Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.

Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species

Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.

Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot

The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.

Systematics of the Trembleya sensu stricto clade of Microlicia (Melastomataceae, Lavoisiereae)

A systematic monograph of the Trembleya s.s. clade is presented, a Brazilian endemic lineage of Melastomataceae comprising 11 species and currently recognised as part of Microlicia s.l. (Melastomataceae). First, we investigate phylogenetic relationships within Lavoisiereae using two nuclear markers and two sampling datasets (102 and 134 terminals). Then, we provide a systematic revision and new circumscription of the Trembleya s.s. clade, including line drawings, photos of living specimens, leaves and floral parts, distribution maps, a key to the 11 accepted species, comments on morphology, reproductive biology, richness, endemism, biogeography and recommended conservation assessments. A nomenclatural update of all taxa previously treated in Trembleya is also provided, including the designation of 45 lectotypes and the proposal of 38 new synonyms.

Predominantly Eastward Long-Distance Dispersal in Pantropical Ochnaceae Inferred From Ancestral Range Estimation and Phylogenomics

Ochnaceae is a pantropical family with multiple transoceanic disjunctions at deep and shallow levels. Earlier attempts to unravel the processes that led to such biogeographic patterns suffered from insufficient phylogenetic resolution and unclear delimitation of some of the genera. In the present study, we estimated divergence time and ancestral ranges based on a phylogenomic framework with a well-resolved phylogenetic backbone to tackle issues of the timing and direction of dispersal that may explain the modern global distribution of Ochnaceae. The nuclear data provided the more robust framework for divergence time estimation compared to the plastome-scale data, although differences in the inferred clade ages were mostly small. While Ochnaceae most likely originated in West Gondwana during the Late Cretaceous, all crown-group disjunctions are inferred as dispersal-based, most of them as transoceanic long-distance dispersal (LDD) during the Cenozoic. All LDDs occurred in an eastward direction except for the SE Asian clade of Sauvagesieae, which was founded by trans-Pacific dispersal from South America. The most species-rich clade by far, Ochninae, originated from either a widespread neotropical-African ancestor or a solely neotropical ancestor which then dispersed to Africa. The ancestors of this clade then diversified in Africa, followed by subsequent dispersal to the Malagasy region and tropical Asia on multiple instances in three genera during the Miocene-Pliocene. In particular, Ochna might have used the South Arabian land corridor to reach South Asia. Thus, the pantropical distribution of Ochnaceae is the result of LDD either transoceanic or via land bridges/corridors, whereas vicariance might have played a role only along the stem of the family.

Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data

While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.

Evolution of Dispersal, Habit, and Pollination in Africa Pushed Apocynaceae Diversification After the Eocene-Oligocene Climate Transition

Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived floral morphological features. These are mainly associated with the development of corolline and/or staminal coronas and a spectrum of integration of floral structures culminating with the formation of a gynostegium and pollinaria—specialized pollen dispersal units. To date, no detailed analysis has been conducted to estimate the origin and diversification of this lineage in space and time. Here, we use the most comprehensive time-calibrated phylogeny of Apocynaceae, which includes approximately 20% of the species covering all major lineages, and information on species number and distributions obtained from the most up-to-date monograph of the family to investigate the biogeographical history of the lineage and its diversification dynamics. South America, Africa, and Southeast Asia (potentially including Oceania), were recovered as the most likely ancestral area of extant Apocynaceae diversity; this tropical climatic belt in the equatorial region retained the oldest extant lineages and these three tropical regions likely represent museums of the family. Africa was confirmed as the cradle of pollinia-bearing lineages and the main source of Apocynaceae intercontinental dispersals. We detected 12 shifts toward accelerated species diversification, of which 11 were in the APSA clade (apocynoids, Periplocoideae, Secamonoideae, and Asclepiadoideae), eight of these in the pollinia-bearing lineages and six within Asclepiadoideae. Wind-dispersed comose seeds, climbing growth form, and pollinia appeared sequentially within the APSA clade and probably work synergistically in the occupation of drier and cooler habitats. Overall, we hypothesize that temporal patterns in diversification of Apocynaceae was mainly shaped by a sequence of morphological innovations that conferred higher capacity to disperse and establish in seasonal, unstable, and open habitats, which have expanded since the Eocene-Oligocene climate transition.

OCBIL theory: a new science for old ecosystems

This paper is an introduction to the special issue of the Biological Journal of the Linnean Society entitled OCBIL theory: a new science for old ecosystems. Firstly, we elaborate on the origins and development of OCBIL theory, which argues that landscape age, climatic buffering and soil fertility are key environmental dimensions shaping ecological and evolutionary processes across different scales. We then consider the 21 contributions made in this special issue in terms of cutting edge advances in the Southern Hemisphere that test, explore and apply aspects of OCBIL theory at the end of its first decade of formal publication. More attempts at refutation are urged, as untested aspects remain controversial. Lastly, a concluding discussion is offered on promising new lines of enquiry to develop the theory further and ensure its global application to pressing conservation issues facing biological and cultural diversity. Although OCBILs are absent or rare in much of the postglacial and periglacial Northern Hemisphere, we demonstrate, in south-west Europe and North America, starting with California, that they are likely to be found, thus extending the implications and applications of OCBIL theory in new directions. We also propose that, in many ways, Noongar Aboriginal cosmology from south-west Australia has developed sophisticated insights about ancient uplands that are precursors to key ideas in OCBIL theory.