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Phylogenetic structure on continents. This penalized likelihood rate-smoothed Bayesian consensus phylogeny and the estimated ages were derived from the data and information provided in Lavin et al. (2003). Robinioid legumes are centred mainly in North America but with two clades in the Greater Antilles, and several clades of South American Coursetia. Average nucleotide substitution parameters estimated for likelihood trees at stationarity are r(GT) ¼ 1:000, r(CT) ¼ 6:274, r(CG) ¼ 0:976, r(AT) ¼ 1:792, r(AG) ¼ 3:170, r(AC) ¼ 1:159, p(A) ¼ 0:200, p(C) ¼ 0:273, p(G) ¼ 0:290, p(T) ¼ 0:236, a ¼ 1:383, iP ¼ 0:217. ITS/5.8S: 3.1-3.5 Â 10 À9 subs site À1 yr À1 ; matK: 3.9 Â 10 À10 subs site À1 yr À1 .
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Penalized likelihood estimated ages of both densely sampled intracontinental and sparsely sampled transcontinental crown clades in the legume family show a mostly Quaternary to Neogene age distribution. The mode ages of the intracontinental crown clades range from 4-6 Myr ago, whereas those of the transcontinental crown clades range from 8-16 Myr a...
Citations
... Our choice is considerably older (c. 20-30 Ma) than previous studies that fixed the stem age of this family to 60-70 Ma (e.g., Lavin et al., 2004;Koenen et al., 2020). Therefore, relaxing the stem node constraints would also bolster the confidence in the age estimation of Fabaceae. ...
The Millettioid/Phaseoloid (or the Millettioid) clade is a major lineage of the subfamily Papilionoideae (Fabaceae) that is poorly understood in terms of its diversification and biogeographic history. To fill this gap, we generated a time‐calibrated phylogeny for 749 species representing c . 80% of the genera of this clade using nrDNA ITS, plastid matK , and plastome sequence (including 38 newly sequenced plastomes). Using this phylogenetic framework, we explored the clade's temporal diversification and reconstructed its ancestral areas and dispersal events. Our phylogenetic analyses support the monophyly of the Millettioid/Phaseoloid clade and four of its tribal lineages (Abreae, Desmodieae, Indigofereae, and Psoraleeae), while two tribal lineages sensu lato millettioids and phaseoloids are polyphyletic. The fossil‐calibrated dating analysis showed a nearly simultaneous divergence between the stem node ( c . 62 Ma) and the crown node ( c . 61 Ma) of the Millettioid/Phaseoloid clade in the Paleocene. The biogeographic analysis suggested that the clade originated in Africa and dispersed to Asia, Europe, Australia, and the Americas at different periods in the Cenozoic. We found evidence for shifts in diversification rates across the phylogeny of the Millettioid/Phaseoloid clade throughout the Cenozoic, with a rapid increase in net diversification rates since c . 10 Ma. Possible explanations for the present‐day species richness and distribution of the Millettioid/Phaseoloid clade include boreotropical migration, frequent intra‐ and intercontinental long‐distance dispersals throughout the Cenozoic, and elevated speciation rates following the Mid‐Miocene Climatic Optimum. Together, these results provide novel insights into major diversification patterns of the Millettioid/Phaseoloid clade, setting the stage for future evolutionary research on this important legume clade.
... Indeed, recent studies have linked the emergence and closure of the Isthmus land bridge to approximately 20 Ma, drawing on geological, paleontological, and molecular evidence of biological diversification (Carvalho and Renner, 2012;Bacon et al., 2015;Hoorn and Flantua, 2015;Montes et al., 2016), despite greatly contradicting the classical picture where a fully closed Panamanian Isthmus formed much more recently, at approximately 3 Ma (O'Dea et al., 2016). Whether Harpalyce successfully colonized Central and North America either by over-barrier dispersal or crossing a possibly much older Isthmus land bridge, long-distance dispersal events across oceanic barriers have been frequently invoked in plant biogeography (e.g., Lavin et al., 2004;Renner, 2004;de Queiroz, 2005). Furthermore, plant lineages with amphitropical disjunct distribution across the New World show divergence time estimates significantly earlier, spanning nearly 50 Myr (Cody et al., 2010), with a marked increase in dispersal rates in the early to mid-Miocene (Willis et al., 2014;Simpson et al., 2017). ...
... Indeed, recent studies have linked the emergence and closure of the Isthmus land bridge to approximately 20 Ma, drawing on geological, paleontological, and molecular evidence of biological diversification (Carvalho and Renner, 2012;Bacon et al., 2015;Hoorn and Flantua, 2015;Montes et al., 2016), despite greatly contradicting the classical picture where a fully closed Panamanian Isthmus formed much more recently, at approximately 3 Ma (O'Dea et al., 2016). Whether Harpalyce successfully colonized Central and North America either by over-barrier dispersal or crossing a possibly much older Isthmus land bridge, long-distance dispersal events across oceanic barriers have been frequently invoked in plant biogeography (e.g., Lavin et al., 2004;Renner, 2004;de Queiroz, 2005). Furthermore, plant lineages with amphitropical disjunct distribution across the New World show divergence time estimates significantly earlier, spanning nearly 50 Myr (Cody et al., 2010), with a marked increase in dispersal rates in the early to mid-Miocene (Willis et al., 2014;Simpson et al., 2017). ...
... There is still one intriguing issue involving the prominence of succulents. It is the identity of the so-called 'succulent biome' (further S-Biome; Lavin et al. 2004;Schrire et al. 2005aSchrire et al. , 2005bGagnon et al. 2019;Ringelberg et al. 2020). The S-Biome has been coined by Lavin et al. (2004;Schrire et al. 2005bSchrire et al. -sometimes cited as '2004. ...
... It is the identity of the so-called 'succulent biome' (further S-Biome; Lavin et al. 2004;Schrire et al. 2005aSchrire et al. , 2005bGagnon et al. 2019;Ringelberg et al. 2020). The S-Biome has been coined by Lavin et al. (2004;Schrire et al. 2005bSchrire et al. -sometimes cited as '2004. Schrire et al. (2005b: 23) claim to have considered three gradients (wet to dry, tropical to temperate, fire-history to no fire-history) to distinguish four biomes: S-Succulent, G-Grass, R-Rainforest, T-temperate. ...
The wet Tropics, home to the zonobiome E1, under the strong influence of the high tropical high temperatures and the Intertropical Convergence Zone controlling high precipitation, are shared between the Northern and Southern Hemisphere. The rainforests are shared between four continents (South America, Africa, Asia, and Australia, as well as neighbouring Mesoamerica, Madagascar, Sundaland archipelagos, and numerous islands of the Indian and Pacific Oceans. The chapter focuses on the nature and delimitation of the subtropical rainforests—a biome often neglected or misunderstood. The biome classification of the tropical and subtropical forests reflects the geographic isolation (continents, oceanic archipelagos). Seasonal Tropics, characterised by alternating precipitation-rich and precipitation-poor periods, support two major biomes known as savanna (SAV) and tropical dry forest (TDF). They form a zonobiome E2. The savannas are multi-faced ecosystems, including grasslands and open and closed woodlands. They can be mesic and arid. The unifying functional element is the understory dominated by C4-grasses and the associated importance of recurrent fires. This chapter presents a consolidated hierarchical classification of the savanna, reflecting the continental idiosyncrasies. This chapter pays special attention to the problem of the natural status of the Madagascan savannas (subtropical-tropical grasslands) and the intriguing nature of so-called ‘underground forests’. On the other hand, the TDF is a grass-poor ecosystem and is usually fire-shy. It is widely distributed in the Tropics, but its bioclimatic underpinnings were, until now, poorly analysed. This chapter mitigates this situation by recognising zonal and azonal TDF types and linking the zonal ones to the climatic anomalies of otherwise clearly defined dynamics of the Intertropical Convergence Zone. Particular attention is paid to the bioclimatic underpinnings of Caatinga (a major South American TDF) and the TDF of the Horn of Africa.KeywordsArid savannaCaatingaHorn of AfricaMadagascarMata AtlanticaMesic savannaSubtropical rainforestTropical dry forestTropical rainforestUnderground forests
... This new phylogeny provides the basis for testing the monophyly of genera (the main focus of this paper and of this Special Issue Advances in Legume Systematics (ALS) 14, Part 1), establishing a new higher-level classification of the subfamily (the focus of ALS 14, Part 2) and for downstream analyses of biogeography, trait evolution and diversification (de Faria et al. 2022;Ringelberg et al. 2022). Caesalpinioideae pro-vides an excellent clade for investigating evolutionary diversification and phylogenetic turnover across the lowland tropics (Lavin et al. 2004;Gagnon et al. 2019;Ringelberg et al. 2020Ringelberg et al. , 2022, as well as the evolution of several prominent plant functional traits including compound leaves, armature, extrafloral nectaries and ant associations (Marazzi et al. 2019), agglomeration of pollen into polyads, plant growth forms (Gagnon et al. 2019), floral morphology and pollination syndromes, fruit morphology and seed dispersal syndromes and the ability to form nitrogen-fixing root nodule symbiosis (Sprent et al. 2017;de Faria et al. 2022). However, all of these opportunities require a robust and well-sampled subfamily-wide phylogeny of Caesalpinioideae. ...
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. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
... A good system for investigating repetitive DNA evolution is the South American genus Arachis (Fabaceae) which diverged around 13.8 ± 1.7 MYA (Lavin et al. 2004). It is a natural group (Moretzsohn et al. 2004(Moretzsohn et al. , 2013Bechara et al. 2010;Wang et al. 2019) of 83 annual and perennial species organized in nine taxonomic sections (Krapovickas and Gregory 1994;Simpson 2005, 2017;Valls et al. 2013;Santana and Valls 2015;Seijo et al. 2021). ...
... Keeping this consideration in mind, the period with the highest activity of Athila in almost all Arachis species (except A. paraguariensis) is observed from 10 to 2 MYA. The initial increase of activity was detected around the initial divergence of the genus Arachis estimated in 13.8 ± 1.7 MYA (Lavin et al. 2004); and the peak of activity was coincident with the beginning of genome divergence within section Arachis, estimated in 2.33-4.99 MYA (Moretzsohn et al. 2013;Nielen et al. 2010). ...
Main conclusion
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids.
The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
... Thus, the finding that Dalbergia arose during the Early Miocene allows us to dismiss the hypotheses based on vicariance, and to take into account LDD as the most possible explanation for the pantropical pattern disjunct distribution of this genus. In addition, some previous legumes studies showed that LDD played an important role in the biogeography of several legume taxa, including Apios [44], Canavalia [45], Zornia [46], the tribe Fabeae [47] and legumes in general [48,49]. ...
The genus Dalbergia has a pantropical distribution and comprises approximately 250 species. Previous phylogenetic studies on the genus revealed that Dalbergia is monophyletic and is sister to Machaerium and Aeschynomene sect. Ochopodium. However, due to limited samples or DNA regions in these studies, relationships among the major clades are still unresolved, and divergence dates and biogeographical history of the genus have not been addressed. In this study, phylogenetic analyses of Dalbergia were conducted using broad taxon sampling and a combined dataset of two plastid DNA markers (matK and rbcL) and one nuclear marker (ITS). We evaluated the infrageneric classification of the genus based on the reconstructed tree, and investigated biogeographical history of this genus through molecular dating and ancestral area reconstruction analyses. The monophyly of Dalbergia was strongly supported and the genus was resolved into five major clades with high support, several of which correspond to the previous recognized sections. We inferred that Dalbergia originated in South America during the Early Miocene (c. 22.9 Ma) and achieved its current pantropical distribution through multiple recent transoceanic long-distance dispersals (LDD). We highlighted the important historical events which may explain the pantropical distribution pattern of Dalbergia.
... Nevertheless, despite high DL, trans-oceanic dispersal has been important in shaping the distribution of Mimosoids: trans-continentally distributed Mimosoid clades are common, including five pantropical genera (Entada, Vachellia, Neptunia, Senegalia and Parkia), with 61 (±27) trans-oceanic disjunctions inferred across the phylogeny (Fig. 1, Table S17). Given the Early to Mid-Eocene crown age of Mimosoids ( Fig. 1), these disjunctions and the strong geographical structuring of global Mimosoid phylogenetic turnover are explained not by vicariance (21), but by stochastic sweepstakes long-distance dispersal (22) followed by in-situ diversification within continents, against a backdrop of DL. The percentage of phylogenetic nodes associated with trans-oceanic dispersal, a measure of DL, varies from 6.9% (±3.5%) between 20 and 35 Mya to 2% (±0.9%) in the last 20 Myr (Fig. 1, Table S17), suggesting an early burst of Mimosoid dispersal establishing their pantropical distribution. ...
Early natural historians - Compte de Buffon, von Humboldt and De Candolle - established ecology 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, an iconic pantropical clade with 3,400 species, we show that the water availability gradient from deserts to rainforests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
... The latter may have been facilitated by island chains between continents (stepping-stone dispersal; e.g., Morley, 2003;Harbaugh and Baldwin, 2007;Kainulainen et al., 2017;Ahlstrand et al., 2019) and can be achieved by transport of diaspores in water (e.g., Gallaher et al., 2015), by wind (Muñoz et al., 2004) or animals (e.g., Nogales et al., 2012;Viana et al., 2016) or by rafting of seeds or plants on floating islands (Renner, 2004;van Duzer, 2004). There are many examples of pantropical distributions with trans-Pacific (e.g., Hernandiaceae, Michalak et al., 2010;Monimiaceae, Renner et al., 2010), trans-Atlantic (e.g., Leguminosae, Lavin et al., 2004;Sapotaceae, Bartish et al., 2011;Clusiaceae, Ruhfel et al., 2016;Melastomataceae, Veranso-Libalah et al., 2018) or dispersal across the Indian Ocean (e.g., Arecaceae, Baker and Couvreur, 2013;Rubiaceae, Kainulainen et al., 2017). We might expect some bias in the direction of transoceanic dispersal due to the predominant wind and sea currents (Renner, 2004;Ali and Huber, 2010), albeit over geological times such dispersal seems to have occurred in all directions across angiosperms (e.g., Renner, 2004;de Queiroz, 2005;Crisp et al., 2009;Christenhusz and Chase, 2013). ...
... Beyond further exploring the impact of geography (e.g., geographic barriers) on the historical biogeography within Ochnaceae, a denser, more complete taxon sampling would also enable us to understand how ecology has shaped the evolutionary history of the family. Lessons from globally distributed plant clades that are ecologically confined within biomes suggest the ease with which lineages can transcend geographic barriers (e.g., Lavin et al., 2004;Crisp et al., 2009;Thiv et al., 2011;Gagnon et al., 2019;Ringelberg et al., 2020), i.e., for such groups it seems to be "easier to move than to evolve" (Donoghue, 2008). More biogeographically realistic models have been developed (Landis et al., 2021a,b) that explicitly model the evolutionary accessibility of distinct environments (biomes) that create geographical opportunity (Edwards and Donoghue, 2013), i.e., permitting to reveal when lineages switch between biomes depending on the temporal availability and geographical connectivity of biomes (Landis et al., 2021a,b). ...
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.
... Indeed, if the density of the vessels is high and the VI is low, indicates resistance to water stress and security of water conduction (Carlquist, 1977(Carlquist, , 2001Carlquist & Hoekman, 1985;Parra, 2009 We present an overview of the possible migration routes of the Caesalpinioideae and Detarioideae compiled by Raven and Axelrod (1974), Gentry (1993), Breteler (1999), Magallón et al. (1999, , , Tiffney and Manchester (2001), Lavin et al. (2004) ...
... Due to the lack of fossil records of Fabaceae with consecutive chronologies, numerous investigations proposed an ancient oceanic dispersal for species distributed on both sides of the Atlantic Ocean, Africa and South America (Magallón et al., 1999;Lavin et al., 2004). This is supported by research on extant flora, such as the analysis developed Malpighiaceae (Anderson, 1990;Davis et al., 2004) and ...
... The Fabaceae analysis performed by Lavin et al. (2004) suggests that long-distance dispersal has been the predominant force shaping the distribution of this family. ...
This article presents an analysis of the affinities of legumes from the upper Cenozoic of the lower La Plata Basin (South America) with extant African genera and their implications for paleoecology and paleophytogeography. Permineralized woods, assigned to Entrerrioxylon victoriensis from the Paraná Formation (Upper Miocene), Gossweilerodendroxylon palmariensis and Paraoxystigma concordiensis from the El Palmar Formation (Upper Pleistocene), and Cylicodiscuxylon paragabunensis from the Arroyo Feliciano Formation (Upper Pleistocene), show affinities with extant genera of the Detarioideae and Caesalpinioideae (mimosoid clade). Today, the taxa of the Detarioideae are distributed mainly in tropical regions of Africa, Central America and South America, and the monotypic genus Cylicodiscus is restricted to West Africa from Sierra Leone to Gabon. Currently, Cylicodiscus, Gossweilerodendron, and Oxystigma are not distributed in South America, which implies that in the past they were widely distributed and became extinct in this region at some point during the Pleistocene–Holocene, presumably related to the climatic changes that occurred during this time. The fossil record of the lower La Plata Basin with taxa related to the Detarioideae and Cylicodiscus supports a wider distribution during the Cenozoic as well as an ancient relationship with the tropical forests of West Africa.
