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In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard‐to‐establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole‐soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole‐soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire‐sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard‐to‐establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long‐term potential consequences for restoration success. [ABSTRACT FROM AUTHOR]

In a landmark comparative phylogeographic study, "Comparative phylogeography of unglaciated eastern North America," Soltis et al. (Molecular Ecology, 2006, 15, 4261) identified geographic discontinuities in genetic variation shared across taxa occupying unglaciated eastern North America and proposed several common biogeographical discontinuities related to past climate fluctuations and geographic barriers. Since 2006, researchers have published many phylogeographical studies and achieved many advances in genotyping and analytical techniques; however, it is unknown how this work has changed our understanding of the factors shaping the phylogeography of eastern North American taxa. We analyzed 184 phylogeographical studies of eastern North American taxa published between 2007 and 2019 to evaluate: (1) the taxonomic focus of studies and whether a previously detected taxonomic bias towards studies focused on vertebrates has changed over time, (2) the extent to which studies have adopted genotyping technologies that improve the resolution of genetic groups (i.e., NGS DNA sequencing) and analytical approaches that facilitate hypothesis‐testing (i.e., divergence time estimation and niche modeling), and (3) whether new studies support the hypothesized biogeographic discontinuities proposed by Soltis et al. (Molecular Ecology, 2006, 15, 4261) or instead support new, previously undetected discontinuities. We observed little change in taxonomic focus over time, with studies still biased toward vertebrates. Although many technological and analytical advances became available during the period, uptake was slow and they were employed in only a small proportion of studies. We found variable support for previously identified discontinuities and identified one new recurrent discontinuity. However, the limited resolution and taxonomic breadth of many studies hindered our ability to clarify the most important climatological or geographical factors affecting taxa in the region. Broadening the taxonomic focus to include more non‐vertebrate taxa, employing technologies that improve genetic resolution, and using analytical approaches that improve hypothesis testing are necessary to strengthen our inference of the forces shaping the phylogeography of eastern North America. [ABSTRACT FROM AUTHOR]

[Display omitted] • General relationships in the group were confirmed, while the large amounts of gene tree discordance are likely due to ILS, reticulation, or both, depending on the subclade. • Of all the major phenomena that may lead to conflicting phylogenetic hypotheses, reticulation and ILS are plausible causes for the incongruence that we detected across perennial Dicerandra. • In parts of the Conradina + allies phylogeny where reticulation indices were lower, both hard incongruence (via ILS and hybridization) and soft incongruence (via gene tree estimation error) likely contributed to poor gene tree concordance. The Scrub Mint clade (Lamiaceae) provides a unique system for investigating the evolutionary processes driving diversification in the North American Coastal Plain from both a systematic and biogeographic context. The clade comprises Dicerandra, Conradina, Piloblephis, Stachydeoma, and four species of the broadly defined genus Clinopodium (Mentheae; Lamiaceae), almost all of which are endemic to the North American Eastern Coastal Plain. Most species of this clade are threatened or endangered and restricted to sandhill or a mosaic of scrub habitats. We analyzed relationships in this clade to understand the evolution of the group and identify evolutionary mechanisms acting on the clade, with important implications for conservation. We used a target-capture method to sequence and analyze 238 nuclear loci across all species of scrub mints, reconstructed the phylogeny, and calculated gene tree concordance, gene tree estimation error, and reticulation indices for every node in the tree using ML methods. Phylogenetic networks were used to determine reticulation events. Our nuclear phylogenetic estimates were consistent with previous results, while greatly increasing the robustness of taxon sampling. The phylogeny resolved the full relationship between Dicerandra and Conradina and the less-studied members of the clade (Piloblephis , Stachydeoma , Clinopodium spp.). We found hotspots of gene tree discordance and reticulation throughout the tree, especially in perennial Dicerandra. Several instances of reticulation events were uncovered between annual and perennial Dicerandra , and within the Conradina + allies clade. Incomplete lineage sorting also likely contributed to phylogenetic discordance. These results clarify phylogenetic relationships in the clade and provide insight on important evolutionary drivers in the clade, such as hybridization. General relationships in the group were confirmed, while the large amount of gene tree discordance is likely due to reticulation across the phylogeny. [ABSTRACT FROM AUTHOR]

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species. [ABSTRACT FROM AUTHOR]

In this study, we evaluated the efficacy of sample collection approaches and DNA metabarcoding to identify plants utilized by nectivorous bats. Samples included guano collected from beneath bat roosts and pollen-swabs from bat fur, both of which were subjected to DNA metabarcoding and visual identification of pollen (microscopy) to measure plant diversity. Our objectives were to determine whether DNA metabarcoding could detect likely food plants of nectivorous bats, whether sample types would produce different estimates of plant diversity, and to compare results of DNA metabarcoding to visual identification. Visual identification found that 99% of pollen was from Agave, which is thought to be the bats' main food source. The dominant taxon found by metabarcoding was also Agavoideae, but a broader diversity of plant species was also detected, many of which are likely "by-catch" from the broader environment. Metabarcoding outcomes differed between sample types, likely because pollen-swabs measured the plant species visited by bats and guano samples measured all items consumed in the bat's diet, even those that were not pollen or nectar. Overall, metabarcoding is a powerful, high-throughput tool to understand bat ecology and species interactions, but careful analysis of results is necessary to derive accurate ecological conclusions. [ABSTRACT FROM AUTHOR]

Increasing genetic diversity and maintaining evolutionary processes are primary goals of conservation translocations, which involve the intentional movement of an at‐risk species to establish new populations or augment existing populations, with the ultimate goal of reversing declines. Much debate has focused on how to select source material for plant translocations, with early approaches focusing primarily on maintaining the genetic uniqueness of populations. However, recent strategies often advocate mixing population sources during translocation to increase genetic diversity and re‐establish connectivity. Yet, despite hundreds of translocations programmes with at‐risk plant species presently underway (e.g. Silcock et al., 2019), few studies have conducted thorough assessments of the effects of mixing population sources on both the genetic diversity and fitness of translocated populations. The study by Van Rossum et al. (2020) in this issue of Molecular Ecology uses detailed assessments of genetic parameters and fitness to understand the outcomes of mixing two genetically differentiated source populations in translocations of the rare, self‐incompatible perennial herb, Arnica montana, whose populations are declining at low elevations in Western Europe. They examine genetic changes throughout the translocation process (source populations to F1 offspring) and demonstrate the maintenance of high genetic diversity in successive generations for all three translocations. Translocated populations exhibited high contemporary pollen flow, substantial admixture between source populations and low inbreeding in F1 offspring. Importantly, they found no evidence of outbreeding depression in F1 offspring. This work shows that genetically mixing source populations can result in optimal genetic outcomes in translocations of declining plant species and exemplifies how multigenerational genetic monitoring and fitness assessments can be used to evaluate the success of experimental translocations. [ABSTRACT FROM AUTHOR]

Extinction is the complete loss of a species, but the accuracy of that status depends on the overall information about the species. Dracaena umbraculifera was described in 1797 from a cultivated plant attributed to Mauritius, but repeated surveys failed to relocate it and it was categorized as Extinct on the IUCN Red List. However, several individuals labelled as D. umbraculifera grow in botanical gardens, suggesting that the species’ IUCN status may be inaccurate. The goal of this study was to understand (1) where D. umbraculifera originated, (2) which species are its close relatives, (3) whether it is extinct, and (4) the identity of the botanical garden accessions and whether they have conservation value. We sequenced a cpDNA region of Dracaena from Mauritius, botanical garden accessions labelled as D. umbraculifera and individuals confirmed to be D. umbraculifera based on morphology, one of which is a living plant in a private garden. We included GenBank accessions of Dracaena from Madagascar and other locations and reconstructed the phylogeny using Bayesian and parsimony approaches. Phylogenies indicated that D. umbraculifera> is more closely related to Dracaena reflexa from Madagascar than to Mauritian Dracaena. As anecdotal information indicated that the living D. umbraculifera originated from Madagascar, we conducted field expeditions there and located five wild populations; the species’ IUCN status should therefore be Critically Endangered because < 50 wild individuals remain. Although the identity of many botanical garden samples remains unresolved, this study highlights the importance of living collections for facilitating new discoveries and the importance of documenting and conserving the flora of Madagascar. [ABSTRACT FROM AUTHOR]

Background: Plant performance in agricultural and natural settings varies with moisture availability, and understanding the range of potential drought responses and the underlying genetic architecture is important for understanding how plants will respond to both natural and artificial selection in various water regimes. Here, we raised genotypes of Brassica rapa under well-watered and drought treatments in the field. Our primary goal was to understand the genetic architecture and yield effects of different drought-escape and dehydration-avoidance strategies. Results: Drought treatments reduced soil moisture by 62 % of field capacity. Drought decreased biomass accumulation and fruit production by as much as 48 %, whereas instantaneous water-use efficiency and root:shoot ratio increased. Genotypes differed in the mean value of all traits and in the sensitivity of biomass accumulation, root:shoot ratio, and fruit production to drought. Bivariate correlations involving gas-exchange and phenology were largely constant across environments, whereas those involving root:shoot varied across treatments. Although root: shoot was typically unrelated to gas-exchange or yield under well-watered conditions, genotypes with low to moderate increases in root:shoot allocation in response to drought survived the growing season, maintained maximum photosynthesis levels, and produced more fruit than genotypes with the greatest root allocation under drought. QTL for gas-exchange and yield components (total biomass or fruit production) had common effects across environments while those for root:shoot were often environment-specific. Conclusions: Increases in root allocation beyond those needed to survive and maintain favorable water relations came at the cost of fruit production. The environment-specific effects of root:shoot ratio on yield and the differential expression of QTL for this trait across water regimes have important implications for efforts to improve crops for drought resistance. [ABSTRACT FROM AUTHOR]

Crop selection often leads to dramatic morphological diversification, in which allocation to the harvestable component increases. Shifts in allocation are predicted to impact (as well as rely on) physiological traits; yet, little is known about the evolution of gas exchange and related anatomical features during crop diversification., In Brassica rapa, we tested for physiological differentiation among three crop morphotypes (leaf, turnip, and oilseed) and for correlated evolution of circadian, gas exchange, and phenological traits. We also examined internal and surficial leaf anatomical features and biochemical limits to photosynthesis., Crop types differed in gas exchange; oilseed varieties had higher net carbon assimilation and stomatal conductance relative to vegetable types. Phylogenetically independent contrasts indicated correlated evolution between circadian traits and both gas exchange and biomass accumulation; shifts to shorter circadian period (closer to 24 h) between phylogenetic nodes are associated with higher stomatal conductance, lower photosynthetic rate (when CO2 supply is factored out), and lower biomass accumulation. Crop type differences in gas exchange are also associated with stomatal density, epidermal thickness, numbers of palisade layers, and biochemical limits to photosynthesis., Brassica crop diversification involves correlated evolution of circadian and physiological traits, which is potentially relevant to understanding mechanistic targets for crop improvement. [ABSTRACT FROM AUTHOR]

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species. [ABSTRACT FROM AUTHOR]

Drought limits light harvesting, resulting in lower plant growth and reproduction. One trait important for plant drought response is water-use efficiency (WUE). We investigated (1) how the joint genetic architecture of WUE, reproductive characters, and vegetative traits changed across drought and well-watered conditions, (2) whether traits with distinct developmental bases (e.g. leaf gas exchange versus reproduction) differed in the environmental sensitivity of their genetic architecture, and (3) whether quantitative variation in circadian period was related to drought response in Brassica rapa. Overall, WUE increased in drought, primarily because stomatal conductance, and thus water loss, declined more than carbon fixation. Genotypes with the highest WUE in drought expressed the lowest WUE in well-watered conditions, and had the largest vegetative and floral organs in both treatments. Thus, large changes in WUE enabled some genotypes to approach vegetative and reproductive trait optima across environments. The genetic architecture differed for gas-exchange and vegetative traits across drought and well-watered conditions, but not for floral traits. Correlations between circadian and leaf gas-exchange traits were significant but did not vary across treatments, indicating that circadian period affects physiological function regardless of water availability. These results suggest that WUE is important for drought tolerance in Brassica rapa and that artificial selection for increased WUE in drought will not result in maladaptive expression of other traits that are correlated with WUE. [ABSTRACT FROM PUBLISHER]

Life history theory predicts the evolution of trait combinations that enhance fitness, and the occurrence of trade-offs depends in part on the magnitude of variation in growth rate or acquisition. Using recombinant inbred lines, we examined the genetic architecture of age and size at reproduction across abiotic conditions encountered by cultivars and naturalized populations of Brassica rapa. We found that genotypes are plastic to seasonal setting, such that reproduction was accelerated under conditions encountered by summer annual populations and genetic variances for age at reproduction varied across simulated seasonal settings. Using an acquisition-allocation model, we predicted the likelihood of trade-offs. Consistent with predicted relationships, we observed a trade-off where early maturity is associated with small size at maturity under simulated summer and fall annual conditions but not under winter annual conditions. The trade-off in the summer annual setting was observed despite significant genotypic variation in growth rate, which is often expected to decouple age and size at reproduction because rapidly growing genotypes could mature early and attain a larger size relative to slowly growing genotypes that mature later. The absence of a trade-off in the winter setting is presumably attributable to the absence of genotypic differences in age at reproduction. We observed QTL for age at reproduction that jointly regulated size at reproduction in both the summer and fall annual settings, but these QTL were environment-specific (i.e. different QTL contributed to the trade-off in the fall vs. summer annual settings). Thus, at least some of the genetic mechanisms underlying observed trade-offs differed across environments. [ABSTRACT FROM AUTHOR]

Developmental mechanisms that enable perception of and response to the environment may enhance fitness. Ecophysiological traits typically vary depending on local conditions and contribute to resource acquisition and allocation, yet correlations may limit adaptive trait expression. Notably, photosynthesis and stomatal conductance vary diurnally, and the circadian clock, which is an internal estimate of time that anticipates diurnal light/dark cycles, may synchronize physiological behaviors with environmental conditions. Using recombinant inbred lines of Brassica rapa, we examined the quantitative-genetic architecture of ecophysiological and phenological traits and tested their association with the circadian clock. We also investigated how trait expression differed across treatments that simulated seasonal settings encountered by crops and naturalized populations. Many ecophysiological traits were correlated, and some correlations were consistent with expected biophysical constraints; for example, stomata jointly regulate photosynthesis and transpiration by affecting carbon dioxide and water vapor diffusion across leaf surfaces, and these traits were correlated. Interestingly, some genotypes had unusual combinations of ecophysiological traits, such as high photosynthesis in combination with low stomatal conductance or leaf nitrogen, and selection on these genotypes could provide a mechanism for crop improvement. At the genotypic and QTL level, circadian period was correlated with leaf nitrogen, instantaneous measures of photosynthesis, and stomatal conductance as well as with a long-term proxy (carbon isotope discrimination) for gas exchange, suggesting that gas exchange is partly regulated by the clock and thus synchronized with daily light cycles. The association between circadian rhythms and ecophysiological traits is relevant to crop improvement and adaptive evolution. [ABSTRACT FROM AUTHOR]

Growth chambers allow measurement of phenotypic differences among genotypes under controlled environment conditions. However, unintended variation in growth chamber air CO2 concentration ([CO2]) may affect the expression of diverse phenotypic traits, and genotypes may differ in their response to variation in [CO2]. We monitored [CO2] and quantified phenotypic responses of 22 Brassica rapa genotypes in growth chambers with either standard or enhanced venting. [CO2] in chambers with standard venting dropped to 280 μmol mol−1 during the period of maximum canopy development, ~80 μmol mol−1 lower than in chambers with enhanced venting. The stable carbon isotope ratio of CO2 in chamber air (δ13Cair) was negatively correlated with [CO2], suggesting that photosynthesis caused observed [CO2] decreases. Significant genotype × chamber-venting interactions were detected for 12 of 20 traits, likely due to differences in the extent to which [CO2] changed in relation to genotypes’ phenology or differential sensitivity of genotypes to low [CO2]. One trait, 13C discrimination (δ13C), was particularly influenced by unaccounted-for fluctuations in δ13Cair and [CO2]. Observed responses to [CO2] suggest that genetic variance components estimated in poorly vented growth chambers may be influenced by the expression of genes involved in CO2 stress responses; genotypic values estimated in these chambers may likewise be misleading such that some mapped quantitative trait loci may regulate responses to CO2 stress rather than a response to the environmental factor of interest. These results underscore the importance of monitoring, and where possible, controlling [CO2]. [ABSTRACT FROM AUTHOR]

The article presents a study which used Population Genetic Data as a tool for species delimitation in a recent radiation of Conradina cygniflora, or lamiceae, from Florida. In this study, patterns of genetic structure based on microsatellites in Conradina were analyzed and a morphological study was then conducted to reveal unique characteristics of these population. It was recommended that Conrandina cygniflora can be considered federally endangered due to its limited geographic distribution.

Phylogeny reconstruction at the species level, especially using organellar markers, is often complicated by problems such as incomplete lineage sorting and interspecific hybridization. Single-copy nuclear genes may be useful for these cases because they have higher mutation rates and are biparentally inherited. One plant group in which hybridization and incomplete lineage sorting have been proposed based on analyses of internal transcribed spacer (ITS) and plastid data is a clade of mints from the southeastern United States: Conradina and the related genera Dicerandra, Piloblephis, Stachydeoma, and Clinopodium (Lamiaceae). To clarify the phylogeny in this clade and investigate the possibility of incomplete lineage sorting and interspecific hybridization, we isolated three members of the nuclear GapC gene family and used two to reconstruct phylogeny. Separate phylogenetic analyses of the two GapC loci did not resolve species relationships. We then used two approaches to concatenate the two heterozygous GapC loci with ITS and plastid data sets from a previous study and carried out combined analyses. Trees resulting from the two concatenation approaches were similar in the resolution and support of generic relationships, but they differed drastically in resolution and support for relationships within Conradina. Conradina species are probably very recently derived, and it may be unreasonable to reconstruct species relationships in Conradina using DNA sequence data due to widespread hybridization or lack of coalescence. Rapidly evolving microsatellite data may be more useful for detecting hybridization and clarifying species boundaries in Conradina. [ABSTRACT FROM AUTHOR]

The article investigates the monophyly of Conradina (Lamiaceae) and its relationship to other endemic mints of the southeastern United States to know the patterns of diversification in Conradina and to clarify species relationships. Conradina has six allopatric species endemic to the southeastern United States. Sequencing of intergenic spacers and plastid regions infered a molecular phylogeny from multiple accessions of each species of Conradina.

Premise: Although ex situ collections of threatened plants are most useful when they contain maximal genetic variation, the conservation and maintenance of genetic diversity in collections are often poorly known. We present a case study using population genomic analyses of an ex situ collection of Karomia gigas, a critically endangered tropical tree from Tanzania. Only ~43 individuals are known in two wild populations, and ex situ collections containing 34 individuals were established in two sites from wild‐collected seed. The study aimed to understand how much diversity is represented in the collection, analyze the parentage of ex situ individuals, and identify efficient strategies to capture and maintain genetic diversity. Methods: We genotyped all known individuals using a 2b‐RADseq approach, compared genetic diversity in wild populations and ex situ collections, and conducted parentage analysis of the collections. Results: Wild populations were found to have greater levels of genetic diversity than ex situ populations as measured by number of private alleles, number of polymorphic sites, observed and expected heterozygosity, nucleotide diversity, and allelic richness. In addition, only 32.6% of wild individuals are represented ex situ and many individuals were found to be the product of selfing by a single wild individual. Discussion: Population genomic analyses provided important insights into the conservation of genetic diversity in K. gigas, identifying gaps and inefficiencies, but also highlighting strategies to conserve genetic diversity ex situ. Genomic analyses provide essential information to ensure that collections effectively conserve genetic diversity in threatened tropical trees. [ABSTRACT FROM AUTHOR]

This essay discusses the use of quantitative genetic experiments to estimate the ability of rare plants to deal with climate change. Topics include the use of neutral genetic markers by most conservation genetics studies, the vulnerability of rare, threatened, or endangered (RTE) species to climate-related extinction, and the need to employ quantitative genetic studies of RTE species across multiple environments.

• Premise of the study: To examine the foraging behavior of nectarivorous bats in southeastern Arizona, we developed microsatellite primers in Agave parryi. These markers were also tested for cross-amplification and applicability to assess patterns of genetic diversity and structure in A. palmeri. • Methods and Results: Utilizing DNA sequence data from 454 shotgun sequencing, we identified seven novel polymorphic microsatellite loci in A. parryi and screened them for cross-amplification in A. palmeri. These markers were characterized in two populations of 30 individuals each for each species. In A. parryi, all primers were polymorphic and amplified between three and 12 alleles per population. In A. palmeri, all primers amplified, six were polymorphic, and allelic diversity ranged from one to 16 alleles per population. • Conclusions: Our results demonstrate the applicability of these microsatellite primers for population genetics studies in both A. parryi and A. palmeri. [ABSTRACT FROM AUTHOR]

Summary: Recent studies have demonstrated that ecological processes that shape community structure and dynamics change along environmental gradients. However, much less is known about how the emergence of the gradients themselves shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments leads to community assembly via two nonmutually exclusive processes: immigration and ecological sorting of pre‐adapted clades (ISPC), and recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes.We develop a novel approach and method based on the decomposition of species turnover into within‐ and among‐clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots.We found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes.Our results suggest that immigration and sorting of clades pre‐adapted to montane habitats is the primary mechanism shaping tree communities across elevations. [ABSTRACT FROM AUTHOR]

Hibiscus liliiflorus , endemic to the Indian Ocean island of Rodrigues, is one of the rarest plant species in the world; only 2 wild individuals remain. Previously, when 4 wild individuals remained, the Mauritian Wildlife Foundation (MWF) in Rodrigues propagated cuttings of them in their nursery, then planted seedlings produced in the nursery into 3 outplanted populations on the island. Our goals were to: 1) assess whether all 4 original wild genotypes are represented in the MWF nursery; 2) determine whether ex situ living collections at international botanical gardens maintain unique genotypes of H. liliiflorus ; 3) assess whether nursery individuals have crossed or self-fertilized to produce seed and quantify their relative contributions to outplanted populations; and 4) provide recommendations for future conservation actions. We used a 2b-RADseq approach to produce 2,711 genome-wide single nucleotide polymorphisms (SNPs) from 98 samples. Genotype identity analysis, principal component analysis, and model-based clustering in STRUCTURE found 4 genotypes extant in Rodrigues but no unique genotypes in ex situ botanic garden collections. Only 3 genotypes are represented in the MWF nursery; the one remaining genotype is represented by an extant wild individual. Parentage analysis showed that seeds produced in the MWF nursery resulted from both self-fertilization and crossing between genotypes, a result supported by internal relatedness and hybrid index calculations. Each outplanted population is dominated by a subset of parental genotypes, and we propose actions to balance the parental contributions to outplanted populations. Our study highlights how genetic assessments of ex situ conservation projects help conserve critically endangered species. [ABSTRACT FROM AUTHOR]

Premise of the Study: Interpreting relationships within groups containing polyploids, which are frequent in angiosperms, can be greatly assisted by genomic techniques. In this study, we used a genome‐skimming approach to investigate the evolutionary relationships and origins of polyploids in the monophyletic group, Ludwigia section Macrocarpon (Onagraceae), which includes diploid, tetraploid, and hexaploid taxa. Methods: We sampled all known taxa and ploidy levels in the section and conducted shotgun sequencing. We assembled plastomes, mitochondrial sequences, and completed nuclear ribosomal regions, reconstructed phylogenies, and conducted comparative genomic analyses for plastomes to gain insights into the relationships among studied taxa. Key Results: Within the section, results showed that the South American diploid taxa L. bonariensis and L. lagunae were closely related. We reported the first chromosome count (2n = 4× = 32) for L. neograndiflora, which is closely related to the two South American diploid taxa, although its exact origin remains unclear. The samples of the widespread, polyploid taxon L. octovalvis do not form a monophyletic group. Both tetraploid and hexaploid L. octovalvis lineages have originated more than once. At least one tetraploid in the L. octovalvis lineage may have been involved in the origins of hexaploids. One or more extinct/unsampled intermediate tetraploids in the L. octovalvis lineages had also likely been involved in the origins of hexaploids. Conclusions: Genome skimming provided important insights into the complex evolutionary relationships within sect. Macrocarpon, but additional sampling and data from single‐copy nuclear regions are necessary to further elucidate the origins of the polyploids in this section. [ABSTRACT FROM AUTHOR]

Premise: The effective ex situ conservation of exceptional plants, whether in living collections or cryo‐collections, requires more resources than the conservation of other species. Because of their expertise with rare plants, botanical gardens are well positioned to lead this effort, but a well‐developed strategy requires a clear understanding of the resources needed. Methods: Grant funding was obtained from the Institute of Museum and Library Services to support a three‐year project on cryobanking, and to provide smaller grants to 10 other botanical gardens for one‐year projects on either (1) seed behavior studies or (2) the development of protocols for in vitro propagation or cryopreservation. Results: Nine of the partner gardens worked on 19 species (one was unable to continue due to the COVID‐19 pandemic), while the larger project focused on 14 species. A point system was developed for tasks accomplished, and the average costs per point of the larger and smaller projects were similar. Labor accounted for half the costs. Projects focused on species in the Asteraceae and Orchidaceae had lower costs per point than other species. Discussion: Both large and small projects can contribute to a strategy for exceptional plant conservation for similar costs. Prioritizing species with lower costs could help advance the field while allowing time for work on more difficult species to develop. [ABSTRACT FROM AUTHOR]

DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next‐generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed‐species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White‐nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto‐ and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain. [ABSTRACT FROM AUTHOR]

Many factors shape the genetic diversity of island-endemic trees, with important implications for conservation. Oceanic island-endemic lineages undergo an initial founding bottleneck during the colonization process and subsequently accumulate diversity following colonization. Moreover, many island endemics occur in small populations and are further threatened by anthropogenic factors that cause population declines, making them susceptible to losses in genetic diversity through genetic drift, inbreeding, and bottlenecks. However, life-history traits commonly found in trees, such as outcrossing mechanisms, long lifespans, and a propensity for interspecific hybridization, may help buffer against losses of genetic variation. To assess the relative importance of colonization history, rarity, and distribution in shaping genetic diversity of island-endemic trees, we conducted a comparative population genomic analysis of 13 species of Diospyros (Ebenaceae) endemic to the Mascarene Islands that differ in island colonization history, distribution, population size, and IUCN threat status. We genotyped 328 individuals across the islands using 2b-RADseq, compared genetic diversity both among and within species, and assessed patterns of genetic structure. Genetic diversity did not vary significantly by IUCN status, but we found that species that co-occur with others on the same intermediate-aged island (Mauritius) had much greater genetic diversity than those that occur solitarily on an island (Réunion and Rodrigues), likely because of greater interspecific hybridization among species with overlapping distributions and processes related to time since island colonization. Results presented here were used to determine priority localities for in situ and ex situ conservation efforts to maximize the genetic diversity of each Mascarene Diospyros species. [ABSTRACT FROM AUTHOR]

• The ability of tree stems to recover from damage is critical for tree survival and may explain species distributions across disturbance regimes. Two primary responses to stem damage, decay compartmentalization and wound closure, act in concert to limit decay and pathogen spread. A previous study demonstrated a tradeoff between wound responses that varied with anatomical traits, but its wide taxonomic range made it hard to analyze responses in an evolutionary context. • Here, we tested the stem wound responses of 13 species of Quercus inhabiting three habitats across a gradient of fire intensity. We also quantified anatomical and structural traits and phylogenetic position, in order to assess the relative contributions of ecological adaptation and phylogenetic history in determining traits. • Xylem anatomical traits were phylogenetically constrained, while phloem traits and damage responses varied with habitat. Across habitats, hammock and sandhill species closed bark wounds effectively, whereas scrub species limited the spread of xylem decay. There was a tradeoff between wound closure and decay compartmentalization within the white+live oaks. • The fact that some wound response traits are phylogenetically constrained while others respond to ecological pressures suggests that damage responses integrate mechanisms operating at several levels within plants. [ABSTRACT FROM AUTHOR]

A common pattern observed in temperate tree clades is that species are often morphologically distinct and partially interfertile but maintain species cohesion despite ongoing hybridization where ranges overlap. Although closely related species commonly occur in sympatry in tropical ecosystems, little is known about patterns of hybridization within a clade over time, and the implications of this hybridization for the maintenance of species boundaries. In this study, we focused on a clade of sympatric trees in the genus Diospyros in the Mascarene islands and investigated whether species are genetically distinct, whether they hybridize, and how patterns of hybridization are related to the time since divergence among species. We sampled multiple populations from each of 12 Mascarene Diospyros species, generated genome‐wide single nucleotide polymorphism data using 2bRADseq, and conducted population genomic and phylogenomic analyses. We found that Mascarene Diospyros species diverged millions of years ago and are today largely genetically distinct from one another. Although hybridization was observed between closely related species belonging to the same subclade, more distantly related species showed little evidence of interspecific hybridization. Phylogenomic analyses also suggested that introgression has occurred during the evolutionary history of the clade. This suggests that, as diversification progressed, interspecific hybridization occurred among species, but became infrequent as lineages diverged from one another and evolved reproductive barriers. Species now coexist in partial sympatry, and experience limited hybridization between close relatives. Additional research is needed to better understand the role that introgression may have played in adaptation and diversification of Mascarene Diospyros, and its relevance for conservation. see also the Perspective by by Charles H. Cannon. [ABSTRACT FROM AUTHOR]

PREMISE: A disjunct distribution, where a species' geographic range is discontinuous, can occur through vicariance or long‐distance dispersal. Approximately 75 North American plant species exhibit a ~650 km disjunction between the Ozark and Appalachian regions. This disjunction is attributed to biogeographic forces including: (1) Eocene–Oligocene vicariance by the formation of the Mississippi embayment; (2) Pleistocene vicariance from interglacial flooding; (3) post‐Pleistocene northward colonization from separate glacial refugia; (4) Hypsithermal vicariance due to climate fluctuations; and (5) recent long‐distance dispersal. We investigated which of these pathways most likely gave rise to the Appalachian‐Ozark disjunction in Delphinium exaltatum. METHODS: We genotyped populations of D. exaltatum from five Ozark and seven Appalachian localities, analyzed genetic structure, tested the order and timing of divergences using DIYABC, and conducted niche reconstructions up to 21,000 years before present (YBP). RESULTS: Populations fell into five main genetic clusters, i.e., a group in the central Appalachians, and four "lowland" groups. DIYABC analyses showed the central Appalachian and lowland lineages diverging 11,300 to17,000 YBP, and the lowland groups diverging 6800 to 10,900 YBP. Niche reconstructions showed that suitable climate for the central Appalachian lineage experienced large spatial discontinuity starting 14,000 YBP, such that divergence and persistence before this period is less plausible than divergence thereafter. CONCLUSIONS: Our results did not fully support any of the original hypotheses. Rather, the oldest divergence likely occurred after 13,500 YBP through expansion into newly opened habitat in the Appalachians. The Appalachian‐Ozark disjunction likely resulted from northward dispersal of the lowland lineage as climate warmed during the Holocene. [ABSTRACT FROM AUTHOR]

Using analyses that exhaustively sampled Mascarene Diospyros and included representative taxa from Madagascar and other regions, we explored: (1) evolutionary relationships among Diospyros spp. across the WIO and (2) biogeographic connections of Malagasy taxa with those in surrounding regions, particularly focusing on connections with taxa in the Mascarene Islands. We obtained plastid sequence data for 146 Diospyros taxa, including 40 species not previously included in molecular analyses, and conducted Bayesian and maximum-likelihood phylogenetic analyses, divergence-time estimation and ancestral area reconstructions. Diospyros sampled from Madagascar fell into two clades, one of which contains all but two Malagasy species. Biogeographic analyses revealed that many clades probably originated in Madagascar and dispersed to locations in Africa and the Mascarenes, indicating that Madagascar may have acted as an important source of diversity for the region. [ABSTRACT FROM AUTHOR]

Abstract: As multiple species of bats are currently experiencing dramatic declines in populations due to white‐nose syndrome (WNS) and other factors, conservation managers have an urgent need for data on the ecology and overall status of populations of once‐common bat species. Standard approaches to obtain data on bat populations often involve capture and handling, requiring extensive expertise and unavoidably resulting in stress to the bats. New methods to rapidly obtain critical data are needed that minimize both the stress on bats and the spread of WNS. Guano provides a noninvasive source of DNA that includes information from the bat, but also dietary items, parasites, and pathogens. DNA metabarcoding is a high‐throughput, DNA‐based identification technique to assess the biodiversity of environmental or fecal samples. We investigated the use of multifaceted DNA metabarcoding (MDM), a technique combining next‐generation DNA sequencing (NGS), DNA barcodes, and bioinformatic analysis, to simultaneously collect data on multiple parameters of interest (bat species composition, individual genotype, sex ratios, diet, parasites, and presence of WNS) from fecal samples using a single NGS run. We tested the accuracy of each MDM assay using samples in which these parameters were previously determined using conventional approaches. We found that assays for bat species identification, insect diet, parasite diversity, and genotype were both sensitive and accurate, the assay to detect WNS was highly sensitive but requires careful sample processing steps to ensure the reliability of results, while assays for nectivorous diet and sex showed lower sensitivity. MDM was able to quantify multiple data classes from fecal samples simultaneously, and results were consistent whether we included assays for a single data class or multiple data classes. Overall, MDM is a useful approach that employs noninvasive sampling and a customizable suite of assays to gain important and largely accurate information on bat ecology and population dynamics. [ABSTRACT FROM AUTHOR]

Spatial genetic structure in plants can be affected by continuity of geographical distribution, cultivation history, pollination and seed dispersal mechanisms. Here, we examined the relative effects of these factors on the genetic structure of Agave palmeri and A. parryi, which share similar pollination syndromes and seed dispersal mechanisms but differ in the continuity of their distributions and cultivation history. Agave parryi has a patchy distribution and was cultivated by Native Americans, whereas A. palmeri has a more continuous distribution and no documented history of cultivation. We sampled populations of each species in their North American ranges, genotyped individuals with microsatellite loci and analysed patterns of genetic structure. No genetic structuring was detected in A. palmeri, but A. parryi formed three distinct genetic clusters, corresponding to geographical locations. One genetic cluster of A. parryi contained populations from lower elevations and had lower levels of genetic diversity, probably indicating anthropogenic origins. We conclude that continuity of distribution, pollinators and cultivation history all may affect patterns of genetic connectivity. [ABSTRACT FROM AUTHOR]

Improved predictions of fitness and yield may be obtained by characterizing the genetic controls and environmental dependencies of organismal ontogeny. Elucidating the shape of growth curves may reveal novel genetic controls that single-time-point ( STP) analyses do not because, in theory, infinite numbers of growth curves can result in the same final measurement., We measured leaf lengths and widths in Brassica rapa recombinant inbred lines ( RILs) throughout ontogeny. We modeled leaf growth and allometry as function valued traits ( FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, circadian rhythms and fitness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci ( QTL)., We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs STPs. We identified leaf shape (allometry) as a genetic module independent of length and width and identified selection on FVT parameters of development., Leaf shape is associated with venation features that affect desiccation resistance. The genetic independence of leaf shape from other leaf traits may therefore enable crop optimization in leaf shape without negative effects on traits such as size, growth rate, duration or gas exchange. [ABSTRACT FROM AUTHOR]