Evolution of geographical place and niche space: Patterns of diversification in the North American sedge (Cyperaceae) flora

Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae

The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification. We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns. Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa. Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.

The evolution of Ericaceae flowers and their pollination syndromes at a global scale

PREMISE

Floral evolution in large clades is difficult to study not only because of the number of species involved, but also because they often are geographically widespread and include a diversity of outcrossing pollination systems. The cosmopolitan blueberry family (Ericaceae) is one such example, most notably pollinated by bees and multiple clades of nectarivorous birds.

METHODS

We combined data on floral traits, pollination ecology, and geography with a comprehensive phylogeny to examine the structuring of floral diversity across pollination systems and continents. We focused on ornithophilous systems to test the hypothesis that some Old World Ericaceae were pollinated by now-extinct hummingbirds.

RESULTS

Despite some support for floral differentiation at a continental scale, we found a large amount of variability within and among landmasses, due to both phylogenetic conservatism and parallel evolution. We found support for floral differentiation in anther and corolla traits across pollination systems, including among different ornithophilous systems. Corolla traits show inconclusive evidence that some Old World Ericaceae were pollinated by hummingbirds, while anther traits show stronger evidence. Some major shifts in floral traits are associated with changes in pollination system, but shifts within bee systems are likely also important.

CONCLUSIONS

Studying the floral evolution of large, morphologically diverse, and widespread clades is feasible. We demonstrate that continent-specific radiations have led to widespread parallel evolution of floral morphology. We show that traits outside of the perianth may hold important clues to the ecological history of lineages.

Complex patterns of ploidy in a holocentric plant clade (Schoenus, Cyperaceae) in the Cape biodiversity hotspot

BACKGROUND AND AIMS

It is unclear how widespread polyploidy is throughout the largest holocentric plant family - the Cyperaceae. Because of the prevalence of chromosomal fusions and fissions, which affect chromosome number but not genome size, it can be impossible to distinguish if individual plants are polyploids in holocentric lineages based on chromosome count data alone. Furthermore, it is unclear how differences in genome size and ploidy levels relate to environmental correlates within holocentric lineages, such as the Cyperaceae.

METHODS

We focus our analyses on tribe Schoeneae, and more specifically the southern African clade of Schoenus. We examine broad-scale patterns of genome size evolution in tribe Schoeneae and focus more intensely on determining the prevalence of polyploidy across the southern African Schoenus by inferring ploidy level with the program ChromEvol, as well as interpreting chromosome number and genome size data. We further investigate whether there are relationships between genome size/ploidy level and environmental variables across the nutrient-poor and summer-arid Cape biodiversity hotspot.

KEY RESULTS

Our results show a large increase in genome size, but not chromosome number, within Schoenus compared to other species in tribe Schoeneae. Across Schoenus, there is a positive relationship between chromosome number and genome size, and our results suggest that polyploidy is a relatively common process throughout the southern African Schoenus. At the regional scale of the Cape, we show that polyploids are more often associated with drier locations that have more variation in precipitation between dry and wet months, but these results are sensitive to the classification of ploidy level.

CONCLUSIONS

Polyploidy is relatively common in the southern African Schoenus, where a positive relationship is observed between chromosome number and genome size. Thus, there may be a high incidence of polyploidy in holocentric plants, whose cell division properties differ from monocentrics.

Phylotranscriptomics reveal the spatio-temporal distribution and morphological evolution of Macrozamia, an Australian endemic genus of Cycadales

BACKGROUND AND AIMS

Cycads are regarded as an ancient lineage of living seed plants, and hold important clues to understand the early evolutionary trends of seed plants. The molecular phylogeny and spatio-temporal diversification of one of the species-rich genera of cycads, Macrozamia, have not been well reconstructed.

METHODS

We analysed a transcriptome dataset of 4740 single-copy nuclear genes (SCGs) of 39 Macrozamia species and two outgroup taxa. Based on concatenated (maximum parsimony, maximum likelihood) and multispecies coalescent analyses, we first establish a well-resolved phylogenetic tree of Macrozamia. To identify cyto-nuclear incongruence, the plastid protein coding genes (PCGs) from transcriptome data are extracted using the software HybPiper. Furthermore, we explore the biogeographical history of the genus and shed light on the pattern of floristic exchange between three distinct areas of Australia. Six key diagnostic characters are traced on the phylogenetic framework using two comparative methods, and infra-generic classification is investigated.

KEY RESULTS

The tree topologies of concatenated and multi-species coalescent analyses of SCGs are mostly congruent with a few conflicting nodes, while those from plastid PCGs show poorly supported relationships. The genus contains three major clades that correspond to their distinct distributional areas in Australia. The crown group of Macrozamia is estimated to around 11.80 Ma, with a major expansion in the last 5-6 Myr. Six morphological characters show homoplasy, and the traditional phenetic sectional division of the genus is inconsistent with this current phylogeny.

CONCLUSIONS

This first detailed phylogenetic investigation of Macrozamia demonstrates promising prospects of SCGs in resolving phylogenetic relationships within cycads. Our study suggests that Macrozamia, once widely distributed in Australia, underwent major extinctions because of fluctuating climatic conditions such as cooling and mesic biome disappearance in the past. The current close placement of morphologically distinct species in the phylogenetic tree may be related to neotenic events that occurred in the genus.

Biodiversity at the global scale: the synthesis continues

Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever-widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad-scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.

Natural history collections are critical resources for contemporary and future studies of urban evolution

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

Diversification in Qinghai-Tibet Plateau: Orchidinae (Orchidaceae) clades exhibiting pre-adaptations play critical role

We explore the origins of the extraordinary plant diversity in the Qinghai-Tibetan Plateau (QTP) using Orchidinae (Orchidaceae) as a model. Our results indicate that six major clades in Orchidinae exhibited substantial variation in the temporal and spatial sequence of diversification. Our time-calibrated phylogenetic model suggests that the species-richness of Orchidinae arose through a combination of in situ diversification, colonisation, and local recruitment. There are multiple origins of species-richness of Orchidinae in the QTP, and pre-adaptations in clades from North Temperate and alpine regions were crucial for in situ diversification. The geographic analysis identified 29 dispersals from Asia, Africa and Europe into the QTP and 15 dispersals out. Most endemic species of Orchidinae evolved within the past six million years.

Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes

To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slow and costly, it is also burdened with significant intercurator variation (including curator-author variation), due to different interpretations of a character by various individuals. This problem is inherent in any human-based intellectual activity. To address this problem, making scientific publications semantically clear (i.e. computable) by the authors at the time of publication is a critical step if we are to avoid postpublication curation. To help authors efficiently produce species phenotypes while producing computable data, we are experimenting with an author-driven ontology development approach and developing and evaluating a series of ontology-aware software modules that would create publishable species descriptions that are readily useable in scientific computations. The first software module prototype called Measurement Recorder has been developed to assist authors in defining continuous measurements and reported in this paper. Two usability studies of the software were conducted with 22 undergraduate students majoring in information science and 32 in biology. Results suggest that participants can use Measurement Recorder without training and they find it easy to use after limited practice. Participants also appreciate the semantic enhancement features. Measurement Recorder's character reuse features facilitate character convergence among participants by 48% and have the potential to further reduce user errors in defining characters. A set of software design issues have also been identified and then corrected. Measurement Recorder enables authors to record measurements in a semantically clear manner and enriches phenotype ontology along the way. Future work includes representing the semantic data as Resource Description Framework (RDF) knowledge graphs and characterizing the division of work between authors as domain knowledge providers and ontology engineers as knowledge formalizers in this new author-driven ontology development approach.

Macroevolutionary analyses indicate that repeated adaptive shifts towards predatory diets affect functional diversity in Neotropical cichlids

During adaptive radiation, diversification within clades is limited by adaptation to the available ecological niches, and this may drive patterns of both trait and species diversity. However, adaptation to disparate niches may result in varied impacts on the timing, pattern and rate of morphological evolution. In this study, we examined the relationship between feeding ecology and functional diversification across a diverse clade of freshwater fishes, the Neotropical cichlids. Species dietary niches were ordinated via multivariate analysis of stomach content data. We investigated changes in the rate and pattern of morphological diversification associated with feeding, including dietary niche and degree of dietary specialization. A major division in dietary niche space was observed between predators that consume fish and macroinvertebrates vs. other groups with diets dominated by small invertebrates, detritus or vegetation. These trophic niches were strongly associated with groupings defined by functional morphospace. Clades within the piscivore/macroinvertivore group rarely transitioned to other dietary niches. Comparatively, high dietary specialization enhanced functional diversification, driving the evolution of more extreme morphologies. Divergent patterns of trophic diversification among Neotropical cichlids appear to derive from different performance demands in regional abiotic and biotic environments associated with biogeographical history.

Timing and ecological priority shaped the diversification of sedges in the Himalayas

BACKGROUND

Diversification patterns in the Himalayas have been important to our understanding of global biodiversity. Despite recent broad-scale studies, the most diverse angiosperm genus of the temperate zone-Carex L. (Cyperaceae), with ca. 2100 species worldwide-has not yet been studied in the Himalayas, which contains 189 Carex species. Here the timing and phylogenetic pattern of lineage and ecological diversification were inferred in this ecologically significant genus. We particularly investigated whether priority, adaptation to ecological conditions, or both explain the highly successful radiation of the Kobresia clade (ca. 60 species, of which around 40 are present in the Himalayas) of Himalayan Carex.

METHODS

Phylogenetic relationships were inferred using maximum likelihood analysis of two nuclear ribosomal DNA (nrDNA) regions (ITS and ETS) and one plastid gene (matK); the resulting tree was time-calibrated using penalized likelihood and a fossil calibration at the root of the tree. Biogeographical reconstruction for estimation of historical events and ancestral ranges was performed using the dispersal-extinction-cladogenesis (DEC) model, and reciprocal effects between biogeography and diversification were inferred using the geographic state speciation and extinction (GeoSSE) model. Climatic envelopes for all species for which mapped specimen data available were estimated using climatic data from WORLDCLIM, and climatic niche evolution was inferred using a combination of Ornstein-Uhlenbeck models of shifting adaptive optima and maximum likelihood inference of ancestral character states under a Brownian motion model.

RESULTS

The Himalayan Carex flora represents three of the five major Carex clades, each represented by multiple origins within the Himalayas. The oldest Carex radiation in the region, dating to ca. 20 Ma, near the time of Himalayan orogeny, gave rise to the now abundant Kobresia clade via long-distance dispersal from the Nearctic. The Himalayan Carex flora comprises a heterogeneous sample of diversifications drawn from throughout the cosmopolitan, but mostly temperate, Carex radiation. Most radiations are relatively recent, but the widespread and diverse Himalayan Kobresia radiation arose at the early Miocene. The timing and predominance of Kobresia in high-elevation Himalayan meadows suggests that Kobresia may have excluded other Carex lineages: the success of Kobresia in the Himalayas, in other words, appears to be a consequence largely of priority, competitive exclusion and historical contingency.

Tracking temporal shifts in area, biomes, and pollinators in the radiation of Salvia (sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

PREMISE OF THE STUDY

A key question in evolutionary biology is why some clades are more successful by being widespread geographically, biome diverse, or species-rich. To extend understanding of how shifts in area, biomes, and pollinators impact diversification in plants, we examined the relationships of these shifts to diversification across the mega-genus Salvia.

METHODS

A chronogram was developed from a supermatrix of anchored hybrid enrichment genomic data and targeted sequence data for over 500 of the nearly 1000 Salvia species. Ancestral areas and biomes were reconstructed using BioGeoBEARS. Pollinator guilds were scored, ancestral pollinators determined, shifts in pollinator guilds identified, and rates of pollinator switches compared.

KEY RESULTS

A well-resolved phylogenetic backbone of Salvia and updated subgeneric designations are presented. Salvia originated in Southwest Asia in the Oligocene and subsequently dispersed worldwide. Biome shifts are frequent from a likely ancestral lineage utilizing broadleaf and/or coniferous forests and/or arid shrublands. None of the four species diversification shifts are correlated to shifts in biomes. Shifts in pollination system are not correlated to species diversification shifts, except for one hummingbird shift that precedes a major shift in diversification near the crown of New World subgen. Calosphace. Multiple reversals back to bee pollination occurred within this hummingbird clade.

CONCLUSIONS

Salvia diversified extensively in different continents, biomes, and with both bee and bird pollinators. The lack of tight correlation of area, biome, and most pollinator shifts to the four documented species diversification shifts points to other important drivers of speciation in Salvia.

Spatial phylogenetics reveals evolutionary constraints on the assembly of a large regional flora

PREMISE OF THE STUDY

We used spatial phylogenetics to analyze the assembly of the Wisconsin flora, linking processes of dispersal and niche evolution to spatial patterns of floristic and phylogenetic diversity and testing whether phylogenetic niche conservatism can account for these patterns.

METHODS

We used digitized records and a new molecular phylogeny for 93% of vascular plants in Wisconsin to estimate spatial variation in species richness and phylogenetic α and β diversity in a native flora shaped mainly by postglacial dispersal and response to environmental gradients. We developed distribution models for all species and used these to infer fine-scale variation in potential diversity, phylogenetic distance, and interspecific range overlaps. We identified 11 bioregions based on floristic composition, mapped areas of neo- and paleo-endemism to establish new conservation priorities and predict how community-assembly patterns should shift with climatic change.

KEY RESULTS

Spatial phylogenetic turnover most strongly reflects differences in temperature and spatial distance. For all vascular plants, assemblages shift from phylogenetically clustered to overdispersed northward, contrary to most other studies. This pattern is lost for angiosperms alone, illustrating the importance of phylogenetic scale.

CONCLUSIONS

Species ranges and assemblage composition appear driven primarily by phylogenetic niche conservatism. Closely related species are ecologically similar and occupy similar territories. The average level and geographic structure of plant phylogenetic diversity within Wisconsin are expected to greatly decline over the next half century, while potential species richness will increase throughout the state. Our methods can be applied to allochthonous communities throughout the world.

Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae)

For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the world's most diverse plant lineages.

Amphitropical disjunctions in New World Menthinae: Three Pliocene dispersals to South America following late Miocene dispersal to North America from the Old World

PREMISE OF THE STUDY

The subtribe Menthinae (Lamiaceae), with 35 genera and 750 species, is among the largest and most economically important subtribes within the mint family. Most genera of Menthinae are found exclusively in the New World, where the group has a virtually continuous distribution ranging from temperate North America to southern South America. In this study, we explored the presence, timing, and origin of amphitropical disjuncts within Menthinae.

METHODS

Our analyses were based on a data set consisting of 89 taxa and the nuclear ribosomal DNA markers ITS and ETS. Phylogenetic relationships were determined under maximum likelihood and Bayesian criteria, divergence times were estimated with the program BEAST, and ancestral range estimated with BioGeoBEARS.

KEY RESULTS

A North Atlantic Land Bridge migration event at about 10.6 Ma is inferred from western Eurasia to North America. New World Menthinae spread rapidly across North America, and then into Central and South America. Several of the large speciose genera are not monophyletic with nuclear rDNA, a finding mirrored with previous chloroplast DNA results. Three amphitropical disjunctions involving North and southern South America clades, one including a southeastern South American clade with several genera, were inferred to have occurred within the past 5 Myr.

CONCLUSIONS

Although three New World Menthinae genera occur in both North and South America, none exhibit an amphitropical disjunction. However, three clades exhibit amphitropical disjunctions, all dating to the early Pliocene, and all involve jump dispersals to either southeastern or southwestern South America from southeastern North America.

Phylogenetic Insights into Chinese Rubus (Rosaceae) from Multiple Chloroplast and Nuclear DNAs

Rubus L. is a large and taxonomically complex genus, species of which exhibit apomixis, polyploidy, and frequent hybridization. Most of Chinese Rubus are assigned in two major sections, Idaeobatus and Malachobatus. To explore the phylogenetic relationships within Chinese Rubus, inferences upon three chloroplast DNA (rbcL, rpl20-rps12, and trnG-trnS), nuclear ribosomal ITS, and two low-copy nuclear markers (GBSSI-2 and PEPC) were deduced in 142 Rubus taxa from 17 subsections in 6 sections. nrITS and GBSSI-2 were the most informative among the six DNA regions assessed. Phylogenetic relationships within Rubus were well-resolved by combined nuclear datasets rather than chloroplast markers. The phylogenetic inferences strongly supported that section Idaeobatus was a polyphyletic group with four distant clades. All samples of sect. Malachobatus formed a monophyletic clade, in which R. tsangorum and R. amphidasys of sect. Dalibardastrum, and R. peltatus from subsection Peltati of sect. Idaeobatus were always nested. Rubus pentagonus (2n = 2x = 14) from subsect. Alpestres of sect. Idaeobatus was a sister group to the polyploid sect. Malachobatus, as well as the polytomy of three sect. Cyalctis members. This suggests that some polyploids of Malachobatus might originate from common ancestors, via polyploidization of hybrids between R. pentagonus and sect. Cylactis species. They had experienced species explosion in a short time. Section Dalibardastrum species have potential parental lineages from subsects. Moluccani and Stipulosi of sect. Malachobatus. Based on molecular phylogenies, we also provided recommendations for the taxonomic treatments of four taxa. In addition, our results showed certain incongruence between chloroplast and nuclear markers, which might be due to hybridization and introgression.

Biogeography and diversification of Brassicales: A 103million year tale

Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.