Evolution of apetaly in the cosmopolitan genus Stellaria.

PREMISE: Apetaly is widespread across distantly related lineages of flowering plants and is associated with abiotic (or self-) pollination. It is particularly prevalent in the carnation family, and the cosmopolitan genus Stellaria contains many lineages that are hypothesized to have lost petals from showy petalous ancestors. But the pollination biology of apetalous species of Stellaria remains unclear. METHODS: Using a substantial species-level sampling (~92% of known taxonomic diversity), we describe the pattern of petal evolution within Stellaria using ancestral character state reconstructions. To help shed light on the reproductive biology of apetalous Stellaria, we conducted a field experiment at an alpine tundra site in the southern Rocky Mountains to test whether an apetalous species (S. irrigua) exhibits higher levels of selfing than a sympatric, showy petalous congener (S. longipes). RESULTS: Analyses indicated that the ancestor of Stellaria was likely showy petalous and that repeated, parallel reductions of petals occurred in clades across much of the world, with uncommon reversal back to showy petals. Field experiments supported high rates of selfing in the apetalous species and high rates of outcrossing in the petalous species. CONCLUSIONS: Petal loss is rampant across major clades of Stellaria and is potentially linked with self-pollination worldwide. Self-pollination occurs within the buds in S. irrigua, and high propensities for this and other forms of selfing known in many other taxa of arctic-alpine habitats may reflect erratic availability of pollinators.

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway.

The flavonoids, one of the largest classes of plant secondary metabolites, are found in lineages that span the land plant phylogeny and play important roles in stress responses and as pigments. Perhaps the most well-studied flavonoids are the anthocyanins that have human health benefits and help plants attract pollinators, regulate hormone production, and confer resistance to abiotic and biotic stresses. The canonical biochemical pathway responsible for the production of these pigments is well-characterized for flowering plants yet its conservation across deep divergences in land plants remains debated and poorly understood. Many early land plants such as mosses, liverworts, and ferns produce flavonoid pigments, but their biosynthetic origins and homologies to the anthocyanin pathway remain uncertain. We conducted phylogenetic analyses using full genome sequences representing nearly all major green plant lineages to reconstruct the evolutionary history of the anthocyanin biosynthetic pathway then test the hypothesis that genes in this pathway are present in early land plants. We found that the entire pathway was not intact until the most recent common ancestor of seed plants and that orthologs of many downstream enzymes are absent from seedless plants including mosses, liverworts, and ferns. Our results also highlight the utility of phylogenetic inference, as compared to pairwise sequence similarity, in orthology assessment within large gene families that have complex duplication-loss histories. We suggest that the production of red-violet flavonoid pigments widespread in seedless plants, including the 3-deoxyanthocyanins, requires the activity of novel, as-yet discovered enzymes, and represents convergent evolution of red-violet coloration across land plants.

A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens.

PREMISE: Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS: We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS: Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS: Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.

Habitat quality and disturbance drive lichen species richness in a temperate biodiversity hotspot.

The impacts of disturbance on biodiversity and distributions have been studied in many systems. Yet, comparatively less is known about how lichens-obligate symbiotic organisms-respond to disturbance. Successful establishment and development of lichens require a minimum of two compatible yet usually unrelated species to be present in an environment, suggesting disturbance might be particularly detrimental. To address this gap, we focused on lichens, which are obligate symbiotic organisms that function as hubs of trophic interactions. Our investigation was conducted in the southern Appalachian Mountains, USA. We conducted complete biodiversity inventories of lichens (all growth forms, reproductive modes, substrates) across 47, 1-ha plots to test classic models of responses to disturbance (e.g., linear, unimodal). Disturbance was quantified in each plot using a standardized suite of habitat quality variables. We additionally quantified woody plant diversity, forest density, rock density, as well as environmental factors (elevation, temperature, precipitation, net primary productivity, slope, aspect) and analyzed their impacts on lichen biodiversity. Our analyses recovered a strong, positive, linear relationship between lichen biodiversity and habitat quality: lower levels of disturbance correlate to higher species diversity. With few exceptions, additional variables failed to significantly explain variation in diversity among plots for the 509 total lichen species, but we caution that total variation in some of these variables was limited in our study area. Strong, detrimental impacts of disturbance on lichen biodiversity raises concerns about conservation and land management practices that fail to incorporate complete estimates of biodiversity, especially from ecologically important organisms such as lichens.

Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses.

Symbioses among co-evolving taxa are often marked by genome reductions such as a loss of protein-coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under-studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and annotated species of lichenized fungi were compared to 167 mitochondrial genomes of nonlichenized fungi. Our results demonstrate the first broad-scale loss of atp9 from mitochondria of lichenized fungi. Despite key functions in mitochondrial energy production, we show that atp9 has been independently lost in three different lineages spanning 10 of the 22 studied species. A search for predicted, functional copies of atp9 among genomes of other symbionts involved in each lichen revealed the full-length, presumably functional copies of atp9 in either the photosynthetic algal partner or in other symbiotic fungi in all 10 instances. Together, these data yield evidence of an obligate symbiotic relationship in which core genomic processes have been streamlined, likely due to co-evolution.

Evolutionary and ecological drivers of plant flavonoids across a large latitudinal gradient.

Flavonoids are important secondary metabolites that play an integral role in protecting plants against UV radiation and other forms of environmental stress. Given widespread impacts of environmental effects associated with latitude on a multitude of biological systems and a well-documented increase in solar radiation towards the equator, plant flavonoid production is expected to increase as a response to factors associated with decreasing latitude. Using data from a Neotropical genus (Ruellia) that spans an exceptionally broad latitudinal gradient, we tested a hypothesis of a positive latitudinal gradient in flavonoid concentration and assessed other factors that influence flavonoid production including habitat type (xeric vs. wet), altitude, phylogenetic relatedness, and pleiotropic effects. Two flavones with peak absorbance in ultraviolet wavelengths, apigenin and luteolin, were detected across all species. Transcriptome data confirm high expression of the gene required for flavone biosynthesis, flavone synthase (FNS). Contrary to our prediction, data revealed a positive correlation between flavone concentration and higher latitudes. Further, we recovered strong impacts of xeric habitat, pleiotropy, and phylogenetic relatedness on flavone concentrations. This study documents a complex interplay of ecological, historical, phylogenetic relatedness, and pleiotropic factors driving plant flavonoid production.

Genome-scale transcriptional study of hybrid effects and regulatory divergence in an F1 hybrid Ruellia (Wild Petunias: Acanthaceae) and its parents.

BACKGROUND: New combinations of divergent genomes can give rise to novel genetic functions in resulting hybrid progeny. Such functions may yield opportunities for ecological divergence, contributing ultimately to reproductive isolation and evolutionary longevity of nascent hybrid lineages. In plants, the degree to which transgressive genotypes contribute to floral novelty remains a question of key interest. Here, we generated an F1 hybrid plant between the red-flowered Ruellia elegans and yellow flowered R. speciosa. RNA-seq technology was used to explore differential gene expression between the hybrid and its two parents, with emphasis on genetic elements involved in the production of floral anthocyanin pigments. RESULTS: The hybrid was purple flowered and produced novel floral delphinidin pigments not manufactured by either parent. We found that nearly a fifth of all 86,475 unigenes expressed were unique to the hybrid. The majority of hybrid unigenes (80.97%) showed a pattern of complete dominance to one parent or the other although this ratio was uneven, suggesting asymmetrical influence of parental genomes on the progeny transcriptome. However, 8.87% of all transcripts within the hybrid were expressed at significantly higher or lower mean levels than observed for either parent. A total of 28 unigenes coding putatively for eight core enzymes in the anthocyanin pathway were recovered, along with three candidate MYBs involved in anthocyanin regulation. CONCLUSION: Our results suggest that models of gene evolution that explain phenotypic novelty and hybrid establishment in plants may need to include transgressive effects. Additionally, our results lend insight into the potential for floral novelty that derives from unions of divergent genomes. These findings serve as a starting point to further investigate molecular mechanisms involved in flower color transitions in Ruellia.

A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions.

More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large ( > 4000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points and experimenting with both fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ∼ 23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineage would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kb of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events explain present-day distributions better than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World (OW) to New World (NW) dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s., which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within the last ∼ 20 myr even though Acanthaceae s.s is over 3 times as old. A simulation study confirmed that these dispersal events were significantly skewed toward the present and not simply a chance occurrence. Finally, we review reports of fossils that have been assigned to Acanthaceae that are substantially older than the lower Cretaceous estimate for Angiosperms as a whole (i.e., the general consensus that has resulted from several recent dating and fossil-based studies in plants). This is the first study to reconstruct divergence times among clades of Acanthaceae and sets the stage for comparative evolutionary research in this and related families that have until now been thought to have extremely poor fossil resources.

Carbon-concentrating mechanisms are a key trait in lichen ecology and distribution.

Carbon-concentrating mechanisms (CCMs) are a widespread phenomenon in photosynthetic organisms. In vascular plants, the evolution of CCMs ([C44-carbon compound] and crassulacean acid metabolism [CAM]) is associated with significant shifts, most often to hot, dry and bright, or aquatic environments. If and how CCMs drive distributions of other terrestrial photosynthetic organisms, remains little studied. Lichens are ecologically important obligate symbioses between fungi and photosynthetic organisms. The primary photosynthetic partner in these symbioses can include CCM-presenting cyanobacteria (as carboxysomes), CCM-presenting green algae (as pyrenoids) or green algae lacking any CCM. We use an extensive dataset of lichen communities from eastern North America, spanning a wide climatic range, to test the importance of CCMs as predictors of lichen ecology and distribution. We show that the presence or absence of CCMs leads to opposite responses to temperature and precipitation in green algal lichens, and different responses in cyanobacterial lichens. These responses contrast with our understanding of lichen physiology, whereby CCMs mitigate carbon limitation by water saturation at the cost of efficient use of vapor hydration. This study demonstrates that CCM status is a key functional trait in obligate lichen symbioses, equivalent in importance to its role in vascular plants, and central for studying present and future climate responses.

Comparative anatomy, morphology, and molecular phylogenetics of the African genus Satanocrater (Acanthaceae).

PREMISE OF THE STUDY: Anatomical and morphological features of Satanocrater were studied to test hypotheses of xeric adaptations in the genus, which is endemic to arid tropical Africa. These features, together with molecular data, were used to test the phylogenetic placement of Satanocrater within the large plant family Acanthaceae. METHODS: We undertook a comparative study of four species of Satanocrater. Carbon isotope ratios were generated to test a hypothesis of C(4) photosynthesis. Molecular data from chloroplast (trnG-trnS, trnG-trnR, psbA-trnH) and nuclear (Eif3E) loci were used to test the placement of Satanocrater within Acanthaceae. KEY RESULTS: Anatomical features reflecting xeric adaptations of species of Satanocrater included a thick-walled epidermis, thick cuticle, abundant trichomes and glandular scales, stomata overarched by subsidiary cells, tightly packed mesophyll cells, and well-developed palisade parenchyma on both leaf surfaces. Although two species had enlarged bundle sheath cells, a feature often implicated in C(4) photosynthesis, isotope ratios indicated all species of Satanocrater use the C(3) pathway. Molecular data resolved Satanocrater within tribe Ruellieae with strong support. Within Ruellieae, our data suggest that pollen morphology of Satanocrater may represent an intermediate stage in a transition series. CONCLUSIONS: Anatomical and morphological features of Satanocrater reflect adaptation to xeric environments and add new information about the biology of xerophytes. Morphological and molecular data place Satanocrater in the tribe Ruellieae with confidence. This study adds to our capacity to test hypotheses of broad evolutionary and ecological interest in a diverse and important family of flowering plants.

Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae).

BACKGROUND: Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data. RESULTS: Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled. Analysis of non-synonymous/synonymous (dn/ds) mutation rates indicated all identified loci are under purifying selection, suggesting overall selection to prevent the accumulation of deleterious mutations. Additionally, upstream enzymes have lower rates of molecular evolution compared to downstream enzymes. However, site-specific tests of selection yielded evidence for positive selection at several sites, including four in F3'H2 and five in DFR3, and these sites are located in protein binding regions. A species-level phylogenetic tree constructed using a newly implemented hybrid transcriptome-RADseq approach implicates several flower color transitions among the 10 species. We found evidence of both regulatory and structural mutations to F3'5'H in helping to explain the evolution of red flowers from purple-flowered ancestors. CONCLUSIONS: Sequence comparisons and co-expression analyses of ABP loci revealed that mutations in regulatory loci are likely to play a greater role in flower color transitions in Ruellia compared to mutations in underlying structural genes.

Reproductive character displacement and potential underlying drivers in a species-rich and florally diverse lineage of tropical angiosperms (Ruellia; Acanthaceae).

Reproductive character displacement is a pattern whereby sympatric lineages diverge more in reproductive character morphology than allopatric lineages. This pattern has been observed in many plant species, but comparably few have sought to disentangle underlying mechanisms. Here, in a diverse lineage of Neotropical plants (Ruellia; Acanthaceae), we present evidence of reproductive character displacement in a macroevolutionary framework (i.e., among species) and document mechanistic underpinnings. In a series of interspecific hand pollinations in a controlled glasshouse environment, we found that crosses between species that differed more in overall flower size, particularly in style length, were significantly less likely to produce viable seeds. Further, species pairs that failed to set seed were more likely to have sympatric distributions in nature. Competition for pollinators and reinforcement to avoid costly interspecific mating could both result in these patterns and are not mutually exclusive processes. Our results add to growing evidence that reproductive character displacement contributes to exceptional floral diversity of angiosperms.

Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria.

Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.

Is floral specialization an evolutionary dead-end? Pollination system transitions in Ruellia (Acanthaceae).

Pollination systems frequently reflect adaptations to particular groups of pollinators. Such systems are indicative of evolutionary specialization and have been important in angiosperm diversification. We studied the evolution of pollination systems in the large genus Ruellia. Phylogenetic analyses, morphological ordinations, ancestral state reconstructions, and a character mapping simulation were conducted to reveal key patterns in the direction and lability of floral characters associated with pollination. We found significant floral morphological differences among species that were generally associated with different groups of floral visitors. Floral evolution has been highly labile and also directional. Some specialized systems such as hawkmoth or bat pollination are likely evolutionary dead-ends. In contrast, specialized pollination by hummingbirds is clearly not a dead-end. We found evidence for multiple reverse transitions from presumed ancestral hummingbird pollination to more derived bee or insect pollination. These repeated origins of insect pollination from hummingbird-pollinated ancestors have not evolved without historical baggage. Flowers of insect-pollinated species derived from hummingbird-pollinated ancestors are morphologically more similar to hummingbird flowers than they are to other more distantly related insect-pollinated flowers. Finally, some pollinator switches were concomitant with changes in floral morphology that are associated with those pollinators. These observations are consistent with the hypothesis that some transitions have been adaptive in the evolution of Ruellia.

The complete mitochondrial genomes of five lichenized fungi in the genus Usnea (Ascomycota: Parmeliaceae).

Known colloquially as 'Old Man's Beard', Usnea is a genus of lichenized Ascomycete fungi characterized by having a fruticose growth form and cartilaginous central axis. The complete mitochondrial genomes of Usnea halei, U. mutabilis, U. subfusca, U. subgracilis, and U. subscabrosa were sequenced using Illumina data and then assembled de novo. These mitogenomes ranged in size from 52,486 bp (U. subfusca) to 94,464 bp (U. subgracilis). All were characterized by having high levels of intronic and intergenic variation, such as ORFs that encode proteins with homology to two homing endonuclease types, LAGLIDADG and GIY-YIG. Genes annotated within these mitogenomes include 14 protein-coding genes, the large and small ribosomal subunits (LSU and SSU), and 23-26 tRNAs. Notably, the atp9 gene was absent from each genome. Genomic synteny was highly conserved across the five species. Five conserved mitochondrial genes (nad2, nad4, cox1, cox2, and cox3) were used to infer a best estimate maximum likelihood phylogeny among these five Usnea and other relatives, which yielded relationships consistent with prior published phylogenies.

Genomic insights into the mitochondria of 11 eastern North American species of Cladonia.

Cladonia is among the most species-rich genera of lichens globally. Species in this lineage, commonly referred to as reindeer lichens, are ecologically important in numerous regions worldwide. In some locations, species of Cladonia can comprise the dominant groundcover, and are a major food source for caribou and other mammals. Additionally, many species are known to produce substances with antimicrobial properties or other characteristics with potentially important medical applications. This exceptional morphological and ecological variation contrasts sharply with the limited molecular divergence often observed among species. As a new resource to facilitate ongoing and future studies of these important species, we analyse here the sequences of 11 Cladonia mitochondrial genomes, including new mitochondrial genome assemblies and annotations representing nine species: C. apodocarpa, C. caroliniana, C. furcata, C. leporina, C. petrophila, C. peziziformis, C. robbinsii, C. stipitata, and C. subtenuis. These 11 genomes varied in size, intron content, and complement of tRNAs. Genes annotated within these mitochondrial genomes include 15 protein-coding genes, the large and small ribosomal subunits (mtLSU and mtSSU), and 23-26 tRNAs. All Cladonia mitochondrial genomes contained atp9, an important energy transport gene that has been lost evolutionarily in some lichen mycobiont mitochondria. Using a concatenated alignment of five mitochondrial genes (nad2, nad4, cox1, cox2, and cox3), a Bayesian phylogeny of relationships among species was inferred and was consistent with previously published phylogenetic relationships, highlighting the utility of these regions in reconstructing phylogenetic history.

The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).

The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.

Disentangling geographical, biotic, and abiotic drivers of plant diversity in neotropical Ruellia (Acanthaceae).

It has long been hypothesized that biotic interactions are important drivers of biodiversity evolution, yet such interactions have been relatively less studied than abiotic factors owing to the inherent complexity in and the number of types of such interactions. Amongst the most prominent of biotic interactions worldwide are those between plants and pollinators. In the Neotropics, the most biodiverse region on Earth, hummingbird and bee pollination have contributed substantially to plant fitness. Using comparative methods, we test the macroevolutionary consequences of bird and bee pollination within a species rich lineage of flowering plants: Ruellia. We additionally explore impacts of species occupancy of ever-wet rainforests vs. dry ecosystems including cerrado and seasonally dry tropical forests. We compared outcomes based on two different methods of model selection: a traditional approach that utilizes a series of transitive likelihood ratio tests as well as a weighted model averaging approach. Analyses yield evidence for increased net diversification rates among Neotropical Ruellia (compared to Paleotropical lineages) as well as among hummingbird-adapted species. In contrast, we recovered no evidence of higher diversification rates among either bee- or non-bee-adapted lineages and no evidence for higher rates among wet or dry habitat lineages. Understanding fully the factors that have contributed to biases in biodiversity across the planet will ultimately depend upon incorporating knowledge of biotic interactions as well as connecting microevolutionary processes to macroevolutionary patterns.

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia.

Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa, and the ingroup. Overall, we found that Petalidium, despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.