Phylogenomic perspectives on speciation and reproductive isolation in a North American biodiversity hotspot: An example using California sages (Salvia subg. Audibertia; Lamiaceae)

BACKGROUND AND AIMS

The California Floristic Province (CA-FP) is the most species-rich region of North America north of Mexico. One of several proposed hypotheses explaining the exceptionally diversity of the region is that the CA-FP harbors myriad recently diverged lineages with nascent reproductive barriers. Salvia subgenus Audibertia is a conspicuous element of the CA-FP, with multiple sympatric and compatible species.

METHODS

Using 305 nuclear loci and both organellar genomes, we reconstruct species trees, examine genomic discordance, conduct divergence-time estimation, and analyze contemporaneous patterns of gene flow and mechanical reproductive isolation.

KEY RESULTS

Despite strong genomic discordance, an underlying bifurcating tree is supported. Organellar genomes capture additional introgression events not detected in the nuclear genome. Most interfertility is found within clades, indicating that reproductive barriers are coincident with genetic divergence. Species are generally not mechanically isolated, suggesting that it is unlikely to be the primary factor leading to reproductive isolation.

CONCLUSIONS

Rapid, recent speciation with some interspecific gene flow in conjunction with the onset of a Mediterranean-like climate is the underlying cause of extant diversity in Salvia subgenus Audibertia. Speciation has largely not been facilitated by gene flow. Its signal in the nuclear genome seems to mostly be erased by backcrossing, but organellar genomes each capture different instances of historical gene flow, likely characteristic of many CA-FP lineages. Mechanical reproductive isolation appears to be only part of a mosaic of factors limiting gene flow.

Seed morphology of Hypericum (Hypericaceae) in China and its taxonomic significance

The seed morphology of 40 taxa within the genus Hypericum (Hypericaceae) from China, representing 9 sections of the genus, was examined using both Light and Scanning Electron Microscopy to evaluate the taxonomic relevance of macro- and micro-morphological features. Details articulating variation in seed size, color, shape, appendages, and seed coat ornamentation are described, illustrated, and compared, and their taxonomic importance is discussed. Seeds were generally brown in color and cylindric-ellipsoid to prolonged cylindric in shape. Seed size displayed wide variation, ranging from 0.37-1.91 mm in length and 0.12-0.75 mm in width. Seed appendages were observed as a characteristic morphological feature. Seed surface ornamentation has high phenotypic plasticity, and four types (reticulate, foveolate, papillose, and ribbed) can be recognized. In general, seed color and shape have limited taxonomic significance. However, some other features represent informative characters that can be used efficiently in distinguishing the studied taxa at the section and/or species levels. The findings illustrate that considerable taxonomic knowledge can be obtained by investigating the seed features of Hypericum, and the use of Scanning Electron Microscopy can reveal inconspicuous morphological affinities among species and play a role in taxonomic and systematic studies of the genus Hypericum. RESEARCH HIGHLIGHTS: Macro- and micro-morphological features of seeds of 40 Hypericum taxa from China were examined using Light and Scanning Electron Microscopy, providing the first broad study regarding seed morphology for Hypericum from China. Details and variations of seed size, shape, color, surface ornamentation, and appendages are fully presented. Seed features and their variation have important taxonomic significance at the section and/or species levels within Hypericum.

East Asian-North American disjunctions and phylogenetic relationships within subtribe Nepetinae (Lamiaceae)

Biogeographic disjunctions, including intercontinental disjunctions, are frequent across plant lineages and have been of considerable interest to biologists for centuries. Their study has been reinvigorated by molecular dating and associated comparative methods. One of the "classic" disjunction patterns is that between Eastern Asia and North America. It has been speculated that this pattern is the result of vicariance following the sundering of a widespread Acrto-Teritary flora. Subtribe Nepetinae in the mint family (Lamiaceae) is noteworthy because it contains three genera with this disjunction pattern: Agastache, Dracocephalum, and Meehania. These disjunctions are ostensibly the result of three separate events, allowing for concurrent testing of the tempo, origin, and type of each biogeographic event. Using four plastid and four nuclear markers, we estimated divergence times and analyzed the historical biogeography of Nepetinae, including comprehensive sampling of all major clades for the first time. We recover a well-supported and largely congruent phylogeny of Nepetinae between genomic compartments, although several cases of cyto-nuclear discordance are evident. We demonstrate that the three disjunctions are pseudo-congruent, with unidirectional movement from East Asia at slightly staggered times during the late Miocene and early Pliocene. With the possible exception of Meehania, we find that vicariance is likely the underlying driver of these disjunctions. The biogeographic history of Meehania in North America may be best explained by long-distance dispersal, but a more complete picture awaits deeper sampling of the nuclear genome and more advanced biogeographical models.

Model selection, hummingbird natural history, and biological hypotheses: a response to Sazatornil et al

We have previously suggested that a shift from bee to hummingbird pollination, in concert with floral architecture modifications, occurred at the crown of Salvia subgenus Calosphace in North America ca. 20 mya (Kriebel et al. 2020 and references therein). Sazatornil et al. (2022), using a hidden states model, challenged these assertions, arguing that bees were the ancestral pollinator of subg. Calosphace and claiming that hummingbirds could not have been the ancestral pollinator of subg. Calosphace because hummingbirds were not contemporaneous with crown subg. Calosphace in North America. Here, using a variety of models, we demonstrate that most analyses support hummingbirds as ancestral pollinators of subg. Calosphace and show that Sazatornil et al. (2022) erroneously concluded that hummingbirds were absent from North America ca. 20 mya. We contend that "biological realism" - based on timing and placement of hummingbirds in Mexico ca. 20 mya and the correlative evolution of hummingbird associated floral traits - must be considered when comparing models based on fit and complexity, including hidden states models.

Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae)

The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.

Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes

Next-generation sequencing technologies have facilitated new phylogenomic approaches to help clarify previously intractable relationships while simultaneously highlighting the pervasive nature of incongruence within and among genomes that can complicate definitive taxonomic conclusions. Salvia L., with ∼1,000 species, makes up nearly 15% of the species diversity in the mint family and has attracted great interest from biologists across subdisciplines. Despite the great progress that has been achieved in discerning the placement of Salvia within Lamiaceae and in clarifying its infrageneric relationships through plastid, nuclear ribosomal, and nuclear single-copy genes, the incomplete resolution has left open major questions regarding the phylogenetic relationships among and within the subgenera, as well as to what extent the infrageneric relationships differ across genomes. We expanded a previously published anchored hybrid enrichment dataset of 35 exemplars of Salvia to 179 terminals. We also reconstructed nearly complete plastomes for these samples from off-target reads. We used these data to examine the concordance and discordance among the nuclear loci and between the nuclear and plastid genomes in detail, elucidating both broad-scale and species-level relationships within Salvia. We found that despite the widespread gene tree discordance, nuclear phylogenies reconstructed using concatenated, coalescent, and network-based approaches recover a common backbone topology. Moreover, all subgenera, except for Audibertia, are strongly supported as monophyletic in all analyses. The plastome genealogy is largely resolved and is congruent with the nuclear backbone. However, multiple analyses suggest that incomplete lineage sorting does not fully explain the gene tree discordance. Instead, horizontal gene flow has been important in both the deep and more recent history of Salvia. Our results provide a robust species tree of Salvia across phylogenetic scales and genomes. Future comparative analyses in the genus will need to account for the impacts of hybridization/introgression and incomplete lineage sorting in topology and divergence time estimation.

Systematic Placement of the Enigmatic Southeast Asian Genus Paralamium and an Updated Phylogeny of Tribe Pogostemoneae (Lamiaceae Subfamily Lamioideae)

Paralamium (Lamiaceae) is a monotypic genus within the subfamily Lamioideae and has a sporadic distribution in subtropical mountains of southeast Asia. Although recent studies have greatly improved our understanding of generic relationships within Lamioideae, the second most species-rich subfamily of Lamiaceae, the systematic position of Paralamium within the subfamily remains unclear. In this study, we investigate the phylogenetic placement of the genus using three datasets: (1) a 69,276 bp plastome alignment of Lamiaceae; (2) a five chloroplast DNA region dataset of tribe Pogostemoneae, and (3) a nuclear ribosomal internal transcribed spacer region dataset of Pogostemoneae. These analyses demonstrate that Paralamium is a member of Pogostemoneae and sister to the monotypic genus Craniotome. In addition, generic-level phylogenetic relationships within Pogostemoneae are also discussed, and a dichotomous key for genera within Pogostemoneae is provided.

An updated tribal classification of Lamiaceae based on plastome phylogenomics

BACKGROUND

A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data.

RESULTS

We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe.

CONCLUSIONS

Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification.

Leveraging plastomes for comparative analysis and phylogenomic inference within Scutellarioideae (Lamiaceae)

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.

Changing Ecological Opportunities Facilitated the Explosive Diversification of New Caledonian Oxera (Lamiaceae)

Phylogenies recurrently demonstrate that oceanic island systems have been home to rapid clade diversification and adaptive radiations. The existence of adaptive radiations posits a central role of natural selection causing ecological divergence and speciation, and some plant radiations have been highlighted as paradigmatic examples of such radiations. However, neutral processes may also drive speciation during clade radiations, with ecological divergence occurring following speciation. Here, we document an exceptionally rapid and unique radiation of Lamiaceae within the New Caledonian biodiversity hotspot. Specifically, we investigated various biological, ecological, and geographical drivers of species diversification within the genus Oxera. We found that Oxera underwent an initial process of rapid cladogenesis likely triggered by a dramatic period of aridity during the early Pliocene. This early diversification of Oxera was associated with an important phase of ecological diversification triggered by significant shifts of pollination syndromes, dispersal modes, and life forms. Finally, recent diversification of Oxera appears to have been further driven by the interplay of allopatry and habitat shifts likely related to climatic oscillations. This suggests that Oxera could be regarded as an adaptive radiation at an early evolutionary stage that has been obscured by more recent joint habitat diversification and neutral geographical processes. Diversification within Oxera has perhaps been triggered by varied ecological and biological drivers acting in a leapfrog pattern, but geographic processes may have been an equally important driver. We suspect that strictly adaptive radiations may be rare in plants and that most events of rapid clade diversification may have involved a mixture of geographical and ecological divergence.

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.

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.

Phylogeny and staminal evolution of Salvia (Lamiaceae, Nepetoideae) in East Asia

BACKGROUND AND AIMS

Salvia is the largest genus within Lamiaceae, with about 980 species currently recognized. East Asia, with approx. 100 species, is one of the three major biodiversity centres of Salvia. However, relationships within this lineage remain unclear, and the staminal lever mechanism, which may represent a key innovation within the genus, has been understudied. By using six genetic markers and nearly comprehensive taxon sampling, this study attempts to elucidate relationships and examine evolutionary trends of staminal development within the East Asia (EA) Salvia clade.

METHODS

Ninety-one taxa of EA Salvia were sampled and 34 taxa representing all other major lineages of Salvia were included for analysis. Two nuclear [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and four chloroplast (psbA-trnH, ycf1-rps15, trnL-trnF and rbcL) DNA markers were used for phylogenetic analysis employing maximum parsimony (MP), maximum likelihood (ML) and BEAST, with the latter also used to estimate divergence times.

KEY RESULTS

All Salvia species native to East Asia form a clade, and eight major subclades (A-G) were recognized. Subclade A, comprising two limestone endemics (S. sonchifolia and S. petrophila), is sister to the remainder of EA Salvia. Six distinct stamen types were observed within the EA clade. Stamen type A, with two fully fertile posterior thecae, only occurs in S. sonchifolia and may represent the ancestral stamen type within EA Salvia. Divergence time estimates showed that the crown of EA Salvia began to diversify approx. 17.4 million years ago.

CONCLUSIONS

This study supports the adoption of a broadly defined Salvia and treats EA Salvia as a subgenus, Glutinaria, recognizing eight sections within this subgenus. Stamen type A is ostensibly plesiomorphic within EA Salvia, and the other five types may have been derived from it. Staminal morphology has evolved in parallel within the EA Salvia, and staminal structure alone is inadequate to delimit infrageneric categories.

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.

How and Why to Build a Unified Tree of Life

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life?

Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny

Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

Which patellofemoral joint imaging features are associated with patellofemoral pain? Systematic review and meta-analysis

OBJECTIVES

To review the association between patellofemoral joint (PFJ) imaging features and patellofemoral pain (PFP).

DESIGN

A systematic review of the literature from AMED, CiNAHL, Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, PEDro, EMBASE and SPORTDiscus was undertaken from their inception to September 2014. Studies were eligible if they used magnetic resonance imaging (MRI), computed tomography (CT), ultrasound (US) or X-ray (XR) to compare PFJ features between a PFP group and an asymptomatic control group in people <45 years of age. A pooled meta-analysis was conducted and data was interpreted using a best evidence synthesis.

RESULTS

Forty studies (all moderate to high quality) describing 1043 people with PFP and 839 controls were included. Two features were deemed to have a large standardised mean difference (SMD) based on meta-analysis: an increased MRI bisect offset at 0° knee flexion under load (0.99; 95% CI: 0.49, 1.49) and an increased CT congruence angle at 15° knee flexion, both under load (1.40 95% CI: 0.04, 2.76) and without load (1.24; 95% CI: 0.37, 2.12). A medium SMD was identified for MRI patella tilt and patellofemoral contact area. Limited evidence was found to support the association of other imaging features with PFP. A sensitivity analysis showed an increase in the SMD for patella bisect offset at 0° knee flexion (1.91; 95% CI: 1.31, 2.52) and patella tilt at 0° knee flexion (0.99; 95% CI: 0.47, 1.52) under full weight bearing.

CONCLUSION

Certain PFJ imaging features were associated with PFP. Future interventional strategies may be targeted at these features.

PROSPERO REGISTRATION NUMBER

CRD 42014009503.

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips-the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics.

Does the Arcto-Tertiary biogeographic hypothesis explain the disjunct distribution of Northern Hemisphere herbaceous plants? The case of Meehania (Lamiaceae)

Despite considerable progress, many details regarding the evolution of the Arcto-Tertiary flora, including the timing, direction, and relative importance of migration routes in the evolution of woody and herbaceous taxa of the Northern Hemisphere, remain poorly understood. Meehania (Lamiaceae) comprises seven species and five subspecies of annual or perennial herbs, and is one of the few Lamiaceae genera known to have an exclusively disjunct distribution between eastern Asia and eastern North America. We analyzed the phylogeny and biogeographical history of Meehania to explore how the Arcto-Tertiary biogeographic hypothesis and two possible migration routes explain the disjunct distribution of Northern Hemisphere herbaceous plants. Parsimony and Bayesian inference were used for phylogenetic analyses based on five plastid sequences (rbcL, rps16, rpl32-trnH, psbA-trnH, and trnL-F) and two nuclear (ITS and ETS) gene regions. Divergence times and biogeographic inferences were performed using Bayesian methods as implemented in BEAST and S-DIVA, respectively. Analyses including 11 of the 12 known Meehania taxa revealed incongruence between the chloroplast and nuclear trees, particularly in the positions of Glechoma and Meehania cordata, possibly indicating allopolyploidy with chloroplast capture in the late Miocene. Based on nrDNA, Meehania is monophyletic, and the North American species M. cordata is sister to a clade containing the eastern Asian species. The divergence time between the North American M. cordata and the eastern Asian species occurred about 9.81 Mya according to the Bayesian relaxed clock methods applied to the combined nuclear data. Biogeographic analyses suggest a primary role of the Arcto-Tertiary flora in the study taxa distribution, with a northeast Asian origin of Meehania. Our results suggest an Arcto-Tertiary origin of Meehania, with its present distribution most probably being a result of vicariance and southward migrations of populations during climatic oscillations in the middle Miocene with subsequent migration into eastern North America via the Bering land bridge in the late Miocene.

Systematics, biogeography, and character evolution of Sparganium (Typhaceae): diversification of a widespread, aquatic lineage

PREMISE OF THE STUDY

Sparganium (Typhaceae) is a genus of aquatic monocots containing ±14 species, with flowers aggregated in unisexual, spherical heads, and habit ranging from floating to emergent. Sparganium presents an opportunity to investigate diversification, character evolution, and biogeographical relationships in a widespread temperate genus of aquatic monocots. We present a fossil-calibrated, molecular phylogeny of Sparganium based on analysis of two chloroplast and two nuclear markers. Within this framework, we examine character evolution in both habit and stigma number and infer the ancestral area and biogeographic history of the genus. •

METHODS

Sequence data from two cpDNA and two nDNA markers were analyzed using maximum parsimony, maximum likelihood, and Bayesian inference. We used the program BEAST to simultaneously estimate phylogeny and divergence times, S-DIVA and Lagrange for biogeographical reconstruction, and BayesTraits to examine locule number and habit evolution. •

KEY RESULTS

Two major clades were recovered with strong support: one composed of S. erectum and S. eurycarpum; and the other containing all remaining Sparganium. We realigned the subgenera to conform to these clades. Divergence time analysis suggests a Miocene crown origin but Pliocene diversification. Importantly, the floating-leaved habit has arisen multiple times in the genus, from emergent ancestors-contrary to past hypotheses. •

CONCLUSIONS

Cooling trends during the Tertiary are correlated with the isolation of temperate Eurasian and North American taxa. Vicariance, long-distance dispersal, and habitat specialization are proposed as mechanisms for Sparganium diversification.

Lost branches on the tree of life

Failure to archive published data can impede reproducibility and inhibit downstream synthesis. Alarmingly, we estimate that ∼70% of existing DNA sequence alignments/phylogenetic trees, representing much of the underpinning of modern phylogenetic analysis, are no longer accessible. The evolutionary biology community needs to adopt policies ensuring that data are publicly archived upon publication.

The diagnostic accuracy of X-ray arthrography for triangular fibrocartilaginous complex injury: a systematic review and meta-analysis

The purpose of this study was to evaluate the diagnostic test accuracy of X-ray arthrography in the detection of TFCC tear. Both published and unpublished databases were searched from their inception to August 2010. All studies comparing the diagnostic accuracy of X-ray arthrography (index test) to arthroscopy (reference standard) for patients with suspected TFCC tears were included in this review. Twelve studies assessing 430 patients (430 wrists) satisfied the eligibility criteria and were included. X-ray arthrography presented with a pooled sensitivity of 76.2% and specificity of 92.5% for the detection of complete TFCC tear. The triple-compartment injection X-ray arthrography was superior to the single-compartment injection technique. To conclude, the diagnostic test accuracy of X-ray arthrography is limited. Neither the single- nor the triple-compartment injection arthrography method is acceptable, given their reported low sensitivities. Further evaluation of the diagnostic test accuracy of Magnetic Resonance Arthrography and Magnetic Resonance Imaging is therefore warranted.

Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae)

PREMISE OF THE STUDY

The mint family (Lamiaceae) is the sixth largest family of flowering plants, with the tribe Mentheae containing about a third of the species. We present a detailed perspective on the evolution of the tribe Mentheae based on a phylogenetic analysis of cpDNA and nrDNA that is the most comprehensive to date, a biogeographic set of analyses using a fossil-calibrated chronogram, and an examination of staminal evolution.

METHODS

Data from four cpDNA and two nrDNA markers representing all extant genera within the tribe Mentheae were analyzed using the programs BEAST, Lagrange, S-DIVA, and BayesTraits. BEAST was used to simultaneously estimate phylogeny and divergence times, Lagrange and S-DIVA were used for biogeographical reconstruction, and BayesTraits was used to infer staminal evolution within the tribe.

KEY RESULTS

Currently accepted subtribal delimitations are shown to be invalid and are updated. The Mentheae and all five of its subtribes have a Mediterranean origin and have dispersed to the New World multiple times. The vast majority of New World species of subtribe Menthinae are the product of a single dispersal event in the mid-late Miocene. At least four transitions from four stamens to two stamens have occurred within Mentheae, once in the subtribe Salviinae, once in the subtribe Lycopinae, and at least twice in the subtribe Menthinae.

CONCLUSIONS

Worldwide cooling trends probably played a large role in the diversification and present day distribution of the tribe Mentheae. Additional work is needed to ascertain relationships within some Mentheae genera, especially in the subtribe Menthinae.