The establishment of Central American migratory corridors and the biogeographic origins of seasonally dry tropical forests in Mexico

A new classification system and taxonomic synopsis for Malpighiaceae (Malpighiales, Rosids) based on molecular phylogenetics, morphology, palynology, and chemistry

Malpighiaceae has undergone unprecedented changes in its traditional classification in the past two decades due to several phylogenetic studies shedding light on the non-monophyly of all subfamilies and most tribes and genera. Even though morphological characters were used to reconstruct the last molecular generic phylogeny of Malpighiaceae, a new classification system has never been proposed for this family. Based on a comprehensive review of the last twenty years of published studies for this family, we propose a new classification system and provide a taxonomic synopsis for Malpighiaceae based on molecular phylogenetics, morphology, palynology, and chemistry as a baseline for the systematics, conservation, and taxonomy of this family worldwide. Malpighiaceae currently comprises two subfamilies (Byrsonimoideae and Malpighioideae), 12 tribes ( Acmanthereae, Acridocarpeaetrib. nov., Barnebyeaetrib. nov., Bunchosieaetrib. nov., Byrsonimeae, Galphimieae, Gaudichaudieae, Hiptageae, Hiraeeae, Malpighieae, Mcvaughieaetrib. nov., and Ptilochaeteaetrib. nov.), 72 genera (incl. Mamedeagen. nov.), and 1,499 accepted species (715 of which are currently under some kind of extinction threat). We present identification keys for all subfamilies, tribes, and genera, a full morphological description for the proposed new genus, the re-circumscription of ten genera alongside the needed new combinations, the proposition of several new synonyms, the typification of several names, and notes on the taxonomy, distribution, conservation, and ecology up to the genus rank. Morphological plates are also provided to illustrate the immense diversity of morphological traits used in the new classification and synopsis.

Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.

The evolutionary history of bees in time and space

Bees are the most significant pollinators of flowering plants. This partnership began ca. 120 million years ago, but the uncertainty of how and when bees spread across the planet has greatly obscured investigations of this key mutualism. We present a novel analysis of bee biogeography using extensive new genomic and fossil data to demonstrate that bees originated in Western Gondwana (Africa and South America). Bees likely originated in the Early Cretaceous, shortly before the breakup of Western Gondwana, and the early evolution of any major bee lineage is associated with either the South American or African land masses. Subsequently, bees colonized northern continents via a complex history of vicariance and dispersal. The notable early absences from large landmasses, particularly in Australia and India, have important implications for understanding the assembly of local floras and diverse modes of pollination. How bees spread around the world from their hypothesized Southern Hemisphere origin parallels the histories of numerous flowering plant clades, providing an essential step to studying the evolution of angiosperm pollination syndromes in space and time.

A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding

Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.

Genetic imprints of Brosimum alicastrum Sw. in Mexico

PREMISE

The mechanisms generating the geographical distributions of genetic diversity are a central theme in evolutionary biology. The amount of genetic diversity and its distribution are controlled by several factors, including dispersal abilities, physical barriers, and environmental and climatic changes. We investigated the patterns of genetic diversity and differentiation among populations of the widespread species Brosimum alicastrum in Mexico.

METHODS

Using nuclear DNA microsatellite data, we tested whether the genetic structure of B. alicastrum was associated with the roles of the Trans-Mexican Volcanic Belt and the Isthmus of Tehuantepec as geographical barriers to gene flow and to infer the role of past events in the genetic diversity patterns. We further used a maximum-likelihood population-effects mixed model (MLPE) to identify the main factor affecting population differentiation in B. alicastrum.

RESULTS

Our results suggested that Mexican B. alicastrum is well differentiated into three main lineages. Patterns of the genetic structure at a finer scale did not fully correspond to the current geographical barriers to gene flow. According to the MLPE mixed model, isolation by distance is the best model for explaining the genetic differentiation of B. alicastrum in Mexico.

CONCLUSIONS

We propose that the differentiation patterns might reflect (1) an ancient differentiation that occurred in Central and South America, (2) the effects of past climatic changes, and (3) the functions of some physical barriers to gene flow. This study provides insights into the possible mechanisms underlying the geographic genetic variation of B. alicastrum along a moisture gradient in tropical lowland forests.

Código de barras de ADN de tres especies de árboles frutales con potencial económico del valle de Huaura, Lima, Perú

El Perú presenta una gran diversidad de recursos genéticos, pero a la vez se desaprovechan especies por desconocimiento o bajo rendimiento económico. Situación que se refleja en el valle de Huaura con los árboles frutales de cansaboca (Bunchosia armeniaca), palillo (Campomanesia lineatifolia) y naranja agria (Citrus aurantium), especies con gran importancia en la gastronomía tradicional local, pero en la actualidad catalogadas en peligro crítico. Con el fin de conservar estas especies se planteó como objetivo establecer código de barras de ADN de tres especies amenazadas con potencial económico del valle de Huaura. Se extrajo ADN de las tres especies con el método CTAB y para las amplificaciones en PCR se emplearon los cebadores de código de barras de ADN universales pertenecientes a cloroplastos: matK, rbcL y trnH-psbA. A partir de los productos purificados y cuantificados se realizó el secuenciamiento de las muestras. Las secuencias fueron analizadas, alineadas y agrupadas con los programas Bioedit, Codon Code Aligner y MEGA respectivamente. Las concentraciones de ADN fueron: palillo (457 ng/μl), cansaboca (433 ng/μl) y naranja agria (442 ng/μl). La amplificación de los cebadores produjo productos de PCR entre 357 y 810 pb. Las secuencias de NCBI que presentaron mayor porcentaje de identidad con cada especie en estudio fueron sometidas a análisis filogenético, los cuales colocaron a las especies en grupos distintos y revelando diferencia genética con las muestras estudiadas. Se proporcionaron las herramientas básicas para implementar códigos de barras de ADN en tres especies de árboles frutales en el valle de Huaura.

Insights into the importance of areas of climatic stability in the evolution and maintenance of avian diversity in the Mesoamerican dry forests

We analysed the phylogeographic structure of five resident bird lineages distributed in the seasonally dry tropical forests (SDTF) of Mesoamerica to test whether they show patterns of synchronous and geographically coincident genetic divergence during the Quaternary. We generated phylogenetic trees, estimated divergence times and analysed the genetic structure of populations (based on sequences of mitochondrial genes), as well as estimating historical distributions (range extension and areas of long-term climate stability) during the Late Pleistocene. We tested and selected the phylogeographic divergence scenarios that best explain the current divergence patterns of taxa using the Approximate Bayesian Computation (ABC) approach. For most species, phylogenetic trees and haplotype networks showed a clear genetic structure associated with geographical distribution. Overall, the divergence times ranged from 0.29–2.0 Mya, suggesting that diversification of populations occurred at different times during the Pleistocene. The palaeodistribution models predicted at least two areas of climatic stability within the current SDTF that probably allowed glacial-interglacial persistence of isolated bird populations along the Mexican Pacific, thus promoting their genetic divergence. The results provide information relevant to the identification of diversification hotspots for the Mesoamerican SDTF avifauna.

Biogeography of Stigmaphyllon (Malpighiaceae) and a Meta-Analysis of Vascular Plant Lineages Diversified in the Brazilian Atlantic Rainforests Point to the Late Eocene Origins of This Megadiverse Biome

We investigated the biogeography of Stigmaphyllon, the second-largest lianescent genus of Malpighiaceae, as a model genus to reconstruct the age and biogeographic history of the Brazilian Atlantic Rainforest (BAF). Few studies to date have focused on the tertiary diversification of plant lineages in the BAFs, especially on Stigmaphyllon. Phylogenetic relationships for 24 species of Stigmaphyllon (18 ssp. From the Atlantic forest (out of 31 spp.), three spp. from the Amazon Rainforest, two spp. from the Caatinga biome, and a single species from the Cerrado biome) were inferred based on one nuclear DNA (PHYC) and two ribosomal DNA (ETS, ITS) regions using parsimony and Bayesian methods. A time-calibrated phylogenetic tree for ancestral area reconstructions was additionally generated, coupled with a meta-analysis of vascular plant lineages diversified in the BAFs. Our results show that: (1) Stigmaphyllon is monophyletic, but its subgenera are paraphyletic; (2) the most recent common ancestor of Stigmaphyllon originated in the Brazilian Atlantic Rainforest/Caatinga region in Northeastern Brazil ca. 26.0 Mya; (3) the genus colonized the Amazon Rainforest at two different times (ca. 22.0 and 6.0 Mya), the Caatinga biome at least four other times (ca. 14.0, 9.0, 7.0, and 1.0 Mya), the Cerrado biome a single time (ca. 15.0 Mya), and the Southern Atlantic Rainforests five times (from 26.0 to 9.0 Mya); (4) a history of at least seven expansion events connecting the Brazilian Atlantic Rainforest to other biomes from 26.0 to 9.0 Mya, and (5) a single dispersion event from South America to Southeastern Asia and Oceania at 22.0 Mya via Antarctica was proposed. Compared to a meta-analysis of time-calibrated phylogenies for 64 lineages of vascular plants diversified in the Brazilian Atlantic Rainforests, our results point to a late Eocene origin for this megadiverse biome.

Multilocus, phenotypic, behavioral, and ecological niche analyses provide evidence for two species within Euphonia affinis (Aves, Fringillidae)

The integration of genetic, morphological, behavioral, and ecological information in the analysis of species boundaries has increased, allowing integrative systematics that better reflect the evolutionary history of biological groups. In this context, the goal of this study was to recognize independent evolutionary lineages within Euphonia affinis at the genetic, morphological, and ecological levels. Three subspecies have been described: E. affinis godmani, distributed in the Pacific slope from southern Sonora to Guerrero; E. affinis affinis, from Oaxaca, Chiapas and the Yucatan Peninsula to Costa Rica; and E. affinis olmecorum from Tamaulipas and San Luis Potosi east to northern Chiapas (not recognized by some authors). A multilocus analysis was performed using mitochondrial and nuclear genes. These analyses suggest two genetic lineages: E. godmani and E. affinis, which diverged between 1.34 and 4.3 My, a period in which the ice ages and global cooling fragmented the tropical forests throughout the Neotropics. To analyze morphometric variations, six morphometric measurements were taken, and the Wilcoxon Test was applied to look for sexual dimorphism and differences between the lineages. Behavioral information was included, by performing vocalization analysis which showed significant differences in the temporal characteristics of calls. Finally, Ecological Niche Models were estimated with MaxEnt, and then compared using the method of Broennimann. These analyses showed that the lineage distributed in western Mexico (E. godmani) has a more restricted niche than the eastern lineage (E. affinis) and thus we rejected the hypotheses of niche equivalence and similarity. Based on the combined evidence from genetic, morphological, behavioral, and ecological data, it is concluded that E. affinis (with E. olmecorum as its synonym) and E. godmani represent two independent evolutionary lineages.

Global Succulent Biome phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae)

The extent to which phylogenetic biome conservatism vs biome shifting determines global patterns of biodiversity remains poorly understood. To address this question, we investigated the biogeography and trajectories of biome and growth form evolution across the Caesalpinia Group (Leguminosae), a clade of 225 species of trees, shrubs and lianas distributed across the Rainforest, Succulent, Temperate and Savanna Biomes. We focused especially on the little-known Succulent Biome, an assemblage of succulent-rich, grass-poor, seasonally dry tropical vegetation distributed disjunctly across the Neotropics, Africa, Arabia and Madagascar. We reconstructed a time-calibrated phylogeny, assembled species occurrence data and assigned species to areas, biomes and growth forms. These data are used to estimate the frequency of transcontinental disjunctions, biome shifts and evolutionary transitions between growth forms and test for phylogenetic biome conservatism and correlated evolution of growth forms and biome shifts. We uncovered a pattern of strong phylogenetic Succulent Biome conservatism. We showed that transcontinental disjunctions confined within the Succulent Biome are frequent and that biome shifts to the Savanna, Rainforest and Temperate Biomes are infrequent and closely associated with shifts in plant growth forms. Our results suggest that the Succulent Biome comprises an ecologically constrained evolutionary arena spanning large geographical disjunctions across the tropics.

Phylogeny of Elatinaceae and the Tropical Gondwanan Origin of the Centroplacaceae(Malpighiaceae, Elatinaceae) Clade

The flowering plant family Elatinaceae is a widespread aquatic lineage inhabiting temperate and tropical latitudes, including ∼35(-50) species. Its phylogeny remains largely unknown, compromising our understanding of its systematics. Moreover, this group is particularly in need of attention because the biogeography of most aquatic plant clades has yet to be investigated, resulting in uncertainty about whether aquatic plants show histories that deviate from terrestrial plants. We inferred the phylogeny of Elatinaceae from four DNA regions spanning 59 accessions across the family. An expanded sampling was used for molecular divergence time estimation and ancestral area reconstruction to infer the biogeography of Elatinaceae and their closest terrestrial relatives, Malpighiaceae and Centroplacaceae. The two genera of Elatinaceae, Bergia and Elatine, are monophyletic, but several traditionally recognized groups within the family are non-monophyletic. Our results suggest two ancient biogeographic events in the Centroplacaceae(Malpighiaceae, Elatinaceae) clade involving western Gondwana, while Elatinaceae shows a more complicated biogeographic history with a high degree of continental endemicity. Our results indicate the need for further taxonomic investigation of Elatinaceae. Further, our study is one of few to implicate ancient Gondwanan biogeography in extant angiosperms, especially significant given the Centroplacaceae(Malpighiaceae, Elatinaceae) clade's largely tropical distribution. Finally, Elatinaceae demonstrates long-term continental in situ diversification, which argues against recent dispersal as a universal explanation commonly invoked for aquatic plant distributions.

Unraveling the biogeographical history of Chrysobalanaceae from plastid genomes

PREMISE OF THE STUDY

The complex geological and climatic history of the Neotropics has had major implications on the diversification of plant lineages. Chrysobalanaceae is a pantropical family of trees and shrubs with 75% of its 531 species found in the Neotropics, and a time-calibrated phylogeny of this family should shed light on the tempo of diversification in the Neotropical flora. Previously published phylogenetic hypotheses of this family were poorly supported, and its biogeography remains unclear.

METHODS

We assembled the complete plastid genome of 51 Chrysobalanaceae species, and increased taxon sampling by Sanger-sequencing of five plastid regions for an additional 88 species. We generated a time-calibrated tree including all 139 Chrsyobalanaceae species and 23 outgroups. We then conducted an ancestral area reconstruction analysis and estimated diversification rates in the family.

KEY RESULTS

The tree generated with the plastid genome alignment was almost fully resolved. It supports the polyphyly of Licania and Hirtella. The family has diversified starting around the Eocene-Oligocene transition. An ancestral area reconstruction confirms a Paleotropical origin for Chrysobalanaceae with several transoceanic dispersal events. The main Neotropical clade likely resulted from a single migration event from Africa around 28 mya ago, which subsequently underwent rapid diversification.

CONCLUSIONS

Given the diverse ecologies exhibited by extant species, we hypothesize that the rapid diversification of Chrysobalanaceae following the colonization of the Neotropics was triggered by habitat specialization during the complex geological and paleoclimatic history of the Neotropics.

Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

PREMISE OF THE STUDY

The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation.

METHODS

Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny.

KEY RESULTS

Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma).

CONCLUSIONS

These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.