A Dated Phylogeny Complements Macroecological Analysis to Explain the Diversity Patterns in Geonoma (Arecaceae)

Hyper-Cryptic radiation of a tropical montane plant lineage

Species are seen as the fundamental unit of biotic diversity, and thus their delimitation is crucial for defining measures for diversity assessments and studying evolution. Differences between species have traditionally been associated with variation in morphology. And yet, the discovery of cryptic diversity suggests that the evolution of distinct lineages does not necessarily involve morphological differences. Here, we analyze 1,684,987 variant sites and over 4,000 genes for more than 400 samples to show how a tropical montane plant lineage (Geonoma undata species complex) is composed of numerous unrecognized genetic groups that are not morphologically distinct. We find that 11 to 14 clades do not correspond to the three currently recognized species. Most clades are genetically different and geographic distance and topography are the most important factors determining this genetic divergence. The genetic structure of this lineage does not match its morphological variation. Instead, this species complex constitutes the first example of a hyper-cryptic plant radiation in tropical mountains.

Targeted Capture of Hundreds of Nuclear Genes Unravels Phylogenetic Relationships of the Diverse Neotropical Palm Tribe Geonomateae

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from complete due to a lack of molecular data. Specifically, the previous Sanger sequencing-based studies used a few informative characters and partial sampling. To overcome these limitations, we used a recently developed Arecaceae-specific target capture bait set to undertake a phylogenomic analysis of the tribe Geonomateae. We sequenced 3,988 genomic regions for 85% of the species of the tribe, including 84% of the species of the largest genus, Geonoma. Phylogenetic relationships were inferred using both concatenation and coalescent methods. Overall, our phylogenetic tree is highly supported and congruent with taxonomic delimitations although several morphological taxa were revealed to be non-monophyletic. It is the first time that such a large genomic dataset is provided for an entire tribe within the Arecaceae. Our study lays the groundwork not only for detailed macro- and micro-evolutionary studies within the group, but also sets a workflow for understanding other species complexes across the tree of life.

A dedicated target capture approach reveals variable genetic markers across micro- and macro-evolutionary time scales in palms

Understanding the genetics of biological diversification across micro- and macro-evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in the tropics, studies of diversification at the population and species levels are still hampered by a lack of genomic markers suitable for the genotyping of large numbers of recently diverged taxa. To fill this gap, we used a whole genome sequencing approach to develop target sequencing for molecular markers in 4,184 genome regions, including 4,051 genes and 133 non-genic putatively neutral regions. These markers were chosen to cover a wide range of evolutionary rates allowing future studies at the family, genus, species and population levels. Special emphasis was given to the avoidance of copy number variation during marker selection. In addition, a set of 149 well-known sequence regions previously used as phylogenetic markers by the palm biological research community were included in the target regions, to open the possibility to combine and jointly analyse already available data sets with genomic data to be produced with this new toolkit. The bait set was effective for species belonging to all three palm sub-families tested (Arecoideae, Ceroxyloideae and Coryphoideae), with high mapping rates, specificity and efficiency. The number of high-quality single nucleotide polymorphisms (SNPs) detected at both the sub-family and population levels facilitates efficient analyses of genomic diversity across micro- and macro-evolutionary time scales.

Plant phylogeny as a window on the evolution of hyperdiversity in the tropical rainforest biome

I. II. III. IV. V. VI. VII. VIII. IX. References SUMMARY: Tropical rainforest (TRF) is the most species-rich terrestrial biome on Earth, harbouring just under half of the world's plant species in c. 7% of the land surface. Phylogenetic trees provide important insights into mechanisms underpinning TRF hyperdiversity that are complementary to those obtained from the fossil record. Phylogenetic studies of TRF plant diversity have mainly focused on whether this biome is an evolutionary 'cradle' or 'museum', emphasizing speciation and extinction rates. However, other explanations, such as biome age, immigration and ecological limits, must also be considered. We present a conceptual framework for addressing the drivers of TRF diversity, and review plant studies that have tested them with phylogenetic data. Although surprisingly few in number, these studies point to old age of TRF, low extinction and high speciation rates as credible drivers of TRF hyperdiversity. There is less evidence for immigration and ecological limits, but these cannot be dismissed owing to the limited number of studies. Rapid methodological developments in DNA sequencing, macroevolutionary analysis and the integration of phylogenetics with other disciplines may improve our grasp of TRF hyperdiversity in the future. However, such advances are critically dependent on fundamental systematic research, yielding numerous, additional, well-sampled phylogenies of TRF lineages.

Shifts in climate foster exceptional opportunities for species radiation: the case of South african geraniums

Climate change is often assumed to be a major driver of biodiversity loss. However, it can also set the stage for novel diversification in lineages with the evolutionary ability to colonize new environments. Here we tested if the extraordinary evolutionary success of the genus Pelargonium was related to the ability of its species to capitalize on the climate niche variation produced by the historical changes in southern Africa. We evaluated the relationship between rates of climate niche evolution and diversification rates in the main Pelargonium lineages and disentangled the roles of deep and recent historical events in the modification of species niches. Pelargonium clades exhibiting higher ecological differentiation along summer precipitation (SPP) gradients also experienced higher diversification rates. Faster rates of niche differentiation in spatially structured variables, along with lower levels of niche overlap among closely related species, suggest recent modification in species niches (e.g. dispersal or range shift) and niche lability. We suggest that highly structured SPP gradients established during the aridification process within southern Africa, in concert with niche lability and low niche overlap, contributed to species divergence. These factors are likely to be responsible for the extensive diversification of other lineages in this diversity hot spot.

Dispersal and niche evolution jointly shape the geographic turnover of phylogenetic clades across continents

The turnover of phylogenetic clades across space is a fundamental biodiversity pattern that may depend on long-term evolutionary processes, and that has downstream effects on other aspects of diversity including species richness and community structure. Limited niche evolution and limited dispersal are two major processes causing spatial restriction, and thus turnover, of clades. We studied the determinants of clade turnover within the World's richest floristic kingdom, the Neotropics, using the palm family (Arecaceae) as a model. We show that continental-scale clade turnover is driven by a combination of limited niche evolution - with respect to temperature and soil tolerances - and limited dispersal. These findings are consistent with strong dispersal barriers within the Neotropics, and the observation that some palm lineages are most diverse in certain biomes or climates. The importance of such deep-time effects suggest that palms might be slow to adapt or disperse in response to anthropogenic climate change.

Geographical ecology of the palms (Arecaceae): determinants of diversity and distributions across spatial scales

BACKGROUND

The palm family occurs in all tropical and sub-tropical regions of the world. Palms are of high ecological and economical importance, and display complex spatial patterns of species distributions and diversity.

SCOPE

This review summarizes empirical evidence for factors that determine palm species distributions, community composition and species richness such as the abiotic environment (climate, soil chemistry, hydrology and topography), the biotic environment (vegetation structure and species interactions) and dispersal. The importance of contemporary vs. historical impacts of these factors and the scale at which they function is discussed. Finally a hierarchical scale framework is developed to guide predictor selection for future studies.

CONCLUSIONS

Determinants of palm distributions, composition and richness vary with spatial scale. For species distributions, climate appears to be important at landscape and broader scales, soil, topography and vegetation at landscape and local scales, hydrology at local scales, and dispersal at all scales. For community composition, soil appears important at regional and finer scales, hydrology, topography and vegetation at landscape and local scales, and dispersal again at all scales. For species richness, climate and dispersal appear to be important at continental to global scales, soil at landscape and broader scales, and topography at landscape and finer scales. Some scale-predictor combinations have not been studied or deserve further attention, e.g. climate on regional to finer scales, and hydrology and topography on landscape and broader scales. The importance of biotic interactions - apart from general vegetation structure effects - for the geographic ecology of palms is generally underexplored. Future studies should target scale-predictor combinations and geographic domains not studied yet. To avoid biased inference, one should ideally include at least all predictors previously found important at the spatial scale of investigation.