Continuous colonization of the Atlantic coastal rain forests of South America from Amazônia.

The two main extensions of rain forest in South America are the Amazon (Amazônia) and the Atlantic rain forest (Mata Atlântica), which are separated by a wide 'dry diagonal' of seasonal vegetation. We used the species-rich tree genus to test if Amazônia-Mata Atlântica dispersals have been clustered during specific time periods corresponding to past, humid climates. We performed hybrid capture DNA sequencing of 810 nuclear loci for 453 accessions representing 164 species that included 62% of Mata Atlântica species and estimated a dated phylogeny for all accessions using maximum likelihood, and a species-level tree using coalescent methods.

Global diversification of the common moonwort ferns (Botrychium lunaria group, Ophioglossaceae) was mainly driven by Pleistocene climatic shifts.

Background And Aims: The cosmopolitan Botrychium lunaria group belong to the most species rich genus of the family Ophioglossaceae and was considered to consist of two species until molecular studies in North America and northern Europe led to the recognition of multiple new taxa. Recently, additional genetic lineages were found scattered in Europe, emphasizing our poor understanding of the global diversity of the B. lunaria group, while the processes involved in the diversification of the group remain unexplored.

Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification.

Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica.

Precipitation is the main axis of tropical plant phylogenetic turnover across space and time.

Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics.

gen. nov. (Leguminosae, Caesalpinioideae), a new genus of mimosoid legumes of tropical Africa.

The genus is here newly described to accommodate three species and one subspecies of African mimosoid legumes. These taxa have previously been included by several authors in , and/or , but they have been shown to be phylogenetically unrelated to any of these, being instead the sister-group of the recently described Neotropical genus , which is similar in vegetative morphology and especially its very similar indumentum, but is decidedly different in pod morphology. A taxonomic treatment of the three species in the genus is presented, with species descriptions, photographs, distribution maps and an identification key.

On the taxonomic affinity of Britton (Leguminosae, Caesalpinioideae-mimosoid clade).

Recent phylogenomic analyses placed Britton as the sister-group of the two currently known species of Harms, clearly outside AlbiziasectionArthrosamanea (Britton & Rose) Barneby & J.W. Grimes where it has until now been included.

Dilemmas in generic delimitation of and allies (Caesalpinioideae, mimosoid clade): how to reconcile phylogenomic evidence with morphology and taxonomy?

comprises 219 species distributed in tropical and subtropical regions of North and South America, Africa, Asia and Australia. Two sections are currently recognised within and these are most readily distinguished by the differences in disposition of their cauline prickles, i.e.

Re-establishment of the genus (Leguminosae, Caesalpinioideae, mimosoid clade): the New World species formerly placed in .

Following recent mimosoid phylogenetic and phylogenomic studies demonstrating the non-monophyly of the genus , we present a new molecular phylogeny focused on the neotropical species in the genus, with much denser taxon sampling than previous studies. Our aims were to test the monophyly of the neotropical section Arthrosamanea, resolve species relationships, and gain insights into the evolution of fruit morphology. We perform a Bayesian phylogenetic analysis of sequences of nuclear internal and external transcribed spacer regions and trace the evolution of fruit dehiscence and lomentiform pods.

Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae).

Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade.

, a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the interior Andean valleys of Bolivia.

Phylogenetic analyses of DNA sequence data sampling all species of alongside representatives of genera of the Inga and Albizia clades of the larger ingoid clade of mimosoid legumes (sensu Koenen et al. 2020) confirm the non-monophyly of the genus . We show that is placed in the Albizia clade, while the remaining four species of are placed in the Inga clade, in line with previous results.

Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation.

Premise: Targeted enrichment methods facilitate sequencing of hundreds of nuclear loci to enhance phylogenetic resolution and elucidate why some parts of the "tree of life" are difficult (if not impossible) to resolve. The mimosoid legumes are a prominent pantropical clade of ~3300 species of woody angiosperms for which previous phylogenies have shown extensive lack of resolution, especially among the species-rich and taxonomically challenging ingoids.

Methods: We generated transcriptomes to select low-copy nuclear genes, enrich these via hybrid capture for representative species of most mimosoid genera, and analyze the resulting data using de novo assembly and various phylogenomic tools for species tree inference.

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event.

The consequences of the Cretaceous-Paleogene (K-Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae).

Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies.

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking.

Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes.

Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity.

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes.

Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world.

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.

The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes.

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae).

Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species.

Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity.

Tropical rainforest hyperdiversity is often suggested to have evolved over a long time-span (the 'museum' model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world-wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved.