We examined global records of accessible natural history voucher collections (with publicly available data) for terrestrial and freshwater vascular plants, fungi, freshwater fishes, birds, mammals, and herpetofauna (amphibians and reptiles) and highlight areas of the world that would be considered undersampled and sometimes called “unexplored” ( i . e ., have relatively low, or no evidence of, past sampling efforts) under typical Western-scientific descriptions. We also question what “unexplored” may actually mean in these contexts and explain how retiring the term in favor of more nuanced phrasing can mitigate future misunderstandings of natural history science.### Competing Interest StatementThe authors have declared no competing interest.

Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.

Premise: Seed dispersal is a critical process impacting individual plants and their communities. Plants have evolved numerous strategies and structures to disperse their seeds, but the evolutionary drivers of this diversity remain poorly understood in most lineages. We tested the hypothesis that the evolution of wind dispersal traits within the melicgrasses (Poaceae: Meliceae Link ex Endl.) was correlated with occupation of open and disturbed habitats. Methods: To evaluate wind dispersal potential, we collected seed dispersal structures (diaspores) from 24 melicgrass species and measured falling velocity and estimated dispersal distances. Species' affinity for open and disturbed habitats were recorded using georeferenced occurrence records and land cover maps. To test whether habitat preference and dispersal traits were correlated, we used phylogenetically informed multilevel models. Results: Melicgrasses display several distinct morphologies associated with wind dispersal, suggesting likely convergence. Open habitat taxa had slower-falling diaspores, consistent with increased wind dispersal potential. However, their shorter stature meant that dispersal distances, at a given wind speed, were not higher than those of their forest-occupying relatives. Species with affinities for disturbed sites had slower-falling diaspores and greater wind dispersal distances, largely explained by lighter diaspores. Conclusions: Our results are consistent with the hypothesized evolutionary relationship between habitat preference and dispersal strategy. However, phylogenetic inertia and other plant functions (e.g., water conservation) likely shaped dispersal trait evolution in melicgrasses. It remains unclear if dispersal trait changes were precipitated by or predated changing habitat preferences. Nevertheless, our study provides promising results and a framework for disentangling dispersal strategy evolution.

The Andes mountains of western South America are a globally important biodiversity hotspot, yet there is a paucity of resolved phylogenies for plant clades from this region. Filling an important gap in our understanding of the World's richest flora, we present the first phylogeny of Freziera (Pentaphylacaceae), an Andean-centered, cloud forest radiation. Our dataset was obtained via hybrid-enriched target sequence capture of Angiosperms353 universal loci for 50 of the ca. 75 spp., obtained almost entirely from herbarium specimens. We identify high phylogenomic complexity in Freziera, including the presence of data artifacts. Via by-eye observation of gene trees, detailed examination of warnings from recently improved assembly pipelines, and gene tree filtering, we identified that artifactual orthologs (i.e., the presence of only one copy of a multicopy gene due to differential assembly) were an important source of gene tree heterogeneity that had a negative impact on phylogenetic inference and support. These artifactual orthologs may be common in plant phylogenomic datasets, where multiple instances of genome duplication are common. After accounting for artifactual orthologs as source of gene tree error, we identified a significant, but nonspecific signal of introgression using Patterson's D and f4 statistics. Despite phylogenomic complexity, we were able to resolve Freziera into 9 well-supported subclades whose evolution has been shaped by multiple evolutionary processes, including incomplete lineage sorting, historical gene flow, and gene duplication. Our results highlight the complexities of plant phylogenomics, which are heightened in Andean radiations, and show the impact of filtering data processing artifacts and standard filtering approaches on phylogenetic inference.

Two species of Podostemaceae, with few previous georeferenced records West of the Andes in northern South America, are reported across the Andes in the region. Our records document a wider range of the Podostemaceae in the tropical Andes and result from recent floristic explorations in Andean rivers in Ecuador and Colombia. These new records are of use for future research in the group, as well as for conservation projects in rivers. We call for international collaborative projects supporting local collectors and institutions in Latin America to bolster research in the under-collected river plants and assess their distribution. We extend the invitation to local scientists to get their feet wet and collect plants in river-rapids and waterfalls.

AbstractPremiseRubiaceae is among the most species‐rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large‐scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single‐copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae‐specific probe set that allows for comparable phylogenetic inference across clades is lacking.MethodsHere, we use publicly accessible genomic resources to identify putatively single‐copy nuclear loci for target enrichment in two Rubiaceae groups: tribe Hillieae (Cinchonoideae) and tribal complex Palicoureeae+Psychotrieae (Rubioideae). We sequenced 2270 exonic regions corresponding to 1059 loci in our target clades and generated in silico target enrichment sequences for other Rubiaceae taxa using our designed probe set. To test the utility of our probe set for phylogenetic inference across Rubiaceae, we performed a coalescent‐aware phylogenetic analysis using a subset of 27 Rubiaceae taxa from 10 different tribes and three subfamilies, and one outgroup in Apocynaceae.ResultsWe recovered an average of 75% and 84% of targeted exons and loci, respectively, per Rubiaceae sample. Probes designed using genomic resources from a particular subfamily were most efficient at targeting sequences from taxa in that subfamily. The number of paralogs recovered during assembly varied for each clade. Phylogenetic inference of Rubiaceae with our target regions resolves relationships at various scales. Relationships are largely consistent with previous studies of relationships in the family with high support (≥0.98 local posterior probability) at nearly all nodes and evidence of gene tree discordance.DiscussionOur probe set, which we call Rubiaceae2270x, was effective for targeting loci in species across and even outside of Rubiaceae. This probe set will facilitate phylogenomic studies in Rubiaceae and advance systematics and macroevolutionary studies in the family.

Recent phylogenetic results strongly suggest that neither Lantana nor Lippia are monophyletic. This has a direct impact on taxonomy and nomenclature in the tribe Lantaneae and it underscores the need to revise its classification. However, any generic recircumscription following the International Code of Nomenclature for algae, fungi, and plants will require substantial nomenclatural changes. As a solution, a phylogenetic classification following the PhyloCode is applied to the whole Lantaneae, and 28 rank-free names are proposed and defined for clades. Clade /Lantaneae is defined to exclude Coelocarpum. Traditional taxon names previously recognized at the ranks of tribe, genus, and section are maintained when associated with clades. Discussion about fruit and corolla morphology, the basis of most previous classifications, within the group is presented along with a key to the clades of /Lantaneae. A useful classification of the plant diversity in tribe Lantaneae consistent with the phylogenetic relationships within the group is provided. This rank-free system promotes name stability as new data become available and avoids name changes to well-known species.

Aquatic plants are generally underrepresented in herbaria due to geographic bias, rarity of species, and sampling bias towards terrestrial vascular plants. This constitutes a limitation to various lines of research (e.g., evolutionary and ecological studies) centered around aquatic plants. Plants in the genus Marathrum (Podostemaceae) have been suggested to be under-collected due to their highly modified phenotypes and to geographic bias. Marathrum (and Podostemaceae in general) live attached to rocks in river-rapids and waterfalls, which are difficult habitats to access. Here, we aimed to assess the number of historical records of Marathrum in Colombia, the country where the genus was first collected and where mountain ranges have been found to constitute a barrier to gene flow across populations. We expand past records with new records for the genus in Colombia and find that Marathrum are not uncommon in river-rapids and waterfalls in the country, but their under-representation in herbaria respond to several collection biases. We discuss the reasons for changes in the number of collections of Marathrum in Colombia through time, sources of collection bias in the group, and the relevance of occurrence records of Marathrum. The herbarium data reported in this study are publicly available in a digital repository to facilitate future research.

Northern South America is a geologically dynamic and species-rich region. Fossil and stratigraphic data show that mountain uplift in the tropical Andes reconfigured river drainages. These landscape changes shaped the evolution of the flora in the region, yet the impacts on aquatic taxa have been overlooked. We explore the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenetic inference, and divergence-dating analyses for two species in the genus Marathrum (Podostemaceae). Mountain uplift and drainage basin formation isolated populations of M. utile and M. foeniculaceum in northern South America and created barriers to gene flow across river drainages. Sympatric species hybridize and the hybrids show the phenotype of one parental line. We propose that the pattern of divergence of populations reflects the formation of river drainages, which was not complete until < 4.1 million yr ago (Ma). Our study provides a clear picture of the role of landscape change on the evolution of plants living strictly in rivers in northern South America. By shifting the focus to aquatic taxa, we provide a novel perspective on the processes shaping the evolution of the Neotropical flora.

PREMISE Lantana and Lippia (Verbenaceae) are two large Linnean genera whose classification has been based on associated fruit traits: fleshy vs. dry fruits and one vs. two seed-bearing units. We reconstruct evolutionary relationships and the evolution of the two fruit traits to test the validity of these traits for classification. METHODS Previous studies of plastid DNA sequences provided limited resolution for this group. Consequently, seven nuclear loci, including ITS, ETS, and five PPR loci, were sequenced for 88 accessions of the Lantana/Lippia clade and three outgroups. RESULTS Neither Lantana nor Lippia is monophyletic. Burroughsia, Nashia, Phyla, and several Aloysia species are included within the clade comprising Lantana and Lippia. We provide a hypothesis for fruit evolution and biogeographic history in the group and their relevance for classification. CONCLUSIONS Fleshy fruits evolved multiple times in the Lantana/Lippia clade and thus are not suitable taxonomic characters. Several sections of Lantana and Lippia and the small genera are monophyletic, but Lippia section Zappania is broadly paraphyletic, making circumscription of genera difficult. Lippia sect. Rhodolippia is a polyphyletic group characterized by convergence in showy bracts. Species of Lantana sect. Sarcolippia, previously transferred to Lippia, are not monophyletic. The clade originated and diversified in South America, with at least four expansions into both Central America and the Caribbean and two to Africa. The types species of Lantana and Lippia occur in small sister clades, rendering any taxonomy that retains either genus similar to its current circumscription impossible.

Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n=36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n=22 to 2n=46 chromosomes. In this study, we present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard ( Sceloporus tristichus ) in order to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n=22 with 6 pairs of macrochromosomes and 5 pairs of microchromosomes with a large pericentric inversion polymorphism on chromosome seven that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84 to 1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in 65,417 annotated genes, 16,426 of which were deduced to have a function. We confirmed the presence of a 4.62 Mb pericentric inversion on chromosome seven, which contains 59 annotated coding genes with known functions. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

[This corrects the article DOI: 10.3389/fpls.2019.01035.].

Summary Northern South America is a geologically dynamic and species-rich region. While fossil and stratigraphic data show that reconfiguration of river drainages resulted from mountain uplift in the tropical Andes, investigations of the impact of landscape change on the evolution of the flora in the region have been restricted to terrestrial taxa. We explore the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenomic, phylogenetic networks, and divergence-dating analyses for populations of riverweeds ( Marathrum , Podostemaceae). We show that mountain uplift and drainage basin formation isolated populations of Marathrum and created barriers to gene flow across rivers drainages. Sympatric species hybridize and the hybrids show the phenotype of one parental line. We propose that the pattern of divergence of populations reflect the formation of river drainages, which was not complete until <4 Ma Our study provides a clear picture of the role of landscape change in shaping the evolution of riverweeds in northern South America, advances our understanding of the reproductive biology of this remarkable group of plants, and spotlights the impact of hybridization in phylogenetic inference.

With the advent of next-generation sequencing technologies, whole-plastome data can be obtained as a byproduct of low-coverage sequencing of the plant genomic DNA. This provides an opportunity to study plastid evolution across groups, as well as testing phylogenetic relationships among taxa. Within the order Malpighiales (∼16,000 spp.), the Podostemaceae (∼300 spp.) stand out for their unique habit, living attached to rocks in fast-flowing aquatic habitats, and displaying highly modified morphologies that confound our understanding of their classification, biology, and evolution. In this study, we used genome skimming data to assemble the full plastid genome of 5 species within Podostemaceae. We analyzed our data in a comparative framework within Malpighiales to determine the structure, gene content, and rearrangements in the plastomes of the family. The Podostemaceae have one of the smallest plastid genomes reported so far for the Malpighiales, possibly due to variation in length of inverted repeat (IR) regions, gene loss, and intergenic region variation. We also detected a major inversion in the large single-copy region unique to the family. The uncommon loss or pseudogenization of ycf1 and ycf2 in angiosperms and in land plants in general is also found to be characteristic of Podostemaceae, but the compensatory mechanisms and implications of this and of the pseudogenization of accD, rpl22, and clpP and loss of rps16 remain to be explained in this group. In addition, we estimated a phylogenetic tree among selected species in Malpighiales. Our findings indicate that the Podostemaceae are a distinct lineage with long branches that suggest faster rates of evolution in the plastome of the group, compared with other taxa in the order. This study lays the foundations for future phylogenomic studies in the family.

This article comments on: Jacqueline Heckenhauer, Ovidiu Paun, Mark W. Chase, Peter S. Ashton, A.S. Kamariah and Rosabelle Samuel. 2019. Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes. Annals of Botany 123(5): 857–865.

The vast floodplains of the Orinoco Basin have the conditions for the proliferation of aquatic vegetation. Despite its ecological importance in the "Llanos Orientales" of Colombia, the aquatic flora in this region has been understudied. Consequently, the knowledge and dissemination of information about the richness and distribution patterns of aquatic plants and aquatic communities is scarce. In addition, the Orinoco Basin of Colombia is among the most over-exploited regions in the country. In order to provide a first insight into the species richness of macrophytes present in the region, plants associated with aquatic habitats were collected, identified, and photographed. For almost two years, 101 localities were visited. These localities were located in six departments (Arauca, Casanare, Guainía, Guaviare, Meta and Vichada) and 19 municipalities. In each locality, dried plant material and silica-dried material were collected. Sampling effort was concentrated towards hydrophytes and helophytes inhabiting lentic and lotic environments. 1167 collected specimens were deposited in the ANDES herbarium (Universidad de los Andes, Bogotá). Among these, 95 families, 221 genera, and 341 species of vascular plants were associated with aquatic habitats. Of the species collected, only 151 had been reported in the study area with 1374 historic occurrences in the "Herbario Nacional Colombiano" (COL) database. The present study aims to contribute to the knowledge and dissemination of information about the richness and distribution patterns of macrophytes in the Orinoco Basin of Colombia. We consider that this information is important in order to propose localities that should be a priority for conservation purposes, and to protect these important and threatened fresh-water ecosystems.

Las extensas llanuras inundables de la cuenca del Orinoco presentan las condiciones adecuadas para la proliferación de vegetación acuática. A pesar de su importancia ecológica en los Llanos Orientales de Colombia, la flora acuática que existe en esta región no ha sido suficientemente estudiada. Así mismo, el conocimiento y divulgación de la riqueza y los patrones de distribución de plantas y comunidades acuáticas son muy reducidas. Adicionalmente, la Orinoquia colombiana es una de las regiones más sobreexplotadas del país. Con el fin de tener una primera aproximación a la riqueza de especies de macrófitas presentes en esta región, se colectaron, identificaron y fotografiaron todas las especies de plantas que fueron encontradas asociadas a cuerpos de agua. Durante casi dos años se visitaron 101 localidades, ubicadas en seis departamentos (Arauca, Casanare, Guainía, Guaviare, Meta y Vichada) y 19 municipios. En cada localidad se colectó material vegetal seco para herbario y tejidos conservados en sílica. El esfuerzo de muestreo se concentró en plantas hidrófitas y helófitas que habitan ambientes lóticos y lénticos. Los 1167 especímenes colectados fueron depositados en el herbario ANDES (Universidad de los Andes, Bogotá). Se identificaron 95 familias de plantas vasculares que incluyeron 221 géneros y 341 especies, que fueron asociadas al agua. Dentro de las especies colectadas, únicamente 151 se encontraron registradas en el área de estudio con 1374 registros históricos en el Herbario Nacional Colombiano (COL). El presente estudio pretende ser una contribución al conocimiento y divulgación sobre la riqueza y patrones de distribución de las macrófitas en la Orinoquia colombiana. Consideramos que esta información es importante para proponer localidades prioritarias para la conservación y proteger estos ecosistemas de agua dulce tan importantes como amenazados.

Ludwigia displays a great variety of life forms adapted to aquatic habitats ranging from humid to water saturated. Morpho-anatomical characters were used to characterize and discriminate among selected Neotropical species of Ludwigia in terms of their root and shoot adaptations. A partial molecular phylogenetic hypothesis was reconstructed using the nrDNA ITS and cpDNA rpl32-trnL(uAG) regions for Neotropical species. ITS accessions of North temperate species were also included to provide a framework for the placement of our sampled taxa. Mapping of morpho-anatomical characters was performed on the resulting phylogenetic tree. We were able to separate the species in three groups according to their morpho-anatomical adaptations to aquatic habitats. Our results strengthen the support for at least two separate origins for the strictly aquatic habit in Neotropical representatives, in line with previous taxonomic classifications. We also suggest that these species experienced convergence of characters, but also diversified into various life forms adequate to live strictly in aquatic environments. We would like to highlight the great value of Ludwigia as a model system for the study of the evolution of characters that respond to pressures imposed by aquatic ecosystems within the dicotyledons, as well as within aquatic plants in general. (C) 2014 Elsevier B.V. All rights reserved.

Este documento hace parte de las memorias de la 5a Jornada Tematica en Finanzas realizada el 3 de abril de 2009 en la Universidad Icesi. En ella se hicieron presentaciones en los campos de Crisis Financiera Mundial, Crisis Empresarial Mundial e Inversion Empresarial. Estas ponencias fueron realizadas por estudiantes de las carreras de Economia y Negocios Internacionales, Administracion de Empresas Diurno, Contaduria Publica y Finanzas Internacionales, Maestria en Finanzas y Especializacion en Finanzas.