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  1. Schemske, D (Ed.)

    We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness inCalochortus(Liliaceae, 74 spp.).Calochortusoccupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades—inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)—began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

     
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    Free, publicly-accessible full text available March 5, 2025
  2. Abstract

    Generalization is difficult to quantify, and many classifications exist. A beta diversity framework can be used to establish a numeric measure of generalist tendencies that jointly describes many important features of species interactions, namely spatiotemporal heterogeneity. This framework is promising for studying generalized symbiotic relationships of any form.

    We formulated a novel index, turnover importance (T).Tdescribes spatiotemporal heterogeneity in interactor assemblages, an inherent feature of generalist relationships that is not captured by available metrics. We simulated the behaviour ofTrelative to other available metrics, calculatedTfor native North American orchid‐insect relationships, and tested correlations betweenTand eco‐geographic variables. We performed case studies to demonstrate applications ofTfor conservation and eco‐evolutionary studies.

    Tbehaves predictably across simulations, and dynamically interacts with site number, gamma diversity, and species range sizes.Tis moderately sensitive to sampling depth. Orchids with higherTscores occupy larger ranges and broader climatic niches.

    Alternative interactor‐specific measures of generalism are best employed for local‐level community networks over short timespans. While these interactor metrics can assess use versus availability in local communities,Tcan be used to measure spatiotemporal patterns of variation in interactor assemblages across a focal species' range. This study provides a roadmap for future work focused on better understanding the patterns and consequences of generalized relationships.

     
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  3. Abstract Winter annuals comprise a large fraction of warm-desert plant species, but the drivers of their diversity are little understood. One factor that has generally been overlooked is the lack of obvious means of long-distance seed dispersal in many desert-annual lineages, which could lead to genetic differentiation at small spatial scales and, ultimately, to speciation and narrow endemism. If our gene-flow hypothesis is correct, individual winter-annual species should have populations with genetic spatial structures implying short distances of gene flow. To test this idea, we sampled six populations of Eschscholzia parishii (Papaveraceae) in three pairs of watersheds within a 28-km radius in southern California. We quantified genetic diversity and structure and inferred the distance of gene flow in these populations using single nucleotide polymorphisms derived from genotyping-by-sequencing. Estimated distances of gene flow were quite small (σ = 10.4–14.9 m), with strong genetic structure observed within and between populations. Kinship declined steeply with ln distance (r2 = 0.85). Petal size and shape differed significantly between the northernmost and southernmost populations. These findings support the hypothesis that the high diversity of warm-desert winter annuals might result, in part, from genetic differentiation within species at small spatial scales driven by poor seed dispersal. 
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  4. Summary

    Poales are one of the most species‐rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution.

    We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalisation analyses, historical biogeography and ancestral state estimations.

    Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species‐rich families Poaceae and Cyperaceae. Smaller families display unique and often divergent evolutionary trajectories.

    The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.

     
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  5. Abstract

    A proactive approach to conservation must be predictive, anticipating how habitats will change and which species are likely to decline or prosper. We use composite species distribution modelling to identify suitable habitats for 18 members of the North American Atlantic Coastal Plain Flora (ACPF) since the Last Glacial Maximum and project these into the future. We then useScirpus longii(Cyperaceae), a globally imperiled ACPF sedge with many of the characteristics of extinction vulnerability, as a case study. We integrate phylogeographical and population genetic analyses and species distribution modelling to develop a broad view of its current condition and prognosis for conservation. We use genotyping‐by‐sequencing to characterize the genomes of 142S. longiiindividuals from 20 populations distributed throughout its range (New Jersey to Nova Scotia). We measure the distribution of genetic diversity in the species and reconstruct its phylogeographical history using thesnappandrasemodels. Extant populations ofS. longiioriginated from a single refugium south of the Laurentide ice sheet around 25 ka. The genetic diversity ofS. longiiis exceedingly low, populations exhibit little genetic structure and the species is slightly inbred. Projected climate scenarios indicate that nearly half of extant populations ofS. longiiwill be exposed to unsuitable climate by 2070. Similar changes in suitable habitat will occur for many other northern ACPF species—centres of diversity will shift northward and Nova Scotia may become the last refuges for those species not extinguished.

     
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  6. Premise

    We tested 25 classic and novel hypotheses regarding trait–origin, trait–trait, and trait–environment relationships to account for flora‐wide variation in life history, habit, and especially reproductive traits using a plastid DNA phylogeny of most native (96.6%, or 1494/1547 species) and introduced (87.5%, or 690/789 species) angiosperms in Wisconsin, USA.

    Methods

    We assembled data on life history, habit, flowering, dispersal, mating system, and occurrence across open/closed/mixed habitats across species in the state phylogeny. We used phylogenetically structured analyses to assess the strength and statistical significance of associations predicted by our models.

    Results

    Introduced species are more likely to be annual herbs, occupy open habitats, have large, visually conspicuous, hermaphroditic flowers, and bear passively dispersed seeds. Among native species, hermaphroditism is associated with larger, more conspicuous flowers; monoecy is associated with small, inconspicuous flowers and passive seed dispersal; and dioecy is associated with small, inconspicuous flowers and fleshy fruits. Larger flowers with more conspicuous colors are more common in open habitats, and in understory species flowering under open (spring) canopies; fleshy fruits are more common in closed habitats. Wind pollination may help favor dioecy in open habitats.

    Conclusions

    These findings support predictions regarding how breeding systems depend on flower size, flower color, and fruit type, and how those traits depend on habitat. This study is the first to combine flora‐wide phylogenies with complete trait databases and phylogenetically structured analyses to provide powerful tests of evolutionary hypotheses about reproductive traits and their variation with geographic source, each other, and environmental conditions.

     
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  7. Abstract

    The amphicarpic annual legumeAmphicarpaea bracteatais unusual in producing aerial and subterranean cleistogamous flowers that always self‐fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterizedSNPvariation in 128 individuals in southern Wisconsin to assess within‐ and among‐population variation at 3928SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among‐group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U‐shaped distribution of pairwiseFSTvalues reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density‐dependent attack by species‐specific strains of pathogenic fungi and/or root‐nodulating bacteria specializing on distinct genotypes.

     
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