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Colonization and Diversification of Melastomataceae in the Atlantic Forest of South America
Abstract
Melastomataceae are the fifth richest plant family in the Atlantic Forest with 544 species belonging to few phylogenetic lineages and present considerable variation in habitat, ecological and reproductive characteristics, and morphology. Some of these lineages are prevailingly centered in the Atlantic Forest, being either endemic (Bertolonieae, Eriocnema, Physeterostemon) and/or highly diverse [Leandra clade (Miconia s.l.), Chaenanthera clade (Miconia s.l.), Discolores clade (Miconia s.l.), Pleroma and Pyramieae] in this biome. In this chapter, we summarize the diversification of Melastomataceae in the Atlantic Forest. Based on the phylogenetic hypothesis generated for the family by Penneys et al. (chapter “A New Melastomataceae Classification Informed by Molecular Phylogenetics and Morphology”), we recovered at least 22 different Melastomataceae lineages currently distributed in the Atlantic Forest, nine of which are highly diverse in the domain. The colonization and diversification events that led to the current distribution of the family in the Atlantic Forest would have occurred during three distinct periods (Miocene, Pliocene and Pleistocene). Moreover, diversification in the AF is heterogeneous, meaning that some AF-centered lineages show higher or lower diversification rates when compared with those outside AF. Future studies on a smaller scale, taking into account putative effects of traits or more specific habitats and regions within and surrounding the AF, should be carried out to explore this diversification heterogeneity.
... This genus also occurs in tropical rainforests in South America, with no significant geographical barriers observed between the Cerrado and Atlantic rainforest (Ratter et al. 2003), where it plays a significant ecological role (Messeder et al. 2021). Miconia stands out as the largest genus in this vegetation but encompassing only three of the 22 lineages of Melastomataceae that diversified in the Atlantic rainforest (Bacci et al. 2022): the Leandra clade (approximately 215 species), Chaenanthera clade (24 species), and Discolores clade (estimated at 77 species) . Consequently, it is expected that the same genus Miconia, observed as an Al-accumulator in the Cerrado, may also exhibit accumulating characteristics in the Atlantic rainforest, where the soil is equally acidic (pH < 4.7) and displays m% above 70% (Mariano et al. 2020). ...
... Cogn., which exhibited Al accumulation exceeding 20,000 mg kg −1 , is phylogenetically distant from the other species (Fig. 5). It belongs to a South-Central American lineage that migrated to the Atlantic coast (Bacci et al. 2022). The other species with extremely high Al accumulation exceeding 20,000 mg kg −1 (Table 3) Bacci et al. 2022), which means that they were until recently placed in the former genus Leandra. ...
... It belongs to a South-Central American lineage that migrated to the Atlantic coast (Bacci et al. 2022). The other species with extremely high Al accumulation exceeding 20,000 mg kg −1 (Table 3) Bacci et al. 2022), which means that they were until recently placed in the former genus Leandra. Similarly, the high Al-accumulating species M. prasina was clustered with M. sellowiana, M. pusilliflora, M. paniculata, M. calvescens, and M. tristis, which showed Al accumulation between 2,000 and 11,000 mg kg −1 , not exceeding 15,000 mg kg −1 (Table 3; Fig. 5). ...
Key message
Miconia predominantly accumulates Al regardless of soil saturation, though certain clades within this high-accumulating group may exhibit distinctly lower Al concentrations in their leaves.
Abstract
In acidic soils (pH < 5.0), aluminum (Al) occurs as Al³⁺, which is toxic to most plants. Tolerant species include Al avoiders and those that accumulate Al in the leaves without toxicity symptoms. The genus Miconia (Melastomataceae), mainly found in moist forests, includes Al-accumulators from the Cerrado vegetation in South America. To explore Al accumulation, we collected Miconia species in four Atlantic rainforest areas, southeastern Brazil, hypothesizing that soil Al saturation (m%) could explain the leaf Al concentration. Both parameters were measured, and a phylogenetic analysis was conducted among the species to ascertain whether Al accumulation resulted from m% or was species dependent. The 27 species found grow on dystrophic soils with m% above 70%. Despite expecting non-accumulators (reported at 15% in the genus), all 27 species were Al-accumulators, some exceeding 25,000 mg Al kg⁻¹ dry leaf, which did not cluster in any specific group in the phylogenetic analysis. Three species (M. willdenowii, M. brunnea, and M. flammea) might have lost the ability to accumulate Al above 1,500 mg kg⁻¹. When the same species occurred at different sites, m% did not drive Al accumulation. Accumulation of Al in Miconia within the Atlantic rainforest stands at a 20-fold higher accumulation range when compared to Miconia spp. from Cerrado. Leaf Al accumulation in Miconia species within the Atlantic rainforest appears to remain unaffected by m%. Within a group where a high capacity for Al accumulation seems to be prevalent, species in certain clades may exhibit distinctly lower Al concentration in their leaves.
Bertolonia crassicaulis is described here as a new species from southeastern areas of the state of Bahia, Brazil. Diagnostic illustrations, field photographs, distribution map, recommended conservation assessment, and a discussion on putative related species based on morphological similarities are provided. This new species can be recognized by the thickened stems in part hidden in the leaf litter and probably with a water storage function, alternate leaves, light green leaf blades with a markedly cordate base, and main veins that are light pink on the abaxial surface. Bertolonia crassicaulis is suggested to be critically endangered (CR).
Evolutionary and ecological processes that influenced the assembly of the New World flora are best understood through investigation of spatio-temporal processes of specific lineages, but some groups still lack a historical overview. Here, we produced a well-sampled dated tree, reconstructed ancestral ranges and performed diversification analyses for Sisyrinchium (Iridaceae) to elucidate its evolution in the Americas. Eight molecular markers and samples representing its full geographical range and morphological diversity were used to estimate divergence times with a Bayesian relaxed clock with secondary calibrations. Ancestral range reconstruction under likelihood methods and diversification analyses were performed. Sisyrinchium originated in a broad range including the Andes and Mesoamerica in the Mid-Miocene. Diversification at high elevations occurred in the early diverging lineages, which feature the highest extinction rates. Increase in diversification rate was detected during the Pliocene/Pleistocene after the colonization of lower elevations. Later sympatric speciation in south-eastern Brazil was followed by movements to other regions, including a long-dispersal event to North America. Higher extinction rates were followed by movements to lower elevations, with periods of accelerated Andean orogeny and global temperature decrease. Our results indicate that palaeoclimate and changes in elevational range influenced diversification in Sisyrinchium.
Systematic studies based on DNA sequences have shown that some traditional tribal delimitations in Melastomataceae remain unresolved, such as the ‘Merianthera and allies’ clade, an informal group which has not been formally assigned to a tribe. This clade includes Behuria, Cambessedesia, Dolichoura, Huberia and Merianthera and occurs mainly at high elevations in the Atlantic Forest and cerrado biomes of Brazil. Behuria, Dolichoura, Huberia and Merianthera were tradionally placed in Merianieae based on overall similar morphology. The assignment of Cambessedesia to Microlicieae has been challenged and its tribal placement needs re-evaluation. To infer the monophyly of the genera and revise generic limits we analysed DNA markers of three plastid (atpF-atpH, psbK-psbL and trnS-trnG), two ribosomal (nrETS and nrITS) and a segment of a low-copy nuclear gene (waxy), using maximum likelihood and Bayesian inference. We also selected 12 morphological characters to reconstruct an ancestral character estimation analysis. Our results recovered Cambessedesia and Merianthera as monophyletic lineages together with monophyletic Huberia and Dolichoura nested in a paraphyletic Behuria. We propose and describe for the first time the tribe Cambessedesieae based on molecular, morphological and geographical data. As recognized here, Cambessedesieae consist of Cambessedesia, Merianthera and an expanded Huberia (including Behuria and Dolichoura).
We propose 31 synonyms for nine South American species of Miconia (Melastomataceae), mostly from the Atlantic Forest in Brazil (with one species in "campos rupestres" and another from the Atlantic Forest in Paraguay); all belong to the 'Miconia discolor clade'. Of these synonyms, 19 are species and 12 are varieties or subspecies, all of them described by the end of the XIX or early XX centuries, and most of them known in herbaria mostly from isotypes or syntypes (except for Miconia cabucu, M. chartacea and M. saldanhae). Miconia flammea var. major is synonymized under M. brunnea; Miconia amambayensis and M. oblongifolia under M. buddlejoides; Miconia augusti, M. divaricata, M. fasciculata subsp. catharinensis, M. fasciculata var. robusta, M. fluminensis, M. gilva, M. rabenii, M. saldanhae, M. saldanhae var. grandifolia and M. saldanhae var. subsessilifolia under M. fasciculata; Miconia chartacea, M. chartacea var. angustifolia, M. chartacea var. brevifolia, M. chartacea var. longifolia and M. chartacea var. miqueliana sob M. flammea; Miconia altissima, M. cabucu, M. formosa var. angustifolia, M. gigantea, M. mourae, and M. ovalifolia under M. formosa; Miconia ovata under M. organensis; Miconia maximowicziana and M. maximowicziana var. major under M. sclerophylla; Miconia eichleri, M. eichleri var. australis, and M. pseudoeichleri under M. valtheri; and Miconia argyraea under M. willdenowii. We also designate lectotypes for all names but M. fasciculata subsp. catharinensis, M. maximowicziana and M. ovata, which already have holotypes designated by the respective authors. We corrected the spelling of M. buddlejoides (previously known as M. budlejoides), M. saldanhae (formerly M. saldanhaei) and M. mourae (formerly M. mouraei). In the present century, 14 species of Miconia s.s. have been described for the Atlantic Forest, and another 43 species, subspecies and varieties have been synonymized (including the ones performed here). This means that a significant inflation of names has been corrected, since the genus has been deflated by 29 taxa. The synonyms proposed here will help students of the family and other researchers employ the correct names in biological studies, which in turn will help to fine tune biodiversity studies and conservation efforts. Resumo Propomos 31 sinônimos para nove espécies sul-americanas de Miconia (Melastomataceae), a maioria delas da Mata Atlântica do Brasil (com uma espécie de campos rupestres e outra da Mata Atlântica do Paraguai); todas do 'clado Miconia discolor'. Desses sinônimos, 19 são espécies e 12 são variedades ou subespécies, todas elas descritas entre o final do século XIX e início do século XX, a maior parte delas conhecidas em herbário por praticamente apenas isótipos ou síntipos (exceções são Miconia cabucu, M. chartacea e M. saldanhae). Miconia flammea var. major é sinonimizada sob M. brunnea; Miconia amambayensis e M. oblongifolia sob M. buddlejoides; Miconia augusti, M. divaricata, M. fasciculata subsp. catharinensis, M. fasciculata var. robusta, M. fluminensis, M. gilva, M. rabenii, M. saldanhae, M. saldanhae var. grandifolia e M. saldanhae var. subsessilifolia sob M. fasciculata; Miconia chartacea, M. chartacea var. angustifolia, M. chartacea var. brevifolia, M. chartacea var. longifolia and M. chartacea var. miqueliana sob M. flammea; Miconia altissima, M. cabucu, M. formosa var. angustifolia, M. gigantea, M. mourae, e M. ovalifolia sob M. formosa; Miconia ovata sob M. organensis; Miconia maximowicziana e M. maximowicziana var. major sob M. sclerophylla; M. eichleri, M. eichleri var. australis e CADDAH ET AL. 284 • Phytotaxa 468 (3) © 2020 Magnolia Press M. pseudoeichleri sob M. valtheri; e Miconia argyraea sob M. willdenowii. Propomos também lectótipos para todos os nomes menos M. fasciculata subsp. catharinensis, M. maximowicziana e M. ovata, que já tinham holótipos designados pelos respectivos autores. Também corrigimos a grafia de M. buddlejoides (conhecida anteriormente por M. budlejoides), M. saldanhae (era M. saldanhaei) e M. mourae (era M. mouraei). Só neste século XXI, 14 espécies de Miconia s.s. já foram descritas para a Mata Atlântica. Por outro lado, outras 43 espécies, subspécies e variedades foram sinonimizadas (incluindo as tratadas aqui). Isso significa que uma inflação relevante de nomes foi corrigida, já que o gênero foi reduzido em 29 táxons. Os sinônimos propostos aqui irão ajudar estudiosos da família e outros pesquisadores a empregar os nomes corretos em estudos biológicos, o que, por sua vez, irá possibilitar um melhor refinamento dos estudos sobre a biodiversidade e dos esforços de conservação.
Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal-extinction-cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder-event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder-event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time-dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non-jump events is assigned a free parameter, j, that when maximized precludes the possibility of non-jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time-dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time-dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state-dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.
Historical biogeography has a diversity of methods for inferring ancestral geographic ranges on phylogenies, but many of the methods have conflicting assumptions, and there is no common statistical framework by which to judge which models are preferable. Probabilistic modeling of geographic range evolution, pioneered by Ree and Smith (2008, Systematic Biology) in their program LAGRANGE, could provide such a framework, but this potential has not been implemented until now.
I have created an R package, "BioGeoBEARS," described in chapter 1 of the dissertation, that implements in a likelihood framework several commonly used models, such as the LAGRANGE Dispersal-Extinction-Cladogenesis (DEC) model and the Dispersal-Vicariance Analysis (DIVA, Ronquist 1997, Systematic Biology) model. Standard DEC is a model with two free parameters specifying the rate of "dispersal" (range expansion) and "extinction" (range contraction). However, while dispersal and extinction rates are free parameters, the cladogenesis model is fixed, such that the geographic range of the ancestral lineage is inherited by the two daughter lineages through a variety of scenarios fixed to have equal probability. This fixed nature of the cladogenesis model means that it has been indiscriminately applied in all DEC analyses, and has not been subjected to any inference or formal model testing.
BioGeoBEARS also adds a number of features not previously available in most historical biogeography software, such as distance-based dispersal, a model of imperfect detection, and the ability to include fossils either as ancestors or tips on a time-calibrated tree.
Several important conclusions may be drawn from this research. First, formal model selection procedures can be applied in phylogenetic inferences of historical biogeography, and the relative importance of different processes can be measured. These techniques have great potential for strengthening quantitative inference in historical biogeography. No longer are biogeographers forced to simply assume, consciously or not, that some processes (such as vicariance or dispersal) are important and others are not; instead, this can be inferred from the data. Second, founder-event speciation appears to be a crucial explanatory process in most clades, the only exception being some intracontinental taxa showing a large degree of sympatry across widespread ranges. This is not the same thing as claiming that founder-event speciation is the only important process; founder event speciation as the only important process is inferred in only one case (Microlophus lava lizards from the Galapagos). The importance of founder-event speciation will not be surprising to most island biogeographers. However, the results are important nonetheless, as there are still some vocal advocates of vicariance-dominated approaches to biogeography, such as Heads (2012, Molecular Panbiogeography of the Tropics), who allows vicariance and range-expansion to play a role in his historical inferences, but explicitly excludes founder-event speciation a priori. The commonly-used LAGRANGE DEC and DIVA programs actually make assumptions very similar to those of Heads, even though many users of these programs likely consider themselves dispersalists or pluralists. Finally, the inclusion of fossils and imperfect detection within the same likelihood and model-choice framework clears the path for integrating paleobiogeography and neontological biogeography, strengthening inference in both.
Model choice is now standard practice in phylogenetic analysis of DNA sequences: a program such as ModelTest is used to compare models such as Jukes-Cantor, HKY, GTR+I+G, and to select the best model before inferring phylogenies or ancestral states. It is clear that the same should now happen in phylogenetic biogeography. BioGeoBEARS enables this procedure. Perhaps more importantly, however, is the potential for users to create and test new models. Probabilistic modeling of geographic range evolution on phylogenies is still in its infancy, and undoubtedly there are better models out there, waiting to be discovered. It is also undoubtedly true that different clades and different regions will favor different processes, and that further improvements will be had by linking the evolution of organismal traits (e.g., loss of flight) with the evolution of geographic range, within a common inference framework. In a world of rapid climate change and habitat loss, biogeographical methods must maximize both flexibility and statistical rigor if they are to play a role. This research takes several steps in that direction.
BioGeoBEARS is open-source and is freely available at the Comprehensive R Archive Network (http://cran.r-project.org/web/packages/BioGeoBEARS/index.html). A step-by-step tutorial, using the Psychotria dataset, is available at PhyloWiki (http://phylo.wikidot.com/biogeobears).
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The effects of global glaciations on the distribution of organisms is an essential element of many diversification models. However, the empirical evidence supporting this idea is mixed, in particular with respect to explaining tropical forest evolution. In the present study, we evaluated the impacts of range shifts associated with Pleistocene global glacial cycles on the evolution of tropical forests. In particular, we tested the predictions: (1) that population genetic structure increases with fragmentation variation between the present and the Last Glacial Maximum (LGM) and also (2) with geographical range instability; and (3) that genetic diversity increases with range stability and (4) decreases with fragmentation variation between periods. To address our predictions, we studied population genetic structures and modelled present and past distributions of 15 Atlantic Forest (AF) endemic birds. Afterwards, we evaluated the relationship of population genetic parameters with metrics of species range shifts between the present and the LGM. We found that geographical ranges of AF birds changed in concert with Pleistocene glacial cycles but, unexpectedly, our findings suggest the novel idea that ranges during glacial maxima were slightly larger on average, as well as equally fragmented and displaced from the interglacial ranges. Our findings suggest that range shifts over the late Pleistocene impacted on the diversification of forest organisms, although they did not show that those range shifts had a strong effect. We found that a combination of fragmentation variation across time, small current range size, and range stability increased population genetic structure. However, neither fragmentation, nor range stability affected genetic diversity. Our study showed that evolutionary responses to range shifts across AF birds have a high variance, which could explain the mixed support given by single-species studies to the action of Pleistocene range shifts on population evolution.
Physeterostemon gomesii is described and illustrated. In addition, a map and a key to all four taxa of this genus are provided. This species can be distinguished from other Physeterostemon species by its non-rhizomatous shrubby habit, 5-merous flowers, 10 stamens, and 3-locular ovary.
The genus Meriania is represented in the Greater Antilles by nine species. Each species is endemic to only one island with five present in Hispaniola, two in Jamaica and two in Cuba. Meriania is absent from Puerto Rico. The two species in Cuba have been traditionally considered as a distinct variety or subspecies of a species also found in Jamaica (M. leucantha), but this study concluded that both deserve status as separate species. Careful examination of the types showed that the most commonly collected Meriania in Cuba had never been formally recognized as a distinct taxon, and it is here described as Meriana albiflora. The other Cuban taxon is here given species status as Meriania angustifolia. We provide a key to species of Meriania in the Greater Antilles, along with complete descriptions and updated nomenclatural and taxonomic notes. Lectotypes are designated for Meriania angustifolia, Meriania bullifera, and Meriania purpurea.
Founder-event speciation, where a rare jump dispersal event founds a new genetically isolated lineage, has long been considered crucial by many historical biogeographers, but its importance is disputed within the vicariance school. Probabilistic modeling of geographic range evolution creates the potential to test different biogeographical models against data using standard statistical model choice procedures, as long as multiple models are available. I re-implement the Dispersal-Extinction-Cladogenesis (DEC) model of LAGRANGE in the R package BioGeoBEARS, and modify it to create a new model, DEC+J, which adds founder-event speciation, the importance of which is governed by a new free parameter, j. The identifiability of DEC and DEC+J is tested on datasets simulated under a wide range of macroevolutionary models where geography evolves jointly with lineage birth/death events. The results confirm that DEC and DEC+J are identifiable even though these models ignore the fact that molecular phylogenies are missing many cladogenesis and extinction events. The simulations also indicate that DEC will have substantially increased errors in ancestral range estimation and parameter inference when the true model includes +J. DEC and DEC+J are compared on 13 empirical datasets drawn from studies of island clades. Likelihood ratio tests indicate that all clades reject DEC, and AICc model weights show large to overwhelming support for DEC+J, for the first time verifying the importance of founder-event speciation in island clades via statistical model choice. Under DEC+J, ancestral nodes are usually estimated to have ranges occupying only one island, rather than the widespread ancestors often favored by DEC. These results indicate that the assumptions of historical biogeography models can have large impacts on inference and require testing and comparison with statistical methods.
The genus Pleiochiton has frequently been recognized by dubious characters and seldom treated in taxonomic and floristic surveys. Nevertheless, monophyly of the genus has been highly supported by recent molecular and morphological data, and it can be morphologically recognized by the epiphytic growth and succulent roots. Following the current circumscription, the genus has 12 species, all endemic to the Atlantic Forest sensu stricto in eastern Brazil. The species occur in well conserved middle elevation forests and most are narrowly distributed, with four recorded from only a single locality. In this paper we present a taxonomic revision of the genus and provide an identification key, distribution maps, descriptions, and illustrations for all species. The new species P. amorimii is described, and the known distribution of the genus is expanded northwards, into the “brejos de altitude” of Pernambuco state.
Studies of the distributions of species of seasonal woodland habitats in South America by means of dot-mapping and phytosociological analyses indicate the presence of three nodal areas: the Caatingas nucleus of arid northeastern Brazil; the Misiones nucleus, comprising a roughly right-angled triangular area enclosed by lines connecting Corumba-Puerto Suarez (Brazil/Bolivia) southward to Resistencia-Corrientes in northern Argentina, and eastward to the upper Uruguay River valley system in Argentinian Misiones and Brazilian Santa Catarina, and thus including most of eastern Paraguay and the west bank of the Paraguay River; and the Piedmont nucleus, which extends from Santa Cruz de la Sierra in Boliva to Tucuman and the sierras of east Catamarca in northwestern Argentina. Distribution maps are presented for over 70 taxa that show this kind of distribution pattern or its modifications. Most of the seasonal woodland species of this affinity are notable by their absence from the cerrado vegetation of central Brazil, although some occur on calcareous outcrops in the general cerrados area, and they also avoid the Chaco of northern Argentina. It is proposed that these fragmentary and mostly disjunct distributional patterns are vestiges of a once extensive and largely contiguous seasonal woodland formation, which may have reached its maximum extension during a dry-cool climatic period ca. 18,000-12,000 BP, coinciding with the contraction of the humid forest.
With 788 species in 67 genera in the Neotropics, Arecaceae are an important ecological and economic component of the region. We review the influence of geological events such as the Pebas system, the Andean uplift and the land connections between South and Central/North America, on the historical assembly of Neotropical palms. We present a case study of the palm genus Astrocaryum (40 species) as a model for evaluating colonization and diversification patterns of lowland Neotropical taxa. We conducted a Bayesian dated phylogenetic analysis based on four low-copy nuclear DNA regions and a biogeographical analysis using the dispersal, extinction and cladogenesis model. Cladogenesis of Western Amazonian Astrocaryum spp. (c. 6 Mya) post-dated the drainage of the aquatic Pebas system, supporting the constraining role of Pebas on in situ diversification and colonization. The ancestral distribution of Astrocaryum spp. in the Guiana Shield supported the hypothesis of an old formation that acted as a source area from which species colonized adjacent regions, but an earliest branching position for Guianan species was not confidently recovered. A twofold increase in diversification rate was found in a clade, the ancestor of which occupied the Guiana Shield (c. 13 Mya, a time of climatic change and Andean uplift).
Historical biogeography is increasingly studied from an explicitly statistical perspective, using stochastic models to describe the evolution of species range as a continuous-time Markov process of dispersal between and extinction within a set of discrete geographic areas. The main constraint of these methods is the computational limit on the number of areas that can be specified. We propose a Bayesian approach for inferring biogeographic history that extends the application of biogeographic models to the analysis of more realistic problems that involve a large number of areas. Our solution is based on a 'data-augmentation' approach, in which we first populate the tree with a history of biogeographic events that is consistent with the observed species ranges at the tips of the tree. We then calculate the likelihood of a given history by adopting a mechanis- tic interpretation of the instantaneous-rate matrix, which specifies both the exponential waiting times between biogeographic events and the relative probabilities of each biogeographic change. We develop this approach in a Bayesian framework, marginalizing over all possible biogeographic histories using Markov chain Monte Carlo (MCMC). Besides dramatically increasing the number of areas that can be accommodated in a biogeographic analysis, our method allows the parameters of a given biogeographic model to be estimated and different biogeographic models to be objectively compared. Our approach is implemented in the program, BayArea.
The Pleistocenic Arc, which must have originated from the climatic
shifts in South America during the late Pleistocene, ranges from the Caatingas
of north-eastern Brazil through south-eastern Brazil to the Paraguay and Paraná
rivers confluence, into south-western Bolivia and north-western Argentina,
and extends sporadically into dry Andean valleys of Peru or coastal western
Ecuador. It is regarded as a new phytogeographic unit for South America, here
named the Tropical Seasonal Forests Region, as it is characterized by a considerable
number of endemic plant taxa at both generic and species level. The paradigm
of the arc is the distribution pattern of Anadenanthera
colubrina
(Fabaceae), which, when superimposed on those of other woody species
of seasonal forests, permits a reasonably accurate mapping of the new region,
which might also have biogeographic implications for endemic bird taxa. The
plant communities of this newly recognized unit are unique in their nature
and floristic composition, when compared with other floristic areas of the
continent by means of classic phytosociological and numerical analyses (PCA).
These ecosystems have remained submerged within other vegetation units in
South American phytogeography (such as the Chaquenian or Amazonian regions),
and have been particularly neglected in conservation policies. An urgent call
is made for these areas to be preserved before they disappear, because they
are located in areas with some of the best agricultural soils of tropical
South America, and therefore subject to clearing for farming.
The relative influence of Neogene geomorphological events and Quaternary climatic changes as causal mechanisms on Neotropical diversification remains largely speculative, as most divergence timing inferences are based on a single locus and have limited taxonomic or geographic sampling. To investigate these influences, we use a multilocus (two mitochondrial and 11 nuclear genes) range-wide sampling of Phyllopezus pollicaris, a gecko complex widely distributed across the poorly studied South American 'dry diagonal' biomes. Our approach couples traditional and model-based phylogeography with geospatial methods, and demonstrates Miocene diversification and limited influence of Pleistocene climatic fluctuations on P. pollicaris. Phylogeographic structure and distribution models highlight that persistence across multiple isolated regions shaped the diversification of this species complex. Approximate Bayesian computation supports hypotheses of allopatric and ecological/sympatric speciation between lineages that largely coincide with genetic clusters associated with Chaco, Cerrado, and Caatinga, standing for complex diversification between the 'dry diagonal' biomes. We recover extremely high genetic diversity and suggest that eight well-supported clades may be valid species, with direct implications for taxonomy and conservation assessments. These patterns exemplify how low-vagility species complexes, characterized by strong genetic structure and pre-Pleistocene divergence histories, represent ideal radiations to investigate broad biogeographic histories of associated biomes.
A new genus, Physeterostemon, with two new species, P. fiaschii and P. jardimii, is described from southern Bahian Atlantic forest of Brazil. The genus can be distinguished from all other Melastomataceae by its 6-merous and diplostemonous flowers, toothed and persistent calyx, inferior ovary and dry, capsular fruits. The androecium consists of stamens that are slightly unequal in size with connectives that are unappendaged or minutely ventrally bituberculate and not prolonged below the thecae but dorsally and apically thickened; the anthers are oblong and rounded apically in ventral view, slightly projecting backwards over the connective in lateral view, but with a single ventral pore.
Gulls (Aves: Larinae) are among the best-studied of birds, yet prior attempts to reconstruct gull relationships have met with little success. In the present study I use 117 characters from the skeleton and 64 from the integument to test gull monophyly and estimate gull phylogeny. One shortest tree, requiring 9747 unweighted changes and having a CI of 0.267, wasLarusis polyphyletic. Although the tree is fully resolved, support for many of the inferred clades is poor. In a comparison of osteological and integumentary evidence, I found that incongruence between the osteological and integumentary character sets accounts for only a minority of the total incongruence observed, and suggest that low between-set incongruence may be a consequence of the low signal-to-noise ratio in each set of characters. I also found that osteological evidence is particularly important for determining higher-level structure, whereas integumentary evidence is important for resolving lower-level relationships within the gull group. Finally, I found that integumentary characters are not dramatically more homoplasious than osteological characters, and argue that casual dismissal of integumentary characters as “too labile”>
Aim To use the method of parsimony analysis of endemism to identify areas of endemism for passerine birds in the Atlantic Forest, South America, and to compare the locations of these areas with areas previously identified for birds as well as other taxa.
Location The Atlantic Forest, eastern South America.
Methods We analysed a matrix composed of the presence (1) or absence (0) of 140 endemic species in 24 quadrats of 1 × 1 degree distributed along the Atlantic Forest to find the most parsimonious area cladogram.
Results Fourteen most parsimonious cladograms were found and then summarized in a single consensus tree. Four areas of endemism were identified: Pernambuco, Central Bahia, Coastal Bahia, and Serra do Mar.
Main conclusions Avian areas of endemism in the Atlantic Forest have significant generality, as they are highly nonrandom and congruent with those of other groups of organisms. A first hypothesis about the historical relationships among the four areas of avian endemism in the Atlantic Forest is delineated. There is a basal dichotomy among areas of endemism in the Atlantic Forest, with Pernambuco forming a northern cluster and Coastal Bahia, Central Bahia and Serra do Mar comprising a southern cluster. Within the southern cluster, Central Bahia and Serra do Mar are more closely related to each other than to Coastal Bahia.
The Neotropical Atlantic Forest is one of the world’s top biodiversity hotspot. Originally, the forest extended over 1.5 million
km2 along the South American Atlantic coast, covering tropical and subtropical climates across highly heterogeneous relief conditions,
which led to outstanding levels of endemism and species richness. Unfortunately, the Atlantic Forest has been historically
altered by humans, which has resulted in severe habitat loss and fragmentation. The forest cover is now reduced to around
12% of its original extent, including regenerating areas and degraded forests, which are mostly spread in small fragments.
As a result, many species are currently threatened to global extinction, with populations collapsing on local and regional
scales. In this chapter, we reviewed the state of the art of Atlantic Forest biodiversity knowledge, pointing out the main
achievements obtained by several research groups during the last decades. Additionally, we (1) propose a new sub-division
of biogeographical sub-regions into 55 sectors considering 2,650 sub-watersheds, using niche theory and bioclimatic data;
(2) describe the original and present distribution of the Atlantic Forest; and (3) relate the forest distribution to elevation
and geomorphometric information (aspect and terrain orientation). Forest protection and restoration efforts, and potential
ecosystem services are also examined as key topics driving the future of the Atlantic Forest biodiversity.
In today's angiosperm-dominated terrestrial ecosystems, leptosporangiate ferns are truly exceptional--accounting for 80% of the approximately 11,000 nonflowering vascular plant species. Recent studies have shown that this remarkable diversity is mostly the result of a major leptosporangiate radiation beginning in the Cretaceous, following the rise of angiosperms. This pattern is suggestive of an ecological opportunistic response, with the proliferation of flowering plants across the landscape resulting in the formation of many new niches--both on forest floors and within forest canopies--into which leptosporangiate ferns could diversify. At present, one-third of leptosporangiate species grow as epiphytes in the canopies of angiosperm-dominated tropical rain forests. However, we know too little about the evolutionary history of epiphytic ferns to assess whether or not their diversification was in fact linked to the establishment of these forests, as would be predicted by the ecological opportunistic response hypothesis. Here we provide new insight into leptosporangiate diversification and the evolution of epiphytism by integrating a 400-taxon molecular dataset with an expanded set of fossil age constraints. We find evidence for a burst of fern diversification in the Cenozoic, apparently driven by the evolution of epiphytism. Whether this explosive radiation was triggered simply by the establishment of modern angiosperm-dominated tropical rain forest canopies, or spurred on by some other large-scale extrinsic factor (e.g., climate change) remains to be determined. In either case, it is clear that in both the Cretaceous and Cenozoic, leptosporangiate ferns were adept at exploiting newly created niches in angiosperm-dominated ecosystems.
Spectral analyses of an uninterrupted 5.5-million-year (My)-long chronology of late Oligocene-early Miocene climate and ocean carbon chemistry from two deep-sea cores recovered in the western equatorial Atlantic reveal variance concentrated at all Milankovitch frequencies. Exceptional spectral power in climate is recorded at the 406-thousand-year (ky) period eccentricity band over a 3.4-million-year period [20 to 23.4 My ago (Ma)] as well as in the 125- and 95-ky bands over a 1.3-million-year period (21.7 to 23.0 Ma) of suspected low greenhouse gas levels. Moreover, a major transient glaciation at the epoch boundary ( approximately 23 Ma), Mi-1, corresponds with a rare orbital congruence involving obliquity and eccentricity. The anomaly, which consists of low-amplitude variance in obliquity (a node) and a minimum in eccentricity, results in an extended period ( approximately 200 ky) of low seasonality orbits favorable to ice-sheet expansion on Antarctica.
The distribution of major clades in Bertolonia (Melastomataceae) is congruent with subareas of the Atlantic Forest, providing an opportunity to estimate ages of historical breaks in the Atlantic Forest, from its major north/south split to more restricted local radiations. The role of niche conservatism in driving diversification of Bertolonia is also analysed and discussed in the light of its historical distribution. We estimated the age of the diversification events, gathered the climatic envelopes of species and clades, generated bioregions for the Atlantic Forest and reconstructed the ancestral areas of speciation for the genus. Our analysis subdivided the Atlantic Forest in five subareas, three of them in the northern and two in the southern Atlantic Forest. We also recovered a deep north/south divergence of the Atlantic Forest in the Oligocene (c. 30 Mya) followed by subsequent local radiations in both regions and a south-eastern/southern division in the Miocene. Later diversification happened mostly from the Mid-Miocene to Pliocene/Pleistocene with several dispersal events, mostly between neighbouring areas. We corroborated this assumption demonstrating that closely related lineages tend to occur in habitats with similar climatic conditions, mainly related to temperature. Our analyses on Bertolonia effectively captured relatively old historical events in the Atlantic Forest, such as the north/south division in the Oligocene and south/south-eastern split in the Miocene, but also recent ones, such as climatic fluctuations and forest fragmentation in the Quaternary. We indicate here for the first time that, for some organisms, the well-known north/south split of the Atlantic Forest could be older than expected. Recent radiation events occurred mainly on a regional basis after this deep division of the domain and the subclades that were recovered showed a significant climatic niche conservatism.
In the past decade, several phylogenetic studies based on molecular data have been generated and changed our view on the evolutionary history and classification of Melastomataceae. Nonetheless, given the size of the family, some groups are still under-sampled and poorly understood, such as the clade formed by Brachyotum and allies in Melastomateae, including three genera, Andesanthus, Brachyotum and Chaetogastra. The principal objective of this work was to further test the relationships in this clade by increasing taxon and locus sampling and by including morphological character reconstructions. In this study, we included nuclear (nrITS, nrETS and waxy) and plastid sequences (accD-psaI, psbK-psbL, trnS-trnG) from 129 species and 29 genera of Melastomataceae, corresponding to c. 46.5% of the species belonging to the clade, and that were used to build phylogenetic hypotheses. We also estimated the evolution of 23 morphological characters through ancestral state reconstruction and the elevational ranges of the species. Our results recovered two major clades: (1) Brachyotum, with species traditionally recognized in Brachyotum, but also including a few species traditionally recognized in Tibouchina; and (2) Chaetogastra, with most species traditionally recognized in Tibouchina, mainly from Tibouchina sections Pseudopterolepis, Diotanthera, Simplicicaules and Purpurella. Andesanthus was placed as sister to Brachyotum and allies in previous phylogenetic analyses; however, in this study it has been recovered as sister to the clades formed by Heterocentron and allies, Monochaetum and allies, and Brachyotum and allies. Four morphological characters can be useful to distinguish genera and clades among Brachyotum and allies: habit; flower position; the angle formed by the petals in relation to the hypanthium; and stamen arrangement. We also find that species in the Brachyotum clade occur at higher elevations (1500–4700 m) than Chaetogastra spp. (sea level to c. 3200 m, but more common at lower elevations, c. 600 to 1800 m). Based on all this evidence we propose the maintenance of Brachyotum as a genus segregated from the recently reinstated Chaetogastra. This work is a contribution to the systematics of Melastomateae, with an improvement in the resolution of the trees in relation to previous phylogenetic analyses, indicating that subclades have a strong relationship with geographical distribution.
We present a new species, a new synonym, the resurrection of a species that has been synonymized before, updates on the distribution of three species, and lectotypifications for two species of Meriania from the Brazilian Atlantic Forest. Meriania baumgratziana is a new species apparently restricted to montane areas in the western portion of the state of Rio de Janeiro. It can be recognized by the sessile to subsessile leaves, these lanceolate, elliptic lanceolate or oblong-lanceolate, with cordate to cordulate, amplexicaul bases (seldom narrowly round), the abaxial surface in young leaves with the union of the primary and the inner pair of secondary veins with a membrane forming pocket domatia, these with trichomes emerging from the inside, then in older leaves the membranes frequently enlarged, globular, these hypertrophied structures sometimes caducous, or easily removed by friction, and by the pendulous inflorescences with 4-merous flowers. Meriania paratyensis Chiavegatto & Baumgratz is synonymized under M. sanchezii R.Goldenb., which in turn is resurrected from what we understand as a mistaken synonymy under M. paniculata DC. We present a discussion and illustrations of leaves and fruits, in order to explain these changes and compare all these three species, plus a fourth similar species, M. glabra (DC.) Naudin. The distributions of Meriania calyptrata (Naudin) Triana and M. sanchezii are updated, the former with the inclusion of specimens collected in the western tip of the state of Rio de Janeiro (it was previously recorded only for eastern São Paulo), and the latter in the exactly opposite way, with new records from Rio de Janeiro added to the previously known specimens from São Paulo. Finally, lectotypes are designated for Meriania calyptrata and M. glabra (DC.) Naudin (this superseding a previous, unnecessary designation of a neotype).
Several centers of endemism have been proposed for Melastomataceae, particularly in Amazonia and Atlantic Forest. Despite the high degree of human-caused degradation in the last 500 years, the Atlantic Forest still presents some of the largest levels of diversity and endemism across all angiosperms. With several recently described species in the last decade, the knowledge on Bertolonia’s distribution and morphological characterization has changed, with most new species found in northern Atlantic Forest and with different flower color patterns than the species from southern Atlantic Forest. We first tested the monophyly of the genus sampling over 85% of its species to generate a reliable phylogenetic hypothesis. Afterwards, we used Bertolonia as a model group to study distribution patterns and morphological evolution of lineages in the Atlantic Forest. Bertolonia is particularly interesting to address such questions because it is endemic to this domain, with species distributed either in the southern, central or northern portions of the Atlantic Forest. The second step of our work aimed to respond (1) Do closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological traits? and (2) Are floral traits more conserved within clades than vegetative characters? We hypothesize that both (1) and (2) are true due to the low dispersal ability and consequent microendemic distribution of most species in the genus. Our results confirm the veracity of the proposed hypotheses. Three major groups were recovered in our analysis: marmorata, formosa and nymphaeifolia clades. Most species that occur in northern Atlantic Forest were recovered in the marmorata clade. Most species distributed in central Atlantic Forest were recovered in the formosa clade, and the ones from the southern Atlantic Forest in the nymphaeifolia clade. A similar pattern was recovered with reproductive characters reconstructed across the phylogeny. Generally, species with pink petals and cream-colored anthers with an extrorse pore occur in northern Atlantic Forest, and species with white petals and yellow anthers with an introrse or apical pore tend to occur in southern Atlantic Forest. Some vegetative characters also have evolutionary congruence and are restricted to one or few lineages, while other characters, such as the texture of the leaf blades surface have a strong taxonomic value, being useful to identify species, but are not homologous. Our analysis also indicates that the division of southern and northern Atlantic Forest could also be related to ancient events, not only linked with recent phylogeographic patterns. Moreover, we suggest that the orientation of the anther’s pore in Bertolonia could be related with diversity of species and stability of its populations. In summary, we corroborate, based on the evolutionary history of Bertolonia, that closely related species endemic to Atlantic Forest tend to have similar distributions and share similar morphological floral traits.
Tibouchina (Melastomataceae: Melastomateae) is an exclusively Neotropical genus that currently includes close to 310 species. These were first described or assigned to 16 other genera, a reflection of the complex taxonomic and phylogenetic history of the genus. Previous phylogenetic analyses have shown that the genus is polyphyletic. Here we present an expanded analysis that includes representatives of 28 genera of New World Melastomateae, as well as representatives of Old World Melastomateae and members of the Marcetieae and Microlicieae. Over 300 species were sequenced for nrITS and the plastid spacers accD‐psaI and psbK‐psbL. We recovered a large clade of Neotropical Melastomateae that contains Tibouchina along with at least 13 other Neotropical genera. Moreover, Tibouchina is not recovered as monophyletic because three mostly Central American and five mostly Andean genera are nested within it, albeit each these genera are recovered as monophyletic. Many of the previously recognized sections of Tibouchina are recovered as monophyletic or paraphyletic providing a basis for a new classification. Tibouchina is here re‐circumscribed into four genera that are each monophyletic and easily diagnosable. This results in a narrowly circumscribed Tibouchina and the re‐establishment of Pleroma and Chaetogastra, and the description of a new genus, Andesanthus. Pleroma now also includes Itatiaia, Microlepis and Svitramia. Brachyotum is maintained until its relationship to Chaetogastra can be further examined. This new taxonomic arrangement is more informative and convenient than merging eight other genera into Tibouchina. An identification key, descriptions of genera, and lists of taxa with their current generic assignment and necessary nomenclatural novelties are also presented here.
Leandra s.str. clade has around 200 species nearly restricted to eastern Brazil. Most species in this group are narrow endemics, but a few present striking disjunct distributions between eastern Brazil and Andes or Mesoamerica. Given the predominantly “montane” distribution observed in most Leandra s.str., we hypothesized that cyclical range expansions during colder Pleistocene periods, followed by local extinctions during warmer interglacial periods, could have shaped the distribution of the disjunct species in this clade. In order to gather support for this biogeographical scenario in a phylogenetic framework, the species that occur outside eastern Brazil were identified, ages of the dispersal events estimated, climatic niche models for the disjuncts were generated, and the climatic envelope of these species compared. Our results place all dispersal events from eastern Brazil to Andes or Mesoamerica during the Pleistocene. Climatic niche modeling indicates a potential range expansion during the Pleistocene colder times for the disjunct species. Although the surpassing of the “dry diagonal” could have been facilitated during glacial periods, this open corridor is an effective barrier for Leandra, given the reduced number of species that dispersed beyond an eastern Brazilian origin. Additionally, the disjunct species do not present significant differences in their climatic envelopes to the non‐disjunct species. Our results provide support to a short‐dispersion/stepping‐stone migration scenario to account for the observed disjunctions in this clade. Range expansions during Pleistocene colder periods followed by local extinctions during interglacial periods could have shaped the distribution of Leandra s.str.
Miconia is the largest genus restricted to the Neotropics, with about 1060 species, and one of the biggest in Mata Atlântica, with 115 species. As currently defined, Miconia is clearly polyphyletic with no clear boundaries to the other genera in the Miconieae. Moreover, the traditional infrageneric classification does not reflect the evolutionary history of the group, thus limiting its utility for identification and monographic purposes. Miconia sect. Chaenanthera and M. sect. Jucunda are two sections mostly restricted to Mata Atlântica that have previously been shown to belong to a single clade (Chaenanthera clade), despite being morphologically distinct from each other. In this paper, we provide a new phylogenetic hypothesis for the Chaenanthera clade with an expanded sampling of both taxa and molecular markers, in order to provide a base for future taxonomic studies. Given the incongruent patterns observed across different markers in our preliminary analyses, a phylogenetic network was also estimated for the group. The history of some morphological characters was reconstructed and the phylogenetic position of a few molecularly unsampled species was estimated based on their morphology. The Chaenanthera clade was corroborated with strong support, although resolution is still unsatisfactory for several relationships within the group. Individual flower-related characters do not reliably predict phylogenetic relationships in this group. Morphological diagnostic characters for above species taxa will demand character combinations and likely the inclusion of other sources of information. We also present the first line of evidence supporting the presence of reticulation shaping the history of the Chaenanthera clade. The concerted effect of incongruent signal, limited variability, incomplete lineage sorting and reticulation events, is certainly a major force driving the phylogenetic support recovered in our analyses, and likely in several other published trees across Melastomataceae. © International Association for Plant Taxonomy (IAPT) 2018, All rights reserved.
Ficus (Moraceae) is well diversified in the Neotropics with two lineages inhabiting the wet forests of this region. The hemiepiphytes of section Americanae are the most diversified with c. 120 species, whereas section Pharmacosycea includes about 20 species mostly with a terrestrial habit. To reconstruct the biogeographical history and diversification of Ficus in the Americas, we produced a dated Bayesian phylogenetic hypothesis of Neotropical Ficus including two thirds of the species sequenced for five nuclear regions (At103, ETS, G3pdh, ITS/5.8S and Tpi). Ancestral range was estimated using all models available in Biogeobears and Binary State Speciation and Extinction analysis was used to evaluate the role of the initial habit and propagule size in diversification. The phylogenetic analyses resolved both Neotropical sections as monophyletic but the internal relationships between species in section Americanae remain unclear. Ficus started their diversification in the Neotropics between the Oligocene and Miocene. The genus experienced two bursts of diversification: in the middle Miocene and the Pliocene.Colonization events from the Amazon to adjacent areas coincide with the end of the Pebas system (10 Mya) and the connection of landmasses. Divergence of endemic species in the Atlantic forest is inferred to have happened after its isolation and the opening and consolidation of the Cerrado. Our results suggest a complex diversification in the Atlantic forest differing between postulated refuges and more instable areas in the South distribution of the forest. Finally the selection for initial hemiepiphytic habit and small to medium propagule size influenced the diversification and current distribution of the species at Neotropical forests marked by the historical instability and long-distance dispersal.
A taxonomic monograph of a re-circumscribed Leandra sect. Leandra is presented. The new circumscription is based on a previous phylogenetic hypothesis, and diagnostic morphological characters are discussed. Four new combinations to Leandra are proposed, one from Clidemia (L. capilliflora) and three from Ossaea (L. capitata, L. cogniauxii and L. loligomorpha). Additionally, eight species are treated as synonyms for the first time, and 15 lectotypes are designated. A review of the 17 recognized species, including descriptions, synonymy, illustrations and distribution maps, is provided. This work also includes an overview of general morphology, leaf and flower anatomy, phenology and geographical distribution. Species with a history of taxonomic problems and/or with distinctive morphotypes are further investigated with morphometrics tools.
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE methods. Specifically, our model, which we refer to as HiSSE (Hidden-State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification (CID) models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.
Gesneriaceae are represented in the New World (NW) by a major clade (c. 1000 species) currently recognized as subfamily Gesnerioideae. Radiation of this group occurred in all biomes of tropical America and was accompanied by extensive phenotypic and ecological diversification. Here we performed phylogenetic analyses using DNA sequences from three plastid loci to reconstruct the evolutionary history of Gesnerioideae and to investigate its relationship with other lineages of Gesneriaceae and Lamiales. Our molecular data confirm the inclusion of the South Pacific Coronanthereae and the Old World (OW) monotypic genus Titanotrichum in Gesnerioideae and the sister-group relationship of this subfamily to the rest of the OW Gesneriaceae. Calceolariaceae and the NW genera Peltanthera and Sanango appeared successively sister to Gesneriaceae, whereas Cubitanthus, which has been previously assigned to Gesneriaceae, is shown to be related to Linderniaceae. Based on molecular dating and biogeographical reconstruction analyses, we suggest that ancestors of Gesneriaceae originated in South America during the Late Cretaceous. Distribution of Gesneriaceae in the Palaeotropics and Australasia was inferred as resulting from two independent long-distance dispersals during the Eocene and Oligocene, respectively. In a short time span starting at 34Mya, ancestors of Gesnerioideae colonized several Neotropical regions including the tropical Andes, Brazilian Atlantic forest, cerrado, Central America and the West Indies. Subsequent diversification within these areas occurred largely in situ and was particularly extensive in the mountainous systems of the Andes, Central America and the Brazilian Atlantic forest. Only two radiations account for 90% of the diversity of Gesneriaceae in the Brazilian Atlantic forest, whereas half of the species richness in the northern Andes and Central America originated during the last 10 Myr from a single radiation.
Molecular phylogenetic studies have become a major area of interest in plant systematics, and their impacts on historical biogeographic hypotheses are not to be disregarded. In Brazil, most historical biogeographic studies have relied on animal phylogenies, whereas plant biogeographic studies have largely lacked a phylogenetic component, having a limited utility for historical biogeography. That country, however, is of great importance for most biogeographic studies of lowland tropical South America, and it includes areas from a number of biogeographic regions of the continent. Important biogeographic reports have been published as part of phylogenetic studies, taxonomic monographs, and regional accounts for small areas or phytogeographic domains, but the available information is subsequently scattered and sometimes hard to find. In this paper we review some relevant angiosperm biogeographic studies in Brazil. Initially we briefly discuss the importance of other continents as source areas for the South American flora. Then we present a subdivision of Brazil into phytogeographic domains, and we cite studies that have explored the detection of biogeographic units (areas of endemism) and how they are historically related among those domains. Examples of plant taxa that could be used to test some biogeographic hypotheses are provided throughout, as well as taxa that exemplify several patterns of endemism and disjunction in the Brazilian angiosperm flora.
Quantification in historical biogeography has usually been based on the search for a single branching relationship among areas of endemism. Unlike organisms, however, areas rarely have a unique hierarchical history. Dispersal barriers appear and disappear and may have different effects on different species. As a result, the biota of an area may consist of several components with separate histories, each of which may be reticulate rather than branching. In an attempt to address these problems, I present a new biogeographic method, dispersal-vicariance analysis, which reconstructs the ancestral distributions in a given phylogeny without any prior assumptions about the form of area relationships. A three-dimensional step matrix based on a simple biogeographic model is used in the reconstruction. Speciation is assumed to subdivide the ranges of widespread species into vicariant components; the optimal ancestral distributions are those that minimize the number of implied dispersal and extinction events. Exact algorithms that find the optimal reconstruction(s) are described. In addition to their use in taxon biogeography, the inferred distribution histories of individual groups serve as a basis for the study of general patterns in historical biogeography, particularly if the relative age of the nodes in the source cladograms is known.
Aim We aim to propose validated, spatially explicit hypotheses for the late Quaternary distribution of the Brazilian Atlantic forest, and thereby provide a framework for integrating analyses of species and genetic diversity in the region.
Location The Atlantic forest, stretching along the Brazilian coast.
Methods We model the spatial range of the forest under three climatic scenarios (current climate, 6000 and 21,000 years ago) with BIOCLIM and MAXENT. Historically stable areas or refugia are identified as the set of grid cells for which forest presence is inferred in all models and time projections. To validate inferred refugia, we test whether our models are matched by the current distribution of the forest and by fossil pollen data. We then investigate whether the location of inferred forest refugia is consistent with current patterns of species endemism and existing phylogeographical data.
Results Forest models agree with pollen records and predict a large area of historical forest stability in the central corridor (Bahia), as well as a smaller refuge (Pernambuco) along the Brazilian coast, matching current centres of endemism in multiple taxa and mtDNA diversity patterns in a subset of the species examined. Less historical stability is predicted in coastal areas south of the Doce river, which agrees with most phylogeographical studies in that region. Yet some widely distributed taxa show high endemism in the southern Atlantic forest. This may be due to limitations of the modelling approach, differences in ecology and dispersal capability, historical processes not contemplated by the current study or inadequacy of the available test data sets.
Main conclusions Palaeoclimatic models predict the presence of historical forest refugia in the Atlantic rain forest and suggest spatial variation in persistence of forests through the Pleistocene, predicting patterns of biodiversity in several local taxa. The results point to the need for further studies to document genetic and species endemism in the relatively poorly known and highly impacted areas of Atlantic rain forests of north‐eastern Brazil.
Until now, Quaternary paleoecologists have regarded evolution as a slow process relative to climate change, predicting that the primary biotic response to changing climate is not adaptation, but instead (1) persistence in situ if changing climate remains within the species' tolerance limits, (2) range shifts (migration) to regions where climate is currently within the species' tolerance limits, or (3) extinction. We argue here that all three of these outcomes involve evolutionary processes. Genetic differentiation within species is ubiquitous, commonly via adaptation of populations to differing environmental conditions. Detectable adaptive divergence evolves on a time scale comparable to change in climate, within decades for herbaceous plant species, and within centuries or millennia for longer-lived trees, implying that biologically significant evolutionary response can ac- company temporal change in climate. Models and empirical studies suggest that the speed with which a population adapts to a changing environment affects invasion rate of new habitat and thus migration rate, population growth rate and thus probability of extinction, and growth and mortality of individual plants and thus productivity of regional vegetation. Recent models and experiments investigate the stability of species tolerance limits, the influence of environmental gradients on marginal populations, and the interplay of de- mography, gene flow, mutation rate, and other genetic processes on the rate of adaptation to changed environments. New techniques enable ecologists to document adaptation to changing conditions directly by resurrecting ancient populations from propagules buried in decades-old sediment. Improved taxonomic resolution from morphological studies of macrofossils and DNA recovered from pollen grains and macroremains provides additional information on range shifts, changes in population sizes, and extinctions. Collaboration between paleoecologists and evolutionary biologists can refine interpretations of paleo- records, and improve predictions of biotic response to anticipated climate change.
The Plio-Pleistocene refugia hypothesis recently gained support in explaining Brazilian Atlantic Forest megadiversity from combined analyses of species paleodistributions and genetic diversity. Here we examine genetic differentiation and historical distributions in the Rhinella crucifer group of toads, endemic to and widely distributed within this biome. We analyzed sequences of mitochondrial (control region, ND1, and ND2) and nuclear (beta-crystallin and rhodopsin) DNA markers from 65 individuals representing five species. We found deep structure across the range at mitochondrial markers; genetic diversity is geographically structured in four main haplotype clades with the oldest divergence, dated to the Pliocene, between the southernmost populations and other regions of the species' range. Remaining populations are distributed in haplotype clades that may have diverged throughout the Pleistocene. Our paleoecological distribution models support a scenario of habitat fragmentation associated with glacial cycling, but we found limited congruence of phylogeographic patterns with the refugia. We found that some genetic breaks geographically coincide with putative barriers associated to neotectonic activity, but finer-scale sampling will be necessary to test the relative importance of distinct isolation mechanisms. Overall, the data refute the recently proposed hypothesis of a southern Holocene colonization of the Atlantic Forest from northern refugia, suggesting instead persistence of forested habitats in the south. Our unexpected results underscore the need to consider distinct organismal histories in planning biome-level conservation. We discuss species correspondence to clades recovered in our phylogenetic analyses.
Conservationists are far from able to assist all species under threat, if only for lack of funding. This places a premium on priorities: how can we support the most species at the least cost? One way is to identify 'biodiversity hotspots' where exceptional concentrations of endemic species are undergoing exceptional loss of habitat. As many as 44% of all species of vascular plants and 35% of all species in four vertebrate groups are confined to 25 hotspots comprising only 1.4% of the land surface of the Earth. This opens the way for a 'silver bullet' strategy on the part of conservation planners, focusing on these hotspots in proportion to their share of the world's species at risk.
At a time when historical biogeography appears to be again expanding its scope after a period of focusing primarily on discerning area relationships using cladograms, new inference methods are needed to bring more kinds of data to bear on questions about the geographic history of lineages. Here we describe a likelihood framework for inferring the evolution of geographic range on phylogenies that models lineage dispersal and local extinction in a set of discrete areas as stochastic events in continuous time. Unlike existing methods for estimating ancestral areas, such as dispersal-vicariance analysis, this approach incorporates information on the timing of both lineage divergences and the availability of connections between areas (dispersal routes). Monte Carlo methods are used to estimate branch-specific transition probabilities for geographic ranges, enabling the likelihood of the data (observed species distributions) to be evaluated for a given phylogeny and parameterized paleogeographic model. We demonstrate how the method can be used to address two biogeographic questions: What were the ancestral geographic ranges on a phylogenetic tree? How were those ancestral ranges affected by speciation and inherited by the daughter lineages at cladogenesis events? For illustration we use hypothetical examples and an analysis of a Northern Hemisphere plant clade (Cercis), comparing and contrasting inferences to those obtained from dispersal-vicariance analysis. Although the particular model we implement is somewhat simplistic, the framework itself is flexible and could readily be modified to incorporate additional sources of information and also be extended to address other aspects of historical biogeography.
Rapid diversification of a species-rich genus of Neotropical rain forest trees
- J E Richardson
- R T Pennington
- T D Pennington
- Hollingsworth
Richardson JE, Pennington RT, Pennington TD, Hollingsworth (2001) Rapid diversification of a
species-rich genus of Neotropical rain forest trees. Science 293:2242-2245
Estudos taxonômicos e filogenéticos em Miconia sect. Discolor (Melastomataceae, Miconieae)
- M K Caddah
Jardim Botânico do Rio de Janeiro
- Jfa Baumgratz
Baumgratz JFA (2020) Leandra in Flora do Brasil 2020. Jardim Botânico do Rio de Janeiro.
Available at: http://floradobrasil.jbrj.gov.br/reflora/floradobrasil/FB9496. Accessed 15
Aug 2021
Revisão taxonômica do gênero Meriania Sw. (Melastomataceae) no Brasil
- B Chiavegatto
Hidden state models improve state-dependent diversification approaches, including biogeographical models
- D S Caetano
- B C Meara
- J M Beaulieu
Melastomataceae in Flora do Brasil 2020
- R Goldenberg
- Jfa Baumgratz
- F A Michelangeli
- Pjf Guimarães
- R Romero
- Afa Versiane
- K Fidanza
- R R Völtz
- D N Silva
- Lfg Lima
- K C Silva-Gonçalves
- L F Bacci
- J C Fontelas
- R Pacifico
- E S Brito
- Mjr Rocha
- M K Caddah
- J Meirelles
- P Rosa
- R Ferreira-Alves
- Aka Santos
- Kvc Moreira
- M Reginato
- Lfa Oliveira
- A Freire-Fierro
- Ama Amorim
- A B Martins
- C Koschnitzke
- Almeda F Jesus
- J C Hinoshita
- Lkr Kriebel
Goldenberg R, Baumgratz JFA, Michelangeli FA, Guimarães PJF, Romero R, Versiane AFA,
Fidanza K, Völtz RR, Silva DN, Lima LFG, Silva-Gonçalves KC, Bacci LF, Fontelas JC,
Pacifico R, Brito ES, Rocha MJR, Caddah MK, Meirelles J, Rosa P, Ferreira-Alves R, Santos
AKA, Moreira KVC, Reginato M, Oliveira LFA, Freire-Fierro A, Amorim AMA, Martins AB,
Koschnitzke C, Almeda F, Jesus JC, Hinoshita LKR, Kriebel R (2020a). Melastomataceae
in Flora do Brasil 2020. Jardim Botânico do Rio de Janeiro. http://floradobrasil.jbrj.gov.br/
reflora/floradobrasil/FB161. Accessed 15 Aug 2021