A two-tier bioinformatic pipeline to develop probes for target capture of nuclear loci with applications in Melastomataceae

Putatively single-copy nuclear (SCN) loci, which are identified using genomic resources of closely related species, are ideal for phylogenomic inference. However, suitable genomic resources are not available for many clades, including Melastomataceae. We introduce a versatile approach to identify SCN loci for clades with few genomic resources and use it to develop probes for target enrichment in the distantly related Memecylon and Tibouchina (Melastomataceae)

Rates of niche and phenotype evolution lag behind diversification in a temperate radiation

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade—Saxifragales—with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, we find that these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (∼15 Mya), followed by increases in niche and phenotypic evolutionary rates by ∼5 Mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages

Milestones toward Majorana-based quantum computing

We introduce a scheme for preparation, manipulation, and read out of Majorana zero modes in semiconducting wires with mesoscopic superconducting islands. Our approach synthesizes recent advances in materials growth with tools commonly used in quantum-dot experiments, including gate control of tunnel barriers and Coulomb effects, charge sensing, and charge pumping. We outline a sequence of milestones interpolating between zero-mode detection and quantum computing that includes (1) detection of fusion rules for non-Abelian anyons using either proximal charge sensors or pumped current, (2) validation of a prototype topological qubit, and (3) demonstration of non-Abelian statistics by braiding in a branched geometry. The first two milestones require only a single wire with two islands, and additionally enable sensitive measurements of the system’s excitation gap, quasiparticle poisoning rates, residual Majorana zero-mode splittings, and topological-qubit coherence times. These pre-braiding experiments can be adapted to other manipulation and read out schemes as well

Climatic and biogeographic processes underlying the diversification of the pantropical flowering plant family Annonaceae

Tropical forests harbor the richest biodiversity among terrestrial ecosystems, but few studies have addressed the underlying processes of species diversification in these ecosystems. We use the pantropical flowering plant family Annonaceae as a study system to investigate how climate and biogeographic events contribute to diversification. A super-matrix phylogeny comprising 835 taxa (34% of Annonaceae species) based on eight chloroplast regions was used in this study. We show that global temperature may better explain the recent rapid diversification in Annonaceae than time and constant models. Accelerated accumulation of niche divergence (around 15 Ma) lags behind the increase of diversification rate (around 25 Ma), reflecting a heterogeneous transition to recent diversity increases. Biogeographic events are related to only two of the five diversification rate shifts detected. Shifts in niche evolution nevertheless appear to be associated with increasingly seasonal environments. Our results do not support the direct correlation of any particular climatic niche shifts or historical biogeographical event with shifts in diversification rate. Instead, we suggest that Annonaceae diversification can lead to later niche divergence as a result of increasing interspecific competition arising from species accumulation. Shifts in niche evolution appear to be associated with increasingly seasonal environments. Our results highlight the complexity of diversification in taxa with long evolutionary histories

Methods for broad-scale plant phenology assessments using citizen scientists’ photographs

© 2020 Barve et al. Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America Premise: Citizen science platforms for sharing photographed digital vouchers, such as iNaturalist, are a promising source of phenology data, but methods and best practices for use have not been developed. Here we introduce methods using Yucca flowering phenology as a case study, because drivers of Yucca phenology are not well understood despite the need to synchronize flowering with obligate pollinators. There is also evidence of recent anomalous winter flowering events, but with unknown spatiotemporal extents. Methods: We collaboratively developed a rigorous, consensus-based approach for annotating and sharing whole plant and flower presence data from iNaturalist and applied it to Yucca records. We compared spatiotemporal flowering coverage from our annotations with other broad-scale monitoring networks (e.g., the National Phenology Network) in order to determine the unique value of photograph-based citizen science resources. Results: Annotations from iNaturalist were uniquely able to delineate extents of unusual flowering events in Yucca. These events, which occurred in two different regions of the Desert Southwest, did not appear to disrupt the typical-period flowering. Discussion: Our work demonstrates that best practice approaches to scoring iNaturalist records provide fine-scale delimitation of phenological events. This approach can be applied to other plant groups to better understand how phenology responds to changing climate

Framing the future for taxonomic monography: Improving recognition, support, and access

No abstract available

Framing the future for taxonomic monography: Improving recognition, support, and access

Taxonomic monographs synthesize biodiversity knowledge and document biodiversity change through recent and geological time for a particular organismal group, sometimes also incorporating cultural and place-based knowledge. They are a vehicle through which broader questions about ecological and evolutionary patterns and processes can be generated and answered (e.g., Muñoz Rodríguez et al., 2019). Chiefly, monography represents the foundational research upon which all biological work is based (Hamilton et al., 2021). Moreover, monography can be a pathway to developing inclusive scientific practices, engaging diverse audiences in expanding and disseminating indigenous and local knowledge and significance of place. Apart from the scientific importance of monography, these comprehensive biodiversity treatments are also crucial for policy, conservation, human wellbeing, and the sustainable use of natural resources. Taxonomic, cultural and biodiversity data within monographs aid in the implementation of law and policy, such as the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), the Nagoya Protocol of the Convention on Biological Diversity (Buck & Hamilton, 2011), and the International Union for Conservation of Nature (IUCN) Red List (e.g., Neo et al., 2017). While vital as a knowledge resource and tool for conservation and research, monographs are not available for many groups of organisms. This is of particular concern for organisms that are threatened with extinction, of medical or economic importance, and those organisms that have the potential to provide insight into biodiversity change over time because they are most susceptible to global change. In discussing the future of collections-based systematics, researchers have highlighted the importance of updated monographic workflows, collaborative teams, and effective ways to educate and disseminate the results of monographs to the public and scientific community (e.g., Wen et al., 2015; Grace et al., 2021). Here, we discuss how improving recognition, support, and access can lead to greater inclusivity while promoting a more active, sustainable, and collaborative outlook for monographic research. </p

Data from: Phylogenetic relationships and character evolution in Heuchera (Saxifragaceae) on the basis of multiple nuclear loci

Premise of the study: The use of multiple genetic regions from the nuclear genome, including low-copy markers, has long been recognized as essential to robust phylogenetic construction, addressing gene tree incongruence, and allowing increased resolution to test current taxonomy and resolve basic hypotheses about character evolution, biogeography, and other organismal traits of interest to biologists. Heuchera, the largest genus of Saxifragaceae endemic to North America, has presented an unusually difficult case for systematists with limited sampling in previous molecular studies. We used morphological and multilocus molecular phylogenetic data to test the monophyly of Heuchera, better resolve hypotheses of relationships, and test hypotheses of character evolution, biogeography, and diversification rates. Methods: Phylogenetic relationships were inferred using sequences from six nuclear loci and 39 morphological characters using concatenation and coalescent analysis. Ancestral state reconstruction, diversification, and correlated evolution of morphological traits were performed using parsimony, BiSSE, and Pagel’s method, respectively. Key results: The concatenation and species tree analyses gave confident support to the monophyly of Heuchera and suggested several well-supported subclades. The addition of morphological data significantly improved support numbers. Ancestral character reconstruction suggested frequent homoplasy and reversal of floral characters and a complex biogeographical history. Conclusions: Heuchera is a natural genus; however, the current subgeneric classification is artificial and requires revision. Biogeographic reconstructions suggest a Pacific Northwest origin for the genus; morphological shifts in stamen exsertion and hypanthium length are hypothesized to have driven diversification in Heuchera in concert with possible pollinator shifts

Supplemental files: Q-Q plots and Shapiro-Wilk tests of normality

Symphyotrichum (Asteraceae) is a well-circumscribed genus on the basis of morphological and molecular data, but species boundaries remain poorly understood. Here, the species delimitation of the contentious Symphyotrichum subulatum group (Symphyotrichum subg. Astropolium) is illuminated using morphometric, phylogenomic, and geographical analyses. Symphyotrichum mexicanum sp. nov., a new species endemic to central Mexico, is described and distinguished from Symphyotrichum expansum based on its morphometric attributes, phylogenetic placement, geographic range, and ecological specialization

Concatenated DNA + morphology tree, maximum likelihood

This tree corresponds to the maximum likelihood tree of Figure 1. The tree was inferred in RAxML using a partitioned GTR-GAMMA model. Please note for interpretation of taxon labels: Heuchera cuneata = Heuchera rubescens var. truncata