-mulleri) in an environmentally heterogeneous region of southern California at three organizational levels: regional species distributions, genetic variation, and phenotypic variation. METHODS: We identified climatic variables influencing regional distribution patterns using species distribution models (SDMs), and then tested whether those individual variables are important in shaping genetic (microsatellite) and phenotypic (leaf morphology) variation. We estimated the relative contributions of geography and climate using multivariate redundancy analyses (RDA) with variance partitioning. KEY RESULTS: The modeled distribution of each species was influenced by climate differently. Our analysis of genetic variation using RDA identified small but significant associations between genetic variation with climate and geography in Q. engelmannii and Q. cornelius-mulleri, but not in Q. berberidifolia, and climate explained more of the variation. Our analysis of phenotypic variation in Q. engelmannii indicated that climate had more impact than geography, but not in Q. berberidifolia. Throughout our analyses, we did not find a consistent pattern in effects of individual climatic variables. CONCLUSIONS: Our comparative analysis illustrates that climate influences tree response at all organizational levels, but the important climate factors vary depending on the level and on the species. Because of these species-specific and level-specific responses, today’s sympatric species are unlikely to have similar distributions in the future

The response of treeline-forming species to global climate change is uncertain. While numerous treeline species have recently experienced range advance along their upper elevational boundary, this has been species- and region-dependent. Making an accurate prediction of how taxa will respond is essential for conservation and land management, as treeline advance is likely to result in a loss of alpine biodiversity through habitat change and fragmentation. Predicting any species response requires an understanding of the current physical and climatic determinants of its distribution. We used the Maxent species distribution modeling software to predict the likelihood of treeline advance in the Nepalese Himalayas by modeling the extent of suitable habitats for 3 dominant treeline species—Abies spectabilis, Betula utilis, and Pinus wallichiana—under present and projected climate conditions. Temperature-related climatic variables and elevation explained the greatest amount of variance in the distribution of the study species. Under projected climate conditions, we found a regional increase in suitable habitat for all 3 treeline species, predicting a potential for northward and upslope advance.

The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in Northeastern Costa Rica dominated by the species Pentaclethra macroloba, which sprouts from the root mass of fallen trees and from snapped trunks. We exam- ined the population structure of juvenile P. macroloba growing in different soil types and across an elevational gradient. Using seven molecular markers, we genotyped 173 juvenile P. macroloba from 18 plots (six plots in seasonally inundated swamps, and 12 plots in upland non-swamp) spanning 50-300m in elevation at La Selva Biological Station and the adjacent Reserva Ecologica Bijagual in Northeastern Costa Rica. We answered two specific questions: (1) How extensive is clonal reproduction? and (2) what is the distribution of genetic diversity and structure?. We found that clonal reproduction occurred exclusively within inundated swamp areas. However, there was no significant difference between genetic diversity measures in swamp and non-swamp plots, which were both generally low when compared with other tropical forest species. Genetic structure was significant across all plots (F ST =0.109). However, genetic structure among swamp plots (F ST =0.128) was higher than among non-swamp upland plots (F ST =0.093). Additionally, spatial autocorrelation among individuals within non-swamp upland plots was significant from the 25 to 100m spatial scale, but not within swamp plots. The degree of overall genetic structure we found in P. macroloba is high for a tropical forest tree. The incidence of clonal reproduction is a contributing factor in genetic differentiation, but the high structure among plots without clonal reproduction indicates that other factors contribute as well. Rev. Biol. Trop. 62 (2): 443-454. Epub 2014 June 01.