Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification.

PREMISE: Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. METHODS: Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. RESULTS: The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. CONCLUSIONS: We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.

Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.

We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization.

Optimum Image Formation for Spaceborne Microwave Radiometer Products.

This paper considers some of the issues of radiometer brightness image formation and reconstruction for use in the NASA-sponsored Calibrated Passive Microwave Daily Equal-Area Scalable Earth Grid 2.0 Brightness Temperature Earth System Data Record project, which generates a multisensor multidecadal time series of high-resolution radiometer products designed to support climate studies. Two primary reconstruction algorithms are considered: the Backus-Gilbert approach and the radiometer form of the scatterometer image reconstruction (SIR) algorithm. These are compared with the conventional drop-in-the-bucket (DIB) gridded image formation approach. Tradeoff study results for the various algorithm options are presented to select optimum values for the grid resolution, the number of SIR iterations, and the BG gamma parameter. We find that although both approaches are effective in improving the spatial resolution of the surface brightness temperature estimates compared to DIB, SIR requires significantly less computation. The sensitivity of the reconstruction to the accuracy of the measurement spatial response function (MRF) is explored. The partial reconstruction of the methods can tolerate errors in the description of the sensor measurement response function, which simplifies the processing of historic sensor data for which the MRF is not known as well as modern sensors. Simulation tradeoff results are confirmed using actual data.

A global urban microwave backscatter time series data set for 1993-2020 using ERS, QuikSCAT, and ASCAT data.

Urban settlements are rapidly growing outward and upward, with consequences for resource use, greenhouse gas emissions, and ecosystem and public health, but rates of change are uneven around the world. Understanding trajectories and predicting consequences of global urban expansion requires quantifying rates of change with consistent, well-calibrated data. Microwave backscatter data provides important information on upward urban growth - essentially the vertical built-up area. We developed a multi-sensor, multi-decadal, gridded (0.05° lat/lon) data set of global urban microwave backscatter, 1993-2020. Comparison of backscatter from two C-band sensors (ERS and ASCAT) and one Ku-band sensor (QuikSCAT) are made at four invariant non-urban sites (~3500 km2) to evaluate instrument stability and multi-decadal pattern. For urban areas, there was a strong linear correlation (overall R2 = 0.69) between 2015 ASCAT urban backscatter and a continental-scale gridded product of building volume, across 8450 urban grid cells (0.05° × 0.05°) in Europe, China, and the USA. This urban backscatter data set provides a time series characterizing global urban change over the past three decades.

A phylogeny of Adelanthaceae (Jungermanniales, Marchantiophyta) based on nuclear and chloroplast DNA markers, with comments on classification, cryptic speciation and biogeography.

Adelanthaceae (including Jamesoniellaceae) represent a major lineage of jungermannialean liverworts that is characterized by ventral-intercalary, often flagelliform branches, succubous leaves, ovoid to cylindrical, plicate perianths with a contracted mouth, often connate bracts and bracteoles, and 4-7 stratose capsule walls. Here we present the first comprehensive molecular phylogeny of Adelanthaceae using five markers (rbcL, psbA, trnL-trnF region, atpB-rbcL spacer, nrITS1-5.8S-ITS2) and 108 accessions from throughout the geographic range of the family. The molecular data support the separation of subfamilies Adelanthoideae and Jamesonielloideae. The Adelanthoideae include the genera Adelanthus, Pseudomarsupidium and Wettsteinia. The Jamesonielloideae include representatives of the genera Anomacaulis, Cryptochila, Cuspidatula, Jamesoniella, and Syzygiella in five main clades. The monophyly of taxa in current morphological classification schemes of Jamesonielloideae is not supported by the molecular data. Based on the outcome of the molecular phylogenetic analyses we propose to include Anomacaulis and Jamesoniella kirkii in Cuspidatula, and to place Cryptochila, Roivainenia, and Jamesoniella in the synonymy of Syzygiella. Molecular data support intercontinental ranges for several species and a range formation of Adelanthaceae by frequent short-distance dispersal, rare long-distance dispersal, extinction, and diversification. Disjunct distribution patterns within the Adelanthaceae cannot be explained by Gondwanan vicariance.

Comparison of SeaWinds Backscatter Imaging Algorithms.

This paper compares the performance and tradeoffs of various backscatter imaging algorithms for the SeaWinds scatterometer when multiple passes over a target are available. Reconstruction methods are compared with conventional gridding algorithms. In particular, the performance and tradeoffs in conventional 'drop in the bucket' (DIB) gridding at the intrinsic sensor resolution are compared to high-spatial-resolution imaging algorithms such as fine-resolution DIB and the scatterometer image reconstruction (SIR) that generate enhanced-resolution backscatter images. Various options for each algorithm are explored, including considering both linear and dB computation. The effects of sampling density and reconstruction quality versus time are explored. Both simulated and actual data results are considered. The results demonstrate the effectiveness of high-resolution reconstruction using SIR as well as its limitations and the limitations of DIB and fDIB.

Polar Applications of Spaceborne Scatterometers.

Wind scatterometers were originally developed for observation of near-surface winds over the ocean. They retrieve wind indirectly by measuring the normalized radar cross section (σo ) of the surface, and estimating the wind via a geophysical model function relating σo to the vector wind. The σo measurements have proven to be remarkably capable in studies of the polar regions where they can map snow cover; detect the freeze/thaw state of forest, tundra, and ice; map and classify sea ice; and track icebergs. Further, a long time series of scatterometer σo observations is available to support climate studies. In addition to fundamental scientific research, scatterometer data are operationally used for sea-ice mapping to support navigation. Scatterometers are, thus, invaluable tools for monitoring the polar regions. In this paper, a brief review of some of the polar applications of spaceborne wind scatterometer data is provided. The paper considers both C-band and Ku-band scatterometers, and the relative merits of fan-beam and pencil-beam scatterometers in polar remote sensing are discussed.

Evaluating and Extending the Ocean Wind Climate Data Record.

Satellite microwave sensors, both active scatterometers and passive radiometers, have been systematically measuring near-surface ocean winds for nearly 40 years, establishing an important legacy in studying and monitoring weather and climate variability. As an aid to such activities, the various wind datasets are being intercalibrated and merged into consistent climate data records (CDRs). The ocean wind CDRs (OW-CDRs) are evaluated by comparisons with ocean buoys and intercomparisons among the different satellite sensors and among the different data providers. Extending the OW-CDR into the future requires exploiting all available datasets, such as OSCAT-2 scheduled to launch in July 2016. Three planned methods of calibrating the OSCAT-2 σo measurements include 1) direct Ku-band σo intercalibration to QuikSCAT and RapidScat; 2) multisensor wind speed intercalibration; and 3) calibration to stable rainforest targets. Unfortunately, RapidScat failed in August 2016 and cannot be used to directly calibrate OSCAT-2. A particular future continuity concern is the absence of scheduled new or continuation radiometer missions capable of measuring wind speed. Specialized model assimilations provide 30-year long high temporal/spatial resolution wind vector grids that composite the satellite wind information from OW-CDRs of multiple satellites viewing the Earth at different local times.

World checklist of hornworts and liverworts.

A working checklist of accepted taxa worldwide is vital in achieving the goal of developing an online flora of all known plants by 2020 as part of the Global Strategy for Plant Conservation. We here present the first-ever worldwide checklist for liverworts (Marchantiophyta) and hornworts (Anthocerotophyta) that includes 7486 species in 398 genera representing 92 families from the two phyla. The checklist has far reaching implications and applications, including providing a valuable tool for taxonomists and systematists, analyzing phytogeographic and diversity patterns, aiding in the assessment of floristic and taxonomic knowledge, and identifying geographical gaps in our understanding of the global liverwort and hornwort flora. The checklist is derived from a working data set centralizing nomenclature, taxonomy and geography on a global scale. Prior to this effort a lack of centralization has been a major impediment for the study and analysis of species richness, conservation and systematic research at both regional and global scales. The success of this checklist, initiated in 2008, has been underpinned by its community approach involving taxonomic specialists working towards a consensus on taxonomy, nomenclature and distribution.

DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species.

DNA barcoding of a group of European liverwort species from the genus Herbertus was undertaken using three plastid (matK, rbcL and trnH-psbA) and one nuclear (ITS) marker. The DNA barcode data were effective in discriminating among the sampled species of Herbertus and contributed towards the detection of a previously overlooked European Herbertus species, described here as H. norenus sp. nov. This species shows clear-cut differences in DNA sequence for multiple barcode regions and is also morphologically distinct. The DNA barcode data were also useful in clarifying taxonomic relationships of the European species with some species from Asia and North America. In terms of the discriminatory power of the different barcode markers, ITS was the most informative region, followed closely by matK. All species were distinguishable by ITS alone, rbcL + matK and various other multimarker combinations.

Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants.

There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH-psbA, atpF-atpH, psbK-psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three-locus combinations involving rpoC1, rbcL, matK and trnH-psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups).

A phylogeny of Porella (Porellaceae, Jungermanniopsida) based on nuclear and chloroplast DNA sequences.

The cosmopolitan family Porellaceae includes about 60 species in two or three genera: the large genus Porella and the monospecific Ascidiota and Macvicaria (alternatively Porella subg. Macvicaria). Maximum parsimony, maximum likelihood and Bayesian inference of phylogeny of a dataset including three markers (rbcL, trnL-trnF region of cp DNA, nrITS region) of 96 accessions resulted in similar topologies supporting the generic status of Ascidiota. Macvicaria is nested in a subclade of Porella. Relationships among species of Porella are in general well resolved and many terminal nodes achieve good statistical support whereas basal relationships are at best moderately supported. Multiple accessions of single species are usually placed in monophyletic lineages. Accessions of P. platyphylla split into a European and a North American clade with one accession from North America embedded within the European samples. The Macaronesian endemic P. inaequalis is closely related to the Asian species P. grandiloba. Porella obtusata and P. canariensis cannot be separated on the basis of the sequence data presented in this study. The molecular topologies indicate a range extension of the Asian P. gracillima subsp. urogea to Eastern North America and of the Neotropical P. swartziana to South Africa. Current supraspecific classifications of Porella are not reflected in the molecular topologies with a correlation between genetic variation and the geographical distribution of the related accessions rather than a correlation between genetic variation and morphology.

Budding speciation and neotropical origin of the Azorean endemic liverwort, Leptoscyphus azoricus.

The origin of plant species endemism in Macaronesia, one of the 25 world biodiversity hotspots, has traditionally been either interpreted as a result of the dramatic reduction of a broader tertiary distribution range during the Ice Age or neoendemism. This hypothesis is tested here in the context of a species-level phylogeny employing chloroplast trnL-trnF and atpB-rbcL sequences in the leafy liverwort genus Leptoscyphus (Lophocoleaceae). The data suggest that the Azorean endemic Leptoscyphus azoricus originated from parental populations of the Neotropical Leptoscyphus porphyrius by long-distance dispersal across the Atlantic and subsequent isolation. Possible reasons for the differences in the origin of endemism in angiosperms, wherein by far most endemic species have their close relatives on the European and North African continents, are discussed.