Calm after the storm? Similar patterns of genetic variation in a riverine foundation species before and after severe disturbance.

In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from five sites just before the storms with 239 shoots collected from nine sites 4 years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.

Predictability of demographic rates based on phylogeny and biological similarity.

Lack of demographic data for most of the world's threatened species is a widespread problem that precludes viability-based status assessments for species conservation. A commonly suggested solution is to use data from species that are closely related or biologically similar to the focal species. This approach assumes similar species and populations of the same species have similar demographic rates, an assumption that has yet to be thoroughly tested. We constructed a Bayesian hierarchical model with data on 425 plant species to predict demographic rates (intrinsic rate of population growth, recruit survival, juvenile survival, adult survival, and fecundity) based on biological traits and phylogenetic relatedness. Generally, we found small effects of species-level traits (except woody polycarpic species tended to have high adult survival rates that increased with plant height) and a weak phylogenetic signal for 4 of the 5 demographic parameters examined. Patterns were stronger in adult survival and fecundity than other demographic rates; however, the unexplained variances at both the species and population levels were high for all demographic rates. For species lacking demographic data, our model produced large, often inaccurate, prediction intervals that may not be useful in a management context. Our findings do not support the assumption that biologically similar or closely related species have similar demographic rates and provide further evidence that direct monitoring of focal species and populations is necessary for informing conservation status assessments.

Limited pollen dispersal, small genetic neighborhoods, and biparental inbreeding in Vallisneria americana.

PREMISE OF THE STUDY: Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system characteristics in Vallisneria americana-a water-pollinated plant with a distribution that has been reduced from historic levels. METHODS: We examined pollen neighborhood size, biparental inbreeding, and pollen dispersal, based on seed paternity using the indirect paternity method KinDist, from samples of 18-39 mothers and 14-20 progeny per mother from three sites across 2 years. KEY RESULTS: On average, fruits contained seeds sired by seven fathers. We found significant biparental inbreeding and limited pollen dispersal distances (0.8-4.34 m). However, in a number of cases, correlated paternity did not decline with distance, and dispersal could not be reliably estimated. CONCLUSIONS: Frequent pollen dispersal is not expected among patches, and even within patches, gene flow via pollen will be limited. Limited pollen dispersal establishes genetic neighborhoods, which, unless overcome by seed and propagule dispersal, will lead to genetic differentiation even in a continuous population. Unless loss and fragmentation drive populations to extreme sex bias, local pollen dispersal is likely to be unaffected by habitat loss and fragmentation per se because the spatial scale of patch isolation already exceeds pollen dispersal distances. Therefore, managing specifically for pollen connectivity is only relevant over very short distances.

Benefits of gene flow are mediated by individual variability in self-compatibility in small isolated populations of an endemic plant species.

Many rare and endemic species experience increased rates of self-fertilization and mating among close relatives as a consequence of existing in small populations within isolated habitat patches. Variability in self-compatibility among individuals within populations may reflect adaptation to local demography and genetic architecture, inbreeding, or drift. We use experimental hand-pollinations under natural field conditions to assess the effects of gene flow in 21 populations of the central Appalachian endemic Trifolium virginicum that varied in population size and degree of isolation. We quantified the effects of distance from pollen source on pollination success and fruit set. Rates of self-compatibility varied dramatically among maternal plants, ranging from 0% to 100%. This variation was unrelated to population size or degree of isolation. Nearly continuous variation in the success of selfing and near-cross-matings via hand pollination suggests that T. virginicum expresses pseudo-self-fertility, whereby plants carrying the same S-allele mate successfully by altering the self-incompatibility reaction. However, outcrossing among populations produced significantly higher fruit set than within populations, an indication of drift load. These results are consistent with strong selection acting to break down self-incompatibility in these small populations and/or early-acting inbreeding depression expressed upon selfing.

Species-level persistence probabilities for recovery and conservation status assessment.

Recovery planning for species listed under the U.S. Endangered Species Act has been hampered by a lack of consistency and transparency, which can be improved by implementing a standardized approach for evaluating species status and developing measurable recovery criteria. However, managers lack an assessment method that integrates threat abatement and can be used when demographic data are limited. To help meet these needs, we demonstrated an approach for evaluating species status based on habitat configuration data. We applied 3 established persistence measures (patch occupancy, metapopulation capacity, and proportion of population lost) to compare 2 conservation strategies (critical habitat designated by the U.S. Fish and Wildlife Service and the Forest Service's Carbonate Habitat Management Strategy) and 2 threat scenarios (maximum limestone mining, removal of all habitat in areas with mining claims; minimum mining, removal of habitat only in areas with existing operations and high-quality ore) against a baseline of existing habitat for 3 federally listed plant species. Protecting all area within the designated critical habitat maintained a similar level (83.9-99.9%) of species persistence as the baseline, whereas maximum mining greatly reduced persistence (0.51-38.4% maintained). The 3 persistence measures provided complementary insights reflecting different aspects of habitat availability (total area, number of patches, patch size, and connectivity). These measures can be used to link recovery criteria developed following the 3 R principles (representation, redundancy, and resilience) to the resulting improvements in species viability. By focusing on amount and distribution of habitat, our method provides a means of assessing the status of data-poor species to inform decision making under the Endangered Species Act.

Actual and potential use of population viability analyses in recovery of plant species listed under the US endangered species act.

Use of population viability analyses (PVAs) in endangered species recovery planning has been met with both support and criticism. Previous reviews promote use of PVA for setting scientifically based, measurable, and objective recovery criteria and recommend improvements to increase the framework's utility. However, others have questioned the value of PVA models for setting recovery criteria and assert that PVAs are more appropriate for understanding relative trade-offs between alternative management actions. We reviewed 258 final recovery plans for 642 plants listed under the U.S. Endangered Species Act to determine the number of plans that used or recommended PVA in recovery planning. We also reviewed 223 publications that describe plant PVAs to assess how these models were designed and whether those designs reflected previous recommendations for improvement of PVAs. Twenty-four percent of listed species had recovery plans that used or recommended PVA. In publications, the typical model was a matrix population model parameterized with ≤5 years of demographic data that did not consider stochasticity, genetics, density dependence, seed banks, vegetative reproduction, dormancy, threats, or management strategies. Population growth rates for different populations of the same species or for the same population at different points in time were often statistically different or varied by >10%. Therefore, PVAs parameterized with underlying vital rates that vary to this degree may not accurately predict recovery objectives across a species' entire distribution or over longer time scales. We assert that PVA, although an important tool as part of an adaptive-management program, can help to determine quantitative recovery criteria only if more long-term data sets that capture spatiotemporal variability in vital rates become available. Lacking this, there is a strong need for viable and comprehensive methods for determining quantitative, science-based recovery criteria for endangered species with minimal data availability. Uso Actual y Potencial del Análisis de Viabilidad Poblacional para la Recuperación de Especies de Plantas Enlistadas en el Acta de Especies En Peligro de E.U.A.

The power to detect recent fragmentation events using genetic differentiation methods.

Habitat loss and fragmentation are imminent threats to biological diversity worldwide and thus are fundamental issues in conservation biology. Increased isolation alone has been implicated as a driver of negative impacts in populations associated with fragmented landscapes. Genetic monitoring and the use of measures of genetic divergence have been proposed as means to detect changes in landscape connectivity. Our goal was to evaluate the sensitivity of Wright's F st, Hedrick' G'st , Sherwin's MI, and Jost's D to recent fragmentation events across a range of population sizes and sampling regimes. We constructed an individual-based model, which used a factorial design to compare effects of varying population size, presence or absence of overlapping generations, and presence or absence of population sub-structuring. Increases in population size, overlapping generations, and population sub-structuring each reduced F st, G'st , MI, and D. The signal of fragmentation was detected within two generations for all metrics. However, the magnitude of the change in each was small in all cases, and when N e was >100 individuals it was extremely small. Multi-generational sampling and population estimates are required to differentiate the signal of background divergence from changes in Fst , G'st , MI, and D associated with fragmentation. Finally, the window during which rapid change in Fst , G'st , MI, and D between generations occurs can be small, and if missed would lead to inconclusive results. For these reasons, use of F st, G'st , MI, or D for detecting and monitoring changes in connectivity is likely to prove difficult in real-world scenarios. We advocate use of genetic monitoring only in conjunction with estimates of actual movement among patches such that one could compare current movement with the genetic signature of past movement to determine there has been a change.

A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems.

Bees provide essential pollination services that are potentially affected both by local farm management and the surrounding landscape. To better understand these different factors, we modelled the relative effects of landscape composition (nesting and floral resources within foraging distances), landscape configuration (patch shape, interpatch connectivity and habitat aggregation) and farm management (organic vs. conventional and local-scale field diversity), and their interactions, on wild bee abundance and richness for 39 crop systems globally. Bee abundance and richness were higher in diversified and organic fields and in landscapes comprising more high-quality habitats; bee richness on conventional fields with low diversity benefited most from high-quality surrounding land cover. Landscape configuration effects were weak. Bee responses varied slightly by biome. Our synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture.

Predicting recovery criteria for threatened and endangered plant species on the basis of past abundances and biological traits.

Recovery plans for species listed under the U.S. Endangered Species Act are required to specify measurable criteria that can be used to determine when the species can be delisted. For the 642 listed endangered and threatened plant species that have recovery plans, we applied recursive partitioning methods to test whether the number of individuals or populations required for delisting can be predicted on the basis of distributional and biological traits, previous abundance at multiple time steps, or a combination of traits and previous abundances. We also tested listing status (threatened or endangered) and the year the recovery plan was written as predictors of recovery criteria. We analyzed separately recovery criteria that were stated as number of populations and as number of individuals (population-based and individual-based criteria, respectively). Previous abundances alone were relatively good predictors of population-based recovery criteria. Fewer populations, but a greater proportion of historically known populations, were required to delist species that had few populations at listing compared with species that had more populations at listing. Previous abundances were also good predictors of individual-based delisting criteria when models included both abundances and traits. The physiographic division in which the species occur was also a good predictor of individual-based criteria. Our results suggest managers are relying on previous abundances and patterns of decline as guidelines for setting recovery criteria. This may be justifiable in that previous abundances inform managers of the effects of both intrinsic traits and extrinsic threats that interact and determine extinction risk.

Testing surrogacy assumptions: can threatened and endangered plants be grouped by biological similarity and abundances?

There is renewed interest in implementing surrogate species approaches in conservation planning due to the large number of species in need of management but limited resources and data. One type of surrogate approach involves selection of one or a few species to represent a larger group of species requiring similar management actions, so that protection and persistence of the selected species would result in conservation of the group of species. However, among the criticisms of surrogate approaches is the need to test underlying assumptions, which remain rarely examined. In this study, we tested one of the fundamental assumptions underlying use of surrogate species in recovery planning: that there exist groups of threatened and endangered species that are sufficiently similar to warrant similar management or recovery criteria. Using a comprehensive database of all plant species listed under the U.S. Endangered Species Act and tree-based random forest analysis, we found no evidence of species groups based on a set of distributional and biological traits or by abundances and patterns of decline. Our results suggested that application of surrogate approaches for endangered species recovery would be unjustified. Thus, conservation planning focused on individual species and their patterns of decline will likely be required to recover listed species.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores.

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical insectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban development, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Taxonomic and geographic patterns of decline for threatened and endangered species in the United States.

Species listed under the U.S. Endangered Species Act (i.e., listed species) have declined to the point that the probability of their extinction is high. The decline of these species, however, may manifest itself in different ways, including reductions in geographic range, number of populations, or overall abundance. Understanding the pattern of decline can help managers assess extinction probability and define recovery objectives. Although quantitative data on changes in geographic range, number of populations, and abundance usually do not exist for listed species, more often qualitative data can be obtained. We used qualitative data in recovery plans for federally listed species to determine whether each listed species declined in range size, number of populations, or abundance relative to historical levels. We calculated the proportion of listed species in each state (or equivalent) that declined in each of those ways. Nearly all listed species declined in abundance, and range size or number of populations declined in approximately 80% of species for which those data were available. Patterns of decline, however, differed taxonomically and geographically. Declines in range were more common among vertebrates than plants, whereas population extirpations were more common among plants. Invertebrates had high incidence of range and population declines. Narrowly distributed plants and invertebrates may be subject to acute threats that may result in population extirpations, whereas vertebrates may be affected by chronic threats that reduce the extent and size of populations. Additionally, in the eastern United States and U.S. coastal areas, where the level of land conversion is high, a greater percentage of species' ranges declined and more populations were extirpated than in other areas. Species in the Southwest, especially plants, had fewer range and population declines than other areas. Such relations may help in the selection of species' recovery criteria.

A sequential approach using genetic and morphological analyses to test species status: the case of United States federally endangered Agalinis acuta (Orobanchaceae).

PREMISE OF THE STUDY: Given that inaccurate taxonomy can have negative consequences for species of conservation concern and result in erroneous conclusions regarding macroecological patterns, efficient methods for resolving taxonomic uncertainty are essential. The primary objective of this study was to assess the evolutionary distinctiveness of the federally endangered plant species Agalinis acuta (Orobanchaceae) to ensure it represents a distinct taxon warranting protection under the United States Endangered Species Act. METHODS: We describe and implement a sequential approach that begins with the most restrictive criteria of genealogical exclusivity within which we first conducted a phylogenetic analysis based on six chloroplast DNA loci assayed from multiple representatives of five putative species. Because of the possibility that incomplete lineage sorting is responsible for the lack of genealogical exclusivity among A. acuta individuals, we then conducted intensive population level analyses based on 21 microsatellite loci and 61 morphological traits. KEY RESULTS: The distinctiveness of A. acuta from Agalinis decemloba and Agalinis tenella was not supported under the genealogical species concept. The results from the analyses of microsatellite loci and morphological characters evaluated under alternative species concepts also did not support the distinctiveness of A. acuta from A. decemloba . CONCLUSIONS: Through this successive approach, we found insufficient evidence to support the evolutionary distinctiveness of the listed taxon A. acuta . We recommend that it be synonymized under A. decemloba and also conclude that the taxon that would now include A. acuta is deserving of protection under the Endangered Species Act.

An evaluation of candidate plant DNA barcodes and assignment methods in diagnosing 29 species in the genus Agalinis (Orobanchaceae).

PREMISE OF THE STUDY: DNA barcoding has been proposed as a useful technique within many disciplines (e.g., conservation biology and forensics) for determining the taxonomic identity of a sample based on nucleotide similarity to samples of known taxonomy. Application of DNA barcoding to plants has primarily focused on evaluating the success of candidate barcodes across a broad spectrum of evolutionary divergence. Less attention has been paid to evaluating performance when distinguishing congeners or to differential success of analytical techniques despite the fact that the practical application and utility of barcoding hinges on the ability to distinguish closely related species. • METHODS: We tested the ability to distinguish among 92 samples representing 29 putative species in the genus Agalinis (Orobanchaceae) using 13 candidate barcodes and three analytical methods (i.e., threshold genetic distances, hierarchical tree-based, and diagnostic character differences). Due to questions regarding evolutionary distinctiveness of some taxa, we evaluated success under two taxonomic hypotheses. • KEY RESULTS: The psbA-trnH and trnT-trnL barcodes in conjunction with the "best close match" distance-based method best met the objectives of DNA barcoding. Success was also a function of the taxonomy used. • CONCLUSIONS: In addition to accurately identifying query sequences, our results showed that DNA barcoding is useful for detecting taxonomic uncertainty; determining whether erroneous taxonomy or incomplete lineage sorting is the cause requires additional information provided by traditional taxonomic approaches. The magnitude of differentiation within and among the Agalinis species sampled suggests that our results inform how DNA barcoding will perform among closely related species in other genera.

Development of 11 polymorphic microsatellite markers in a macrophyte of conservation concern, Vallisneria americana Michaux (Hydrocharitaceae).

Vallisneria americana Michaux (wild celery) is currently a target of submersed aquatic vegetation restoration efforts in the Chesapeake Bay watershed. To aid these efforts, we have developed 11 polymorphic microsatellite markers to assess the distribution and degree of genetic diversity in both restored and naturally occurring populations in the Chesapeake Bay. In 59 individuals from two populations, we detected two to 10 total alleles per locus. Observed heterozygosity ranged from 0.125 to 0.929, and two loci exhibited significant deviations from Hardy-Weinberg equilibrium in at least one of the populations assayed.

Phylogenetic patterns and conservation among North American members of the genus Agalinis (Orobanchaceae).

BACKGROUND: North American Agalinis Raf. species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range. RESULTS: Phylogenetic relationships estimated using maximum likelihood analyses of seven chloroplast DNA loci (aligned length = 11,076 base pairs (bp) and the nuclear ribosomal DNA ITS (internal transcribed spacer) locus (733 bp); indicated no support for the historically recognized sections except for Section Erectae. Our results suggest that North American members of the genus comprise six major lineages, however we were not able to resolve branching order among many of these lineages. Monophyly of 24 of the 29 sampled species was supported based on significant branch lengths of and high bootstrap support for subtending branches. However, there was no statistical support for the monophyly of A. acuta with respect to Agalinis tenella and Agalinis decemloba. Although most species were supported, deeper relationships among many species remain ambiguous. CONCLUSION: The North American Agalinis species sampled form a well supported, monophyletic group within the family Orobanchaceae relative to the outgroups sampled. Most hypotheses regarding section- and subsection-level relationships based on morphology were not supported and taxonomic revisions are warranted. Lack of support for monophyly of Agalinis acuta leaves the important question regarding its taxonomic status unanswered. Lack of resolution is potentially due to incomplete lineage sorting of ancestral polymorphisms among recently diverged species; however the gene regions examined did distinguish among almost all other species in the genus. Due to the important policy implications of this finding we are further evaluating the evolutionary distinctiveness of A. acuta using morphological data and loci with higher mutation rates.

A genealogical approach to quantifying lineage divergence.

We introduce a statistic, the genealogical sorting index (gsi), for quantifying the degree of exclusive ancestry of labeled groups on a rooted genealogy and demonstrate its application. The statistic is simple, intuitive, and easily calculated. It has a normalized range to facilitate comparisons among different groups, trees, or studies and it provides information on individual groups rather than a composite measure for all groups. It naturally handles polytomies and accommodates measures of uncertainty in phylogenetic relationships. We use coalescent simulations to explore the behavior of the gsi across a range of divergence times, with the mean value increasing to 1, the maximum value when exclusivity within a group reached monophyly. Simulations also demonstrate that the power to reject the null hypothesis of mixed genealogical ancestry increased markedly as sample size increased, and that the gsi provides a statistically more powerful measure of divergence than FST. Applications to data from published studies demonstrated that the gsi provides a useful way to detect significant exclusivity even when groups are not monophyletic. Although we describe this statistic in the context of divergence, it is more broadly applicable to quantify and assess the significance of clustering of observations in labeled groups on any tree.

Biased data reduce efficiency and effectiveness of conservation reserve networks.

Complementarity-based reserve selection algorithms efficiently prioritize sites for biodiversity conservation, but they are data-intensive and most regions lack accurate distribution maps for the majority of species. We explored implications of basing conservation planning decisions on incomplete and biased data using occurrence records of the plant family Proteaceae in South Africa. Treating this high-quality database as 'complete', we introduced three realistic sampling biases characteristic of biodiversity databases: a detectability sampling bias and two forms of roads sampling bias. We then compared reserve networks constructed using complete, biased, and randomly sampled data. All forms of biased sampling performed worse than both the complete data set and equal-effort random sampling. Biased sampling failed to detect a median of 1-5% of species, and resulted in reserve networks that were 9-17% larger than those designed with complete data. Spatial congruence and the correlation of irreplaceability scores between reserve networks selected with biased and complete data were low. Thus, reserve networks based on biased data require more area to protect fewer species and identify different locations than those selected with randomly sampled or complete data.

Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions.

BACKGROUND: The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsections and sections). Previous presentations of relationships have been ambiguous and have not conformed to modern phylogenetic standards (e.g., were not presented as phylogenetic trees). Agalinis contains a large number of putatively rare taxa that have some degree of taxonomic uncertainty. We used DNA sequence data from three chloroplast genes to examine phylogenetic relationships among sections within the genus Agalinis Raf. (=Gerardia), and between Agalinis and closely related genera within Orobanchaceae. RESULTS: Maximum likelihood analysis of sequences data from rbcL, ndhF, and matK gene regions (total aligned length 7323 bp) yielded a phylogenetic tree with high bootstrap values for most branches. Likelihood ratio tests showed that all but a few branch lengths were significantly greater than zero, and an additional likelihood ratio test rejected the molecular clock hypothesis. Comparisons of substitution rates between gene regions based on linear models of pairwise distance estimates between taxa show both ndhF and matK evolve more rapidly than rbcL, although the there is substantial rate heterogeneity within gene regions due in part to rate differences among codon positions. CONCLUSIONS: Phylogenetic analysis supports the monophyly of Agalinis, including species formerly in Tomanthera, and this group is sister to a group formed by the genera Aureolaria, Brachystigma, Dasistoma, and Seymeria. Many of the previously described sections within Agalinis are polyphyletic, although many of the subsections appear to form natural groups. The analysis reveals a single evolutionary event leading to a reduction in chromosome number from n = 14 to n = 13 based on the sister group relationship of section Erectae and section Purpureae subsection Pedunculares. Our results establish the evolutionary distinctiveness of A. tenella from the more widespread and common A. obtusifolia. However, further data are required to clearly resolve the relationship between A. acuta and A. tenella.