Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota).

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology.

Reconstructing Terrestrial Paleoclimate and Paleoecology with Fossil Leaves Using Digital Leaf Physiognomy and Leaf Mass Per Area.

Climate and environment strongly influence the size, shape, and toothiness (physiognomy) of plants' leaves. These relationships, particularly in woody non-monocotyledonous angiosperms, have been used to develop leaf-based proxies for paleoclimate and paleoecology that have been applied to reconstruct ancient terrestrial ecosystems for the last ~120 million years of Earth's history. Additionally, given that these relationships have been documented in living plants, they are important for understanding aspects of plant evolution and how plants respond to climatic and environmental changes.

Amphibian as an experimental model for infection studies with the chytrid fungus .

Model organisms are crucial in research as they can provide key insights applicable to other species. This study proposes the use of the amphibian species , widely available through the aquarium trade, as a model organism for the study of chytridiomycosis, a disease caused by the fungus (Bd) and linked to amphibian decline and extinction globally. Currently, no model organisms are used in the study of chytridiomycosis, particularly because of the lack of availability and nonstandardized methods.

Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet.

The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information.

Estimating herbarium specimen digitization rates: Accounting for human experience.

Premise: Herbaria are invaluable sources for understanding the natural world, and in recent years there has been a concerted effort to digitize these collections. To organize such efforts, a method for estimating the necessary labor is desired. This work analyzes digitization productivity reports of 105 participants from eight herbaria, deriving generalized labor estimates that account for human experience.

Molecular and morphological analyses reveal new taxa additions to the tribe Streblocladieae (Rhodomelaceae, Rhodophyta).

The recent segregation of 12 genera in the tribe Streblocladieae suggests that the taxonomy of some species belonging to Polysiphonia sensu lato is updated with the transfer and the proposal of new combinations. Accordingly, six new additions to the tribe Streblocladieae on the basis of morphological and molecular analyses are presented as a consequence of this new segregation. These additions include the description of the new species Carradoriella platensis sp.

Corrigendum: Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales.

[This corrects the article DOI: 10.3389/fpls.2019.

New Guinea has the world's richest island flora.

New Guinea is the world's largest tropical island and has fascinated naturalists for centuries. Home to some of the best-preserved ecosystems on the planet and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region, it is a globally recognized centre of biological and cultural diversity. So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea.

Plastid Genomes of Five Species of Riverweeds (Podostemaceae): Structural Organization and Comparative Analysis in Malpighiales.

With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (∼16,000 spp.

Tracking microhabitat temperature variation with iButton data loggers.

Premise Of The Study: Fine-scale variation in temperature and soil moisture contribute to microhabitats across the landscape, affecting plant phenology, distribution, and fitness. The recent availability of compact and inexpensive temperature and humidity data loggers such as iButtons has facilitated research on microclimates.

Methods And Results: Here, we highlight the use of iButtons in three distinct settings: comparisons of empirical data to modeled climate data for rare rock ferns in the genus in eastern North America; generation of fine-scale data to predict flowering time and vernalization responsiveness of crop wild relatives of chickpea from southeastern Anatolia; and measurements of extreme thermal variation of solar array installations in Vermont.

Repeated range expansion and niche shift in a volcanic hotspot archipelago: Radiation of C Hawaiian subgenus (Euphorbiaceae).

Woody perennial plants on islands have repeatedly evolved from herbaceous mainland ancestors. Although the majority of species in subgenus section (Euphorbiaceae) are small and herbaceous, a clade of 16 woody species diversified on the Hawaiian Islands. They are found in a broad range of habitats, including the only known C plants adapted to wet forest understories.

Historical biogeography and phylogeny of the pantropical Psychotrieae alliance (Rubiaceae), with particular emphasis on the Western Indian Ocean Region.

Premise Of The Study: The Western Indian Ocean Region (WIOR) is a biodiversity hotspot providing an ideal setting for exploring the origins of insular biodiversity and dynamics of island colonization. We aimed to investigate the origins of the WIOR Psychotrieae alliance (Rubiaceae) with typically small, probably mainly bird-dispersed drupes, and the timing and direction or sequence of its colonization events in the region.

Methods: We used the program BEAST to estimate divergence times and Lagrange for biogeographic reconstruction.

New combinations in Odontostemma (Caryophyllaceae).

Sixty-three new combinations in Odontostemma (Alsineae, Caryophyllaceae) are made to accommodate placement of all currently recognized taxa of Arenaria subg. Odontostemma within the genus Odontostemma.

Digitization workflows for flat sheets and packets of plants, algae, and fungi.

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.

Eremogone (Caryophyllaceae): new combinations for Old World species.

Twenty-one new combinations in Eremogone (Eremogoneae, Caryophyllaceae) are proposed to accommodate placement of all Old World taxa of Arenariasubg.Eremogone and Eremogoneastrum within Eremogone.

Characterization of 14 microsatellite DNA markers for the tropical forest tree Virola surinamensis (Rol.) Warb. (Myristicaceae).

Fourteen microsatellite DNA markers were developed for studies of gene flow in the Neotropical rain forest tree Virola surinamensis. The loci were unlinked and polymorphic in a sample of 21 individuals, with two to 10 alleles per locus and observed heterozygosity ranging from 0.14 to 0.

Does secotioid inertia drive the evolution of false-truffles?

Secotioid inertia is a model implemented to explain the prevalence of highly derived false-truffles with no obvious connection to the Homobasidiomycetes. The model accommodates the apparent lack of epigeous sister taxa for some highly derived hypogeous lineages by assuming that gasteromycetation in some fungi leads to the extinction of their epigeous sister population. The derived state of some hypogeous lineages suggests that they arose early in the evolution of Homobasidiomycetes and that those groups were subject to conditions that favoured hypogeous lineages such that the hypogeous fruit body form became the predominant form for some lineages.

The phylogenetic placement of the Leucogastrales, including Mycolevis siccigleba (Cribbeaceae), in the Albatrellaceae using morphological and molecular data.

The morphology of many hypogeous fungi converges on a homogeneous reduced form, suggesting that disparate lineages are subject to a uniform selection pressure. The primary goal of this study was to evaluate the morphology and infer the phylogeny of the Leucogastrales with Mycolevis siccigleba using a Bayesian methodology. A comprehensive morphological assessment was used for an a priori phylogenetic inference to guide the sequencing effort.

Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests.

Fossil data have been interpreted as indicating that Late Cretaceous tropical forests were open and dry adapted and that modern closed-canopy rain forest did not originate until after the Cretaceous-Tertiary (K/T) boundary. However, some mid-Cretaceous leaf floras have been interpreted as rain forest. Molecular divergence-time estimates within the clade Malpighiales, which constitute a large percentage of species in the shaded, shrub, and small tree layer in tropical rain forests worldwide, provide new tests of these hypotheses.

Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales.

Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales.

Elatinaceae are sister to Malpighiaceae; Peridiscaceae belong to Saxifragales.

Phylogenetic data from plastid (ndhF and rbcL) and nuclear (PHYC) genes indicate that, within the order Malpighiales, Elatinaceae are strongly supported as sister to Malpighiaceae. There are several putative morphological synapomorphies for this clade; most notably, they both have a base chromosome number of X = 6 (or some multiple of three or six), opposite or whorled leaves with stipules, unicellular hairs (also uniseriate in some Elatinaceae), multicellular glands on the leaves, and resin (Elatinacae) or latex (Malpighiaceae). Further study is needed to determine if these features are synapomorphic within the order.

Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography.

A major tenet of African Tertiary biogeography posits that lowland rainforest dominated much of Africa in the late Cretaceous and was replaced by xeric vegetation as a response to continental uplift and consequent widespread aridification beginning in the late Paleogene. The aridification of Africa is thought to have been a major factor in the extinction of many African humid-tropical lineages, and in the present-day disparity of species diversity between Africa and other tropical regions. This primarily geologically based model can be tested with independent phylogenetic evidence from widespread African plant groups containing both humid- and xeric-adapted species.

Structural rearrangements, including parallel inversions, within the chloroplast genome of Anemone and related genera.

Chloroplast DNA cleavage sites for 10 restriction enzymes were mapped for 46 species representing all sections of Anemone, four closely related genera (Clematis, Pulsatilla, Hepatica, and Knowltonia), and three more distantly related outgroups (Caltha, Ranunculus, and Adonis). Comparison of the maps revealed that the chloroplast genomes of Anemone and related genera have sustained an unusual number and variety of rearrangements. A single inversion of a 42-kb segment was found in the large single-copy region of Adonis aestivalis.