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.
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, ...morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
At present, tropical arid biomes house less woody plant species diversity than tropical moist biomes, which could be due to lower rates of evolutionary diversification in the recent or distant past. ...Here, we study the evolutionary diversification of
Petalidium
(Acanthaceae), a genus of 36 species of woody shrubs found in the Namib Desert of southwest Africa, and surrounding areas. We generated a new, nearly fully sampled and temporally calibrated phylogeny for
Petalidium
using RADseq SNP data and secondary calibrations. We then investigated variation in net diversification rate across the phylogeny, the ancestral climatic niche of lineages and the link between the two. We find that arid climatic conditions are linked with increased rates of net species diversification in the genus. Despite its great age, the Namib Desert clearly hosts young plant radiations. This apparent contradiction can be explained by a scenario of high evolutionary turnover, in this case potentially caused by alternating hyper-arid and relatively mesic phases. Hyper-arid phases could result in high plant mortality and extinction of species, leading to ecological opportunity and diversification during mesic phases. Taken together, our results contribute to a growing body of literature that shows evidence for elevated rates of plant diversification in the Quaternary in arid biomes across the globe.
SUMMARY
Thermogenesis – the ability to generate metabolic heat – is much more common in animals than in plants, but it has been documented in several plant families, most prominently the Araceae. ...Metabolic heat is produced in floral organs during the flowering time (anthesis), with the hypothesised primary functions being to increase scent volatilisation for pollinator attraction, and/or to provide a heat reward for invertebrate pollinators. Despite in‐depth studies on the thermogenesis of single species, no attempts have yet been made to examine plant thermogenesis across an entire clade. Here, we apply time‐series clustering algorithms to 119 measurements of the full thermogenic patterns in inflorescences of 80 Amorphophallus species. We infer a new time‐calibrated phylogeny of this genus and use phylogenetic comparative methods to investigate the evolutionary determinants of thermogenesis. We find striking phenotypic variation across the phylogeny, with heat production in multiple clades reaching up to 15°C, and in one case 21.7°C above ambient temperature. Our results show that the thermogenic capacity is phylogenetically conserved and is also associated with inflorescence thickness. Our study paves the way for further investigations of the eco‐evolutionary benefits of thermogenesis in plants.
Significance Statement
Metabolic heat production is a common phenomenon in two important animal groups (birds and mammals), but rare in plants. Here, we investigat the thermogenic patterns in the genus Amorphophallus (Araceae). This is the first study to provide a detailed assessment of thermogenic patterns of a plant genus on a large scale and our methodological approach to investigate thermogenic patterns in an evolutionary context is unprecedented.
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.
Abstract
Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of ...Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear gene phyC and plastid data obtained from genome skimming. We investigate evolutionary relationships at the intergeneric level in Vrieseeae and at the intrageneric level in Vriesea s.s. We sampled a comprehensive dataset, including 11 genera of Tillandsioideae and nearly 50% of all known Vriesea spp. Using a genome skimming approach, we obtained a 78 483-bp plastome alignment containing 35 complete and 55 partial protein-coding genes. Phylogenetic trees were reconstructed using maximum-likelihood based on three datasets: (1) the 78 483 bp plastome alignment; (2) the nuclear gene phyC and (3) a concatenated alignment of 18 subselected plastid genes + phyC. Additionally, a Bayesian inference was performed on the second and third datasets. These analyses revealed that Vriesea s.s. forms a well-supported clade encompassing most of the species of the genus. However, our results also identified several remaining issues in the systematics of Vriesea, including a few species nested in Tillandsia and Stigmatodon. Finally, we recognize some putative groups within Vriesea s.s., which we discuss in the light of their morphological and ecological characteristics.
The tremendously unbalanced distribution of species richness across clades in the tree of life is often interpreted as the result of variation in the rates of diversification, which may themselves ...respond to trait evolution. Even though this is likely a widespread pattern, not all diverse groups of organisms exhibit heterogeneity in their dynamics of diversification. Testing and characterizing the processes driving the evolution of clades with steady rates of diversification over long periods of time are of importance in order to have a full understanding of the build-up of biodiversity through time.
We studied the macroevolutionary history of the species-rich tree fern family Cyatheaceae and inferred a time-calibrated phylogeny of the family including extinct and extant species using the recently developed fossilized birth-death method. We tested whether the high diversity of Cyatheaceae is the result of episodes of rapid diversification associated with phenotypic and ecological differentiation or driven by stable but low rates of diversification. We compared the rates of diversification across clades, modelled the evolution of body size and climatic preferences and tested for trait-dependent diversification.
This ancient group diversified at a low and constant rate during its long evolutionary history. Morphological and climatic niche evolution were found to be overall highly conserved, although we detected several shifts in the rates of evolution of climatic preferences, linked to changes in elevation. The diversification of the family occurred gradually, within limited phenotypic and ecological boundaries, and yet resulted in a remarkable species richness.
Our study indicates that Cyatheaceae is a diverse clade which slowly accumulated morphological, ecological and taxonomic diversity over a long evolutionary period and provides a compelling example of the tropics as a museum of biodiversity.
The metabolic theory of ecology stipulates that molecular evolutionary rates should correlate with temperature and latitude in ectothermic organisms. Previous studies have shown that most groups of ...vertebrates, such as amphibians, turtles and even endothermic mammals, have higher molecular evolutionary rates in regions where temperature is high. However, the association between molecular evolutionary rates and temperature or latitude has never been tested in Squamata.
We used a large dataset including the spatial distributions and environmental variables for 1,651 species of Squamata and compared the contrast of the rates of molecular evolution with the contrast of temperature and latitude between sister species. Using major axis regressions and a new algorithm to choose independent sister species pairs, we found that temperature and absolute latitude were not associated with molecular evolutionary rates.
This absence of association in such a diverse ectothermic group questions the mechanisms explaining current pattern of species diversity in Squamata and challenges the presupposed universality of the metabolic theory of ecology.
The outstanding diversity of Amazonian forests is predicted to be the result of several processes. While tree lineages have dispersed repeatedly across the Amazon, interactions between plants and ...insects may be the principal mechanism structuring the communities at local scales.
Using metabolomic and phylogenetic approaches, we investigated the patterns of historical assembly of plant communities across the Amazon based on the Neotropical genus of trees Inga (Leguminosae) at four, widely separated sites.
Our results show a low degree of phylogenetic structure and a mixing of chemotypes across the whole Amazon basin, suggesting that although biogeography may play a role, the metacommunity for any local community in the Amazon is the entire basin. Yet, local communities are assembled by ecological processes, with the suite of Inga at a given site more divergent in chemical defences than expected by chance
Synthesis. To our knowledge, this is the first study to present metabolomic data for nearly 100 species in a diverse Neotropical plant clade across the whole Amazonia. Our results demonstrate a role for plant–herbivore interactions in shaping the clade's community assembly at a local scale, and suggest that the high alpha diversity in Amazonian tree communities must be due in part to the interactions of diverse tree lineages with their natural enemies providing a high number of niche dimensions.
Resumen
La increíble diversidad de los bosques Amazónicos se cree es el resultado de varios procesos. Aunque los linajes de Inga se han dispersado repetidamente a lo largo de la Amazonía, las interacciones entre plantas e insectos podrían ser el mecanismo más importante en el ensamblaje de comunidades a escala local.
Usando métodos metabolómicos y filogenéticos, investigamos los patrones históricos de ensamblaje de comunidades de plantas a lo largo de la Amazonía basándonos en el género neotropical de árboles Inga (Leguminosae) en cuatro sitios, ampliamente separados.
Nuestros resultados demuestran un grado de estructura filogenética y una mezcla de chemotipos a lo largo de la Amazonía, sugiriendo que aunque la biogeografía juegue un rol, la metacomunidad para cualquier comunidad regional en la Amazonía es toda la cuenca Amazónica. Comunidades locales son ensambladas por procesos ecológicos, donde todas las especies de Inga coexistiendo en un mismo sitio son más divergentes en defensas químicas que al azar.
Síntesis. Este es el primer estudio que presenta datos metabolómicos para casi 100 especies de árboles pertenecientes a un grupo Neotropical diverso a lo largo de su rango de distribución. Nuestros resultados demuestran un rol para las interacciones entre plantas y herbívoros en el ensamblaje de la comunidad de este clado a escala local, y sugiere que la alta diversidad alfa en las comunidades de árboles Amazónicos puede deberse en parte a las interacciones de grupos de árboles diversos con sus enemigos naturales.
Using metabolomic and phylogenetic approaches, we show that species of the Neotropical tree genus Inga, have dispersed freely across the Amazon. However, the subset of Inga species that coexist in any given forest community differ dramatically from each other in their chemical defences. Thus, interactions between plants and herbivores are a major factor shaping community composition in tropical rain forests.
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