Search

Premise: Biological outliers (observations that fall outside of a previously understood norm, e.g., in phenology or distribution) may indicate early stages of a transformative change that merits immediate attention. Collectors of biodiversity specimens such as plants, fungi, and animals are on the front lines of discovering outliers, yet the role collectors currently play in providing such data is unclear. Methods: We surveyed 222 collectors of a broad range of taxa, searched 47 training materials, and explored the use of 170 outlier terms in 75 million specimen records to determine the current state of outlier detection and documentation in this community. Results: Collectors reported observing outliers (e.g., about 80% of respondents observed morphological and distributional outliers at least occasionally). However, relatively few specimen records include outlier terms, and imprecision in their use and handling in data records complicates data discovery by stakeholders. This current state appears to be at least partly due to the absence of protocols: only one of the training materials addressed documenting and reporting outliers. Conclusions: We suggest next steps to mobilize this largely untapped, yet ideally suited, community for early detection of biotic change in the Anthropocene, including community activities for building relevant best practices. [ABSTRACT FROM AUTHOR]

The article aims at motivating professional botanists to get new success as a result of public participation in their research.

PREMISE OF THE STUDY: Subtribe Hakeinae (526 spp.) represents a large Australian plant radiation central to our understanding of that flora's evolution and ecology. It contains Grevillea--the third largest plant genus in Australia and a group inferred to have among the highest diversification rates in the angiosperms. However, we lack a robust phylogenetic framework for understanding subtribe Hakeinae and recognize that Grevillea lacks an unambiguous synapomorphy supporting its monophyly. METHODS: We used four plastid and one nuclear DNA region from a taxonomically even sampling of a third of the species to infer a time-calibrated phylogeny of Hakeinae and absolute diversification rates of major clades. We developed the R package addTaxa to add unsampled taxa to the tree for diversification rate inference. KEY RESULTS: Grevillea is paraphyletic with respect to Hakea and Finschia. Under most parameter combinations, Hakea contains the major clade with the highest diversification rate in Hakeinae, rather than Grevillea. The crown age of the Grevillea+Hakea+Finschia crown group is about double that of prior estimates. CONCLUSIONS: We demonstrate that the paraphyly of Grevillea considerably enlarges the number of Australian descendants from its most recent common ancestor but has also misled investigators who considered a single operational taxonomic unit as adequate to represent the genus for inferences of diversification rate and timing. Our time-calibrated phylogeny can form the basis of future evolutionary, comparative ecology, and biogeography studies involving this large Australian plant radiation, as well as nomenclatural changes. [ABSTRACT FROM AUTHOR]

* Premise of the study: A past study based on morphological data alone showed that the means by which plants of the Australian genus Hakea reduce florivory is related to the evolution of bird pollination. For example, bird pollination was shown to have arisen only in insect-pollinated lineages that already produced greater amounts of floral cyanide, a feature that reduces florivory. We examine a central conclusion of that study, and a common assumption in the literature, that bird pollination arose in insect-pollinated lineages, rather than the reverse. * Methods: We combined morphological and DNA data to infer the phylogeny and age of the Australian genus Hakea, using 9.2 kilobases of plastid and nuclear DNA and 46 morphological characters from a taxonomically even sampling of 55 of the 149 species. * Key results : Hakea is rooted confidently in a position that has not been suggested before. The phylogeny implies that bird pollination is primitive in Hakea and that multiple shifts to insect pollination have occurred. The unexpectedly young age of Hakea (a crown age of ca. 10 Ma) makes it coincident with its primary bird pollinators (honeyeaters) throughout its history. * Conclusions: Our study demonstrates that Hakea is an exception to the more commonly described shift from insect to bird pollination. However, we note that only one previous phylogenetic study involved Australian plants and their honeyeater pollinators and that our finding might prove to be more common on that continent. [ABSTRACT FROM AUTHOR]

Tribe Macadamieae (91 spp., 16 genera; Proteaceae) is widespread across the southern hemisphere on all major fragments of Gondwana except New Zealand and India. Macadamia is cultivated outside its natural range as a "nut" crop (notably in Hawaii, where it is the principal orchard crop). We sampled seven DNA regions and 53 morphological characters from the tribe to infer its phylogeny and address the common assumption that the distribution of the extant diversity of the tribe arose by the rafting of ancestors on Gondwanan fragments. Macadamia proves to be paraphyletic with respect to the African genus Brabejum, the South American genus Panopsis, and the Australian species Orites megacarpus. We erect two new generic names, Nothorites and Lasjia, to produce monophyly at that rank. The earliest disjunctions in the tribe are inferred to be the result of long-distance dispersal out of Australia (with one possible exception), rather than vicariance. Evolution of tardy fruit dehiscence is correlated with these dispersals, and the onset of the Antarctic Circumpolar Current (ACC) precedes them. We suggest that the ancestors of extant diversity arrived on their respective continents via the ACC, and we recognize that this is a mechanism precluded, rather than facilitated,by Gondwana's terrestrial continuity. [ABSTRACT FROM AUTHOR]

We sequenced seven cpDNA regions from 70 spp. in Dodecatheon, Primula subgenus Auriculastrum, and outgroups, reconstructed their cpDNA phylogeny with maximum parsimony, and determined branch support with bootstrap frequencies and Bayesian posterior probabilities. Strongly supported conclusions include the (1) paraphyly of Primula subgenus Auriculastrum with respect to a monophyletic Dodecatheon, (2) sister relationship between the North American Dodecatheon and the Californian P. suffrutescens, (3) novel basal split in Dodecatheon to produce one clade with rugose and one clade with smooth anther connectives, (4) monophyly of all sections of Primula subgenus Auriculastrum, and (5) exclusion of the enigmatic Primula section Amethystina from the similar Primula subgenus Auriculastrum. These results support the origin of the monomorphic, buzz-pollinated flower of Dodecatheon from the heterostylous flower of Primula. We marshal evidence to support the novel hypothesis that the solanoid flower of Dodecatheon represents the fixation of recessive alleles at the heterostyly linkage group (pin phenotype). Of the remaining traits associated with their solanoid flowers, we recognize at least six likely to have arisen with the origin of Dodecatheon, one that preceded it (flower coloration, a transfer exaptation in Dodecatheon), and one that followed it (rugose anther connectives, an adaptation to buzz pollination). [ABSTRACT FROM AUTHOR]

Focuses on the use of a null model to recognize significant co-occurrence prior to identifying candidate areas of endemism. Disputed use of co-occurrence; Description of the null model; Exploration of the usefulness of the null model with Morrone's (1994) distributional data set for the species of the southern African weevil Sciobius.

Investigates the biogeography and origin of stomatal distribution in Banksia and Dryandra based on their chloroplast DNA phylogeny. Floristic interchange between Australia and the Southwest Botanica Provinence; Hypothesis of sclerophylly-pre-adaptation lineage to xeromorphy; Paraphyly of Banksia with respect to Dryandra; Consensus sequence.

We sequenced the trnL and rpl16 introns of the chloroplast DNA from 95 of the ca. 425 species (30 of 37 sections, seven of eight subgenera) of Primula L. in order to reconstruct the phylogenetic history of the group. Among the 24 additional taxa sampled are representatives of all genera that are likely to be embedded in Primula, as well as outgroups from the Maesaceae, Theophrastaceae, and Myrsinaceae. In the strict consensus of the most parsimonious trees, Primula and the genera embedded in it (Dionysia Fenzl., Sredinskya [Stein] Fedorov, Dodecatheon L., and Cortusa L.) are sister to a clade of several genera previously suspected to be embedded in Primula (Hottonia L., Omphalogramma [Franchet] Franch., and Soldanella L.). In recognition of this, two new rankless names are defined for these clades (/Primula and/Soldanella). Close relationships are inferred between Dionysia and Primula subgenus Sphondylia (Duby) Rupr., Sredinskya and Primula subgenus Primula, Dodecatheon and Primula subgenus Auriculastrum Schott, and Cortusa and Primula subgenus Auganthus (Link) Wendelbo. The largest subgenus, Aleuritia (Duby) Wendelbo, is dispersed among three clades that are not each other's closest relatives. Primula sections Muscarioides Balf. f., Soldanelloides Pax, Denticulata Watt, Armerina Lindley, and Aleuritia Duby are resolved as para- or polyphyletic with moderate to strong support. Throughout, we consider the striking morphological and cytological variation seen in Primula within a phylogenetic context, particularly as it relates to the close relationship implied here between Dionysia and Primula subgenus Sphondylia. The homology of involute leaf vernation in Primula is reconsidered in light of its two independent origins, and we come to the conclusion that vernation in subgenus Sphondylia is better characterized as conduplicate. [ABSTRACT FROM AUTHOR]

Plant-associated microbial communities may be important sources of functional diversity and genetic variation that influence host evolution. Bacteria provide benefits for their hosts, yet in most plant systems we know little about their taxonomic composition or variation across tissues and host range. Red Mangrove (Rhizophora mangle L.) is a vital coastal plant species that is currently expanding poleward and with it, perhaps, its microbiome. We explored variability in bacterial communities across tissues, individuals, and populations. We collected samples from six sample types from 5 to 10 individuals at each of three populations and used 16S rRNA gene (iTag) sequencing to describe their bacterial communities. Core community members and dominant bacterial classes were determined for each sample type. Pairwise PERMANOVA of Bray–Curtis dissimilarity and Indicator Species Analysis revealed significant differences in bacterial communities between sample types and populations. We described the previously unexplored microbiome of the reproductive tissues of R. mangle. Populations and most sample types were associated with distinct communities. Bacterial communities associated with R. mangle are influenced by host geography and sample type. Our study provides a foundation for future work exploring the functional roles of these microbes and their relevance to biogeochemical cycling. [ABSTRACT FROM AUTHOR]

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. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery. [ABSTRACT FROM AUTHOR]

The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model-based estimation of ancestral regions indicates that Hakea began diversifying in the Mediterranean biome of southern Australia in the Middle Eocene-Early Oligocene, and dispersed repeatedly into other biomes across the continent. We infer around 47 shifts between biomes. Frequencies of shifts between pairs of biomes are usually similar to those expected from their geographic connectedness or climatic similarity, but in some cases are substantially higher or lower than expected, perhaps reflecting how readily key physiological traits can be modified to adapt lineages to new environments. The history of frequent biome-shifting is reflected in the structure of present-day assemblages, which tend to be more phylogenetically diverse than null-model expectations. The case of Hakea demonstrates that the radiation of large plant clades across wide geographic areas need not be constrained by dispersal limitation or conserved adaptations to particular environments. [ABSTRACT FROM AUTHOR]

A goal of the biodiversity research community is to digitize the majority of the one billion specimens in US collections by 2020. Meeting this ambitious goal requires increased collaboration and technological innovation and broader engagement beyond the walls of universities and museums. Engaging the public in digitization promises to both serve the digitizing institutions and further the public understanding of biodiversity science. We discuss three broad areas accessible to public participants that will accelerate research progress: label and ledger transcription, georeferencing from locality descriptions, and specimen annotation from images. We illustrate each activity, compare useful tools, present best practices and standards, and identify gaps in our knowledge and areas for improvement. The field of public participation in digitization of biodiversity research specimens is in a growth phase with many emerging opportunities for scientists, educators, and the public, as well as broader communication with complementary projects in other areas (e.g., the digital humanities). [ABSTRACT FROM AUTHOR]

This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation's National Resource for Advancing Digitization of Biological Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) predigitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs. [ABSTRACT FROM AUTHOR]

Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn; stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates. [ABSTRACT FROM AUTHOR]