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1. Clonality, local population structure and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

   https://doi.org/10.1093/aob/mcad077  

   Shaw, A Jonathan; Duffy, Aaron M; Nieto-Lugilde, Marta; Aguero, Blanka; Schuette, Scott; Robinson, Sean; Loveland, James; Hicks, Karen A; Weston, David; Piatkowski, Bryan; et al (July 2023, Annals of Botany)

   Abstract Background and AimsSphagnum (peatmoss) comprises a moss (Bryophyta) clade with ~300–500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. We assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. MethodsFour hundred and five samples of the four species, representing 57 populations, were subjected to restriction site-associated DNA sequencing (RADseq). Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Difference in fitness between genets was estimated as the numbers of ramets each genet comprised. Degrees of clonality [numbers of genets/numbers of ramets (samples)] within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. Key ResultsAll four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but two to eight ramets were dsumbers ansd text etected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets and sexes were not detected. Within S. divinum, however, female gametophytes harboured two to three times the number of microbial taxa as males. ConclusionsThese four Sphagnum species all exhibit similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns, where genets abut one another but do not extensively mix because of limited ramet fragmentation, and the guerrilla patterns, where extensive genet fragmentation and dispersal result in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases. 

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2. Adaptation to lower latitudes and lower elevations precedes the evolution of hummingbird pollination in western North American Penstemon

   https://doi.org/10.1002/ajb2.1857  

   Hamilton, Ashley M.; Wessinger, Carolyn A. (June 2022, American Journal of Botany)

   Abstract PremiseA switch in pollinator can occur when a plant lineage enters a new habitat where the ancestral pollinator is less common, and a novel pollinator is more common. Because pollinator communities vary according to environmental tolerances and availability of resources, there may be consistent associations between pollination mode and specific regions and habitats. Such associations can be studied in lineages that have experienced multiple pollinator transitions, representing evolutionary replicates. MethodsOur study focused on a large clade ofPenstemonwildflower species in western North America, which has repeatedly evolved hummingbird‐adapted flowers from ancestral bee‐adapted flowers. For each species, we estimated geographic ranges from occurrence data and inferred environmental niches from climate, topographical, and soil data. Using a phylogenetic comparative approach, we investigated whether hummingbird‐adapted species occupy distinct geographic regions or habitats relative to bee‐adapted species. ResultsHummingbird‐adapted species occur at lower latitudes and lower elevations than bee‐adapted species, resulting in a difference in their environmental niche. Bee‐adapted species sister to hummingbird‐adapted species are also found in relatively low elevations and latitudes, similar to their hummingbird‐adapted sister species, suggesting ecogeographic shifts precede pollinator divergence. Sister species pairs—regardless of whether they differ in pollinator—show relatively little geographic range overlap. ConclusionsAdaptation to a novel pollinator may often occur in geographic and ecological isolation from ancestral populations. The ability of a given lineage to adapt to novel pollinators may critically depend on its ability to colonize regions and habitats associated with novel pollinator communities. 

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3. Convergent niche shifts of endangered parrots (genus Amazona ) during successful establishment in urban southern California

   https://doi.org/10.1111/ddi.13817  

   Ramirez, Brenda R.; Freeland, Rowdy J.; Muhlheim, Allison; Zellmer, Amanda J.; DeRaad, Devon A.; Kirsch, Eliza J.; Mutchler, Marquette J.; Secor, Maeve B.; Reckling, Kelsey R.; Schedl, Margaret E.; et al (April 2024, Diversity and Distributions)

   Abstract AimIntroduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genusAmazonaoffers a clear test case, where sister species Red‐crowned (A. viridigenalis) and Lilac‐crowned Parrots (A. finschi) have established breeding populations in southern California following introduction via the pet trade from Mexico where they do not coexist. After establishment in the 1980s, introduced population sizes have increased, with mixed species flocks found throughout urban Los Angeles. Here, we investigate the differences between the environmental conditions of the native and introduced ranges of these now co‐occurring species. LocationSouthern California and Mexico. MethodsUsing environmental data on climate and habitat from their native and introduced ranges, we tested whether Red‐crowned and Lilac‐crowned Parrots have divergent realized niches between their native ranges, and whether each species has significantly shifted its realized niche to inhabit urban southern California. We also analysed data from Texas and Florida introductions of Red‐crowned Parrots for comparative analysis. ResultsThere are significant differences in the native‐range niches of both parrot species, but a convergence into a novel, shared environmental niche into urban southern California, characterized by colder temperatures, less tree cover and lower rainfall. Texas and Florida Red‐crowned Parrots also show evidence for niche shifts with varying levels of niche conservatism through the establishment of somewhat different realized niches. Main ConclusionsDespite significant niche shifts, introduced parrots are thriving, suggesting a broad fundamental niche and an ability to exploit urban resources. Unique niche shifts in different U.S. introductions indicate thatAmazonaparrots can adapt to diverse environmental conditions, with cities offering a resource niche and the timing of introduction playing a crucial role. Cities can potentially serve as refugia for threatened parrot species, but the risk of hybridization between species emphasizes the need for ongoing monitoring and genetic investigations. 

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4. Unprecedented distribution data for Joshua trees (Yucca brevifolia and Y. jaegeriana) reveal contemporary climate associations of a Mojave Desert icon

   https://doi.org/10.3389/fevo.2023.1266892  

   Esque, Todd C; Shryock, Daniel F; Berry, Gabrielle A; Chen, Felicia C; DeFalco, Lesley A; Lewicki, Sabrina M; Cunningham, Brent L; Gaylord, Eddie J; Poage, Caitlan S; Gantz, Gretchen E; et al (December 2023, Frontiers in Ecology and Evolution)

   IntroductionForecasting range shifts in response to climate change requires accurate species distribution models (SDMs), particularly at the margins of species' ranges. However, most studies producing SDMs rely on sparse species occurrence datasets from herbarium records and public databases, along with random pseudoabsences. While environmental covariates used to fit SDMS are increasingly precise due to satellite data, the availability of species occurrence records is still a large source of bias in model predictions. We developed distribution models for hybridizing sister species of western and eastern Joshua trees (Yucca brevifoliaandY. jaegeriana, respectively), iconic Mojave Desert species that are threatened by climate change and habitat loss. MethodsWe conducted an intensive visual grid search of online satellite imagery for 672,043 0.25 km²grid cells to identify the two species' presences and absences on the landscape with exceptional resolution, and field validated 29,050 cells in 15,001 km of driving. We used the resulting presence/absence data to train SDMs for each Joshua tree species, revealing the contemporary environmental gradients (during the past 40 years) with greatest influence on the current distribution of adult trees. ResultsWhile the environments occupied byY. brevifoliaandY. jaegerianawere similar in total aridity, they differed with respect to seasonal precipitation and temperature ranges, suggesting the two species may have differing responses to climate change. Moreover, the species showed differing potential to occupy each other's geographic ranges: modeled potential habitat forY. jaegerianaextends throughout the range ofY. brevifolia, while potential habitat forY. brevifoliais not well represented within the range ofY. jaegeriana. DiscussionBy reproducing the current range of the Joshua trees with high fidelity, our dataset can serve as a baseline for future research, monitoring, and management of this species, including an increased understanding of dynamics at the trailing and leading margins of the species' ranges and potential for climate refugia. 

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5. occTest : An integrated approach for quality control of species occurrence data

   https://doi.org/10.1111/geb.13847  

   Serra‐Diaz, Josep M; Borderieux, Jeremy; Maitner, Brian; Boonman, Coline_C F; Park, Daniel; Guo, Wen‐Yong; Callebaut, Arnaud; Enquist, Brian J; Svenning, Jens‐C; Merow, Cory (July 2024, Global Ecology and Biogeography)

   Abstract AimSpecies occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses. InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases(i.e. cleaning vs. testing)that encompass different testBlocksgrouping differenttestTypes(e.g.environmental outlier detection), which may use differenttestMethods(e.g.Rosner test, jacknife,etc.). Four differenttestBlockscharacterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed. Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application. 

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