Diversity in habit expands the environmental niche of Ziziphus (Rhamnaceae)

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: The data that support the findings of this study are openly available in the Dryad Digital Repository: https://doi.org/10.5061/dryad.34tmpg4p0 (Rickenback et al., 2022).Ziziphus (Rhamnaceae) is a widely distributed genus across the Australasian and African tropics with unusual diversity in habit, and many species of significance to people. Here, we quantify the environmental limits of Ziziphus species and examine inter-specific relationships among functional traits, environment, biome, and range size. We developed a curated geolocation database for Ziziphus and used it to examine the environmental limits of the genus relative to temperature, rainfall, and seasonality. To assess the relationship between biome and habit, permutational analysis of variance was used, while hierarchical clustering was used to determine whether habit, leaves, and fruit traits were related to biome. For 40 species with adequate geolocation data, range size was calculated to assess its relationship with habit, biomes, and cultivation. Finally, niche identity tests were used to determine niche equivalency among cultivated and non-cultivated species. Liana species are restricted to closed forests and the geoxylic habit is found only in open grasslands. Further, habit is significantly associated with range size, with trees having on average larger range sizes than shrubs, lianas, and geoxyles, but biome was not correlated with range size. Cultivated species have ranges ~10 times that of non-cultivated tree species and with significantly different and broader environmental niches. The unusually wide distribution of Ziziphus can be explained by its diversity of habits associated with different biomes spanning continents. This, along with the usage of many Ziziphus species by people for their fruits, expands the range and environmental occupation of the genus

Hybridisation:A ‘double-edged sword’ for neotropical plant diversity

Hybridization can facilitate both evolutionary diversification and extinction and has had a critical role in plant evolution, with c. 25% of species known to hybridize in some temperate floras. However, in the species-rich Neotropical flora, the role of hybridization in the evolution of diversity remains unclear. Our review examines studies of hybridization in seed plants from across the Neotropics and explores its outcomes on Neotropical plant evolution. We review studies on a per-biome basis and a spectrum of evolutionary outcomes from hybridization are evident across Neotropical biomes and taxa. These range from short-term impacts, such as the broadening of ecological amplitude in hybrid progeny with transgressive phenotypes and genetic swamping, through to long term impacts, such as the generation of new lineages. Among these studies certain themes emerge, such as the pervasive hybridization among species-rich plant radiations from the Andean páramos, suggesting a role for hybridization in rapid diversification events. Finally, we highlight that hybridization is relatively understudied in the Neotropical flora, despite its remarkable species richness. The advent of genomic techniques can facilitate the study of hybridization and its effects in understudied biomes and plant groups. The increasing availability of genomic resources will eventually allow comparisons between tropical and temperate floras and therefore shed light on the evolutionary impacts of hybridization across the latitudinal biodiversity gradient

History and Geography of Neotropical Tree Diversity

Early botanical explorers invoked biogeographic history to explain the remarkable tree diversity of Neotropical forests. In this context, we review the history of Neotropical tree diversity over the past 100 million years, focusing on biomes with significant tree diversity. We evaluate hypotheses for rain forest origins, intercontinental disjunctions, and models of Neotropical tree diversification. To assess the impact of biotic interchange on the Amazon tree flora, we examined biogeographic histories of trees in Ecuador’s Yasuní Forest,which suggest that nearly 50% of its species descend from immigrant lineages that colonized South America during the Cenozoic. Long-distance and intercontinental dispersal, combined with trait filtering and niche evolution, are important factors in the community assembly of Neotropical forests.We evaluate the role of pre-Columbian people on Neotropical tree diversity and discuss the future of Neotropical forests in the Anthropocene.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151936/1/Dick&Pennington2019.pdf85Description of Dick&Pennington2019.pdf : Main articl

Molecular systematic perspectives on biome origins and dynamics

invited commentary on the following article:De-Nova JA, Medina R, Montero JC, Weeks A, Rosell JA, Olson ME, Eguiarte LE, Magallo ́n S. 2011. Insights into the historical construction of species-rich Mesoamerican seasonally dry tropical forests: the diversification of Bursera (Burseraceae, Sapindales). New Phytologist 193: 276–287.Phylogenetic reconstructions of diverse tropical groups have yielded biological insights that extend well beyond the field of systematics, illuminating such topics as biome assembly and plant–insect coevolution. In this issue of New Phytologist, De-Nova et al. (pp. 276–287) present a rigorous time-calibrated phylogeny of the Neotropical tree genus Bursera in order to estimate lineage ages, and to investigate how geography and ecology have structured its species diversification. Because Bursera is a dominant component of Mesoamerican seasonally dry tropical forests (SDTFs), the study provides evidence relating to the origin and expansion of this important biome. The study also sets the record straight on the age of a well-known plant– herbivore interaction.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/88158/1/Dick&Pennington2012.pdf-

The unintended impact of Colombia's covid-19 lockdown on forest fires

The covid-19 pandemic led to rapid and large-scale government intervention in economies and societies. A common policy response to covid-19 outbreaks has been the lockdown or quarantine. Designed to slow the spread of the disease, lockdowns have unintended consequences for the environment. This article examines the impact of Colombia’s lockdown on forest fires, motivated by satellite data showing a particularly large upsurge of fires at around the time of lockdown implementation. We find that Colombia’s lockdown is associated with an increase in forest fires compared to three different counterfactuals, constructed to simulate the expected number of fires in the absence of the lockdown. To varying degrees across Colombia’s regions, the presence of armed groups is correlated with this fire upsurge. Mechanisms through which the lockdown might influence fire rates are discussed, including the mobilisation of armed groups and the reduction in the monitoring capacity of state and conservation organisations during the covid-19 outbreak. Given the fast-developing situation in Colombia, we conclude with some ideas for further research

Amazonian White-Sand Forests Show Strong Floristic Links with Surrounding Oligotrophic Habitats and the Guiana Shield

Recognizing and understanding historical patterns and processes that have influenced the diversification of organisms on earth is one of the central goals of evolutionary biology. Within this broad area, studies within the disciplines of molecular systematics (i.e. phylogeography, phylogenetics and population genetics), allow us to address evolutionary questions from different biological, spatial and temporal scales. Phylogeography and molecular phylogenetics help us to understand aspects related to events that have given rise to patterns of genetic variation in organisms, as well as to understand the assembly of biological communities in a given area. These types of studies provide crucial information to increase knowledge about the biodiversity of little-studied ecoregions. One such ecoregion is Colombian Guyana. This ecoregion, which is located between three putative centers of speciation; Amazonia, the Andes and Guyana, is one of the least explored areas of the country. As a result of their geological composition, the western enclaves of the Guiana Shield have been described as a "heterogeneous entity", composed of savannas, catingas, lowland forests, and even white sand forests. Using bats as a biological study group, this paper presents two approaches focused on understanding how biogeographic events that have shaped the diversity of the continent have affected different lineages that inhabit Colombian Guiana. Bats are a group of vertebrates sensitive to biogeographic events that have shaped the diversity of the continent, which play different functional roles in the ecosystems they inhabit. High degrees of association with habitat have been described for numerous bat species, mainly in terms of foraging characteristics and diet types. In a first project, we comparatively analyzed the phylogeographic patterns of three widely distributed bat species, with the aim of identifying the patterns of genetic divergence of the bats that inhabit the area today. Using mitochondrial DNA sequences, we revealed the existence of bat populations established in the area, which showed different degrees of gene flow with surrounding biogeographic areas, especially with the Guiana provinces of Oriente and Pantepui and the Amazon. Additionally, we identified different demographic histories for each species, which were probably influenced to different extents by climatic changes during the Pleistocene and differential ecological characteristics. Our results highlight the influence of Colombian Guiana ecosystems on the formation and spatial configuration of bat diversity and genetic structure, and the importance of these ecosystems for bat conservation. In a second project, from a phylogenetic perspective, we evaluated the phylogenetic structure of bat communities inhabiting different eco-regions of northern South America, using mitochondrial and nuclear DNA sequences. The results of the analysis allowed us to demonstrate that the bat populations of the Western Guayana Province (which includes the Colombian portion of the Guiana Shield), are phylogenetically clustered, that is, the species that compose the communities are evolutionarily closer than expected by chance. We conclude that factors such as the high heterogeneity of habitats in the region, the high diversity of fruit bats in the sampled communities, and interspecific competition have shaped the species composition of the communities in this area. In a final chapter, a general discussion of the results obtained from the two research projects carried out is developed. Chapters one and two of this thesis will be submitted to international indexed journals, which is why they are written in English and in scientific article format.Reconocer y entender patrones y procesos históricos que han influenciado la diversificación de los organismos sobre la tierra, es uno de los objetivos centrales de la biología evolutiva. Dentro de esta gran área, estudios enmarcados en las disciplinas de la sistemática molecular (i.e. filogeografía, filogenética y genética de poblaciones), nos permiten abordar preguntas evolutivas desde diferentes escalas biológicas, espaciales y temporales. La filogeografía y la filogenética molecular nos ayudan a entender aspectos relacionados con eventos que han dado lugar a patrones de variación genética de los organismos, así como entender el ensamblaje de comunidades biológicas en un área determinada. Este tipo de estudios aportan información crucial para aumentar el conocimiento acerca de biodiversidad de eco regiones poco estudiadas. Una de estas eco regiones es la Guyana colombiana. Esta eco región, la cual se encuentra ubicada entre tres centros putativos de especiación; Amazonía, Andes y Guayana, es una de las zonas menos exploradas del país. Como resultado de su composición geológica, los enclaves occidentales del escudo Guayanés han sido descritos como una "entidad heterogénea", compuesta de sabanas, catingas, bosques bajos, e inclusive bosques de arena blanca. Usando como grupo biológico de estudio los murciélagos, este trabajo de grado presentan dos aproximaciones enfocadas a entender como eventos biogeográficos que han moldeado la diversidad del continente, han afectado diferentes linajes que habitan la Guayana colombiana. Los murciélagos son un grupo de vertebrados sensibles a los eventos biogeográficos que han moldeado la diversidad del continente, el cuál cumple diferentes roles funcionales en los ecosistemas que habitan. Altos grados de asociación con el hábitat han sido descritos para numerosas especies de murciélagos, principalmente en cuanto a características de forrajeo y tipos de dieta. En un primer proyecto, analizamos comparativamente los patrones filogeográficos de tres especies de murciélagos de amplia distribución, con el objetivo de identificar los patrones de divergencia genética de los murciélagos que habitan el área en la actualidad. Utilizando secuencias de ADN mitocondrial, revelamos la existencia de poblaciones de murciélagos establecidas en el área, las cuales mostraron diferentes grados de flujo genético con áreas biogeográficas circundantes, en especial con las provincias guayanesas del Oriente y Pantepui y el Amazonas. Adicionalmente identificamos diferentes historias demográficas para cada especie, las cuales probablemente fueron influenciadas en diferente medida por cambios climáticos durante el pleistoceno y características ecológicas diferenciales. Nuestros resultados destacan la influencia de los ecosistemas guayaneses colombianos en la formación y configuración espacial de la diversidad y estructura genética en murciélagos, y la importancia de estos ecosistemas para la conservación dicha diversidad. En un segundo proyecto, desde una perspectiva filogenética, evaluamos la estructura filogenética de la comunidad de murciélagos de diferentes eco-regiones del norte de sur américa, usando secuencia de ADN mitocondrial. Los resultados de los análisis nos permitieron demostrar que las poblaciones de murciélagos de la Provincia Guayanesa del Occidente (la cual incluye la porción colombiana del escudo guayanés), se encuentran filogenéticamente agregadas, es decir, las especies que componen las comunidades son más cercanas evolutivamente de lo esperado por el azar. Concluimos que factores como la alta heterogeneidad de hábitats en la región, la alta diversidad de murciélagos frugívoros en las comunidades muestreadas, y la competencia interespecífica han moldeado la composición de especies de las comunidades en esta zona. En un capítulo final, se desarrolla una discusión general de los resultados obtenidos de los dos proyectos de investigación realizados. Los capítulos uno y dos de esta tesis serán sometidos a revistas indexadas internacionales, razón por la cual están escritos en idioma inglés y en formato de artículo científico.Línea de Investigación: Biología EvolutivaMaestrí

Underground trees inhabit varied environmental extremes across the Afrotropics

This is the final version. Available on open access from Oxford University Press via the DOI in this recordAbstract Background and Aims Geoxyles, a distinctive feature of Afrotropical savannas and grasslands, survive recurrent disturbances by resprouting subshrub branches from large below-ground woody structures. Underground trees are a type of geoxyle that independently evolved within woody genera of at least 40 plant families in Africa. The environmental limits and determinants of underground tree biogeography are poorly understood, with the relative influence of frost and fire debated in particular. We aim to quantify variability in the niche of underground tree species relative to their taller, woody tree/shrub congeners. Methods Using occurrence records of four Afrotropical genera, Parinari (Chrysobalanaceae), Ozoroa (Anacardiaceae), Syzygium (Myrtaceae) and Lannea (Anacardiaceae), and environmental data of nine climate and disturbance variables, the biogeography and niche of underground trees are compared with their open and closed ecosystem congeners. Key Results Along multiple environmental gradients and in a multidimensional environmental space, underground trees inhabit significantly distinct and extreme environments relative to open and closed ecosystem congeners. Niche overlap is low among underground trees and their congeners, and also among underground trees of the four genera. Of the study taxa, Parinari underground trees inhabit hotter, drier and more seasonal environments where herbivory pressure is greatest. Ozoroa underground trees occupy relatively more fire-prone environments, while Syzygium underground trees sustain the highest frost frequency and occur in relatively wetter conditions with seasonal waterlogging. Lannea underground trees are associated with the lowest temperatures, highest precipitation, and varying exposure to disturbance. Conclusions While underground trees exhibit repeated convergent evolution, varied environments shape the ecology and biogeography of this iconic plant functional group. The multiplicity of extreme environments related to fire, frost, herbivory and waterlogging that different underground tree taxa occupy, and the distinctiveness of these environments, should be recognized in the management of African grassy ecosystems

Systematics, biogeography, and character evolution of the legume tribe Fabeae with special focus on the middle-Atlantic island lineages

Background: Tribe Fabeae comprises about 380 legume species, including some of the most ancient and important crops like lentil, pea, and broad bean. Breeding efforts in legume crops rely on a detailed knowledge of closest wild relatives and geographic origin. Relationships within the tribe, however, are incompletely known and previous molecular results conflicted with the traditional morphology-based classification. Here we analyse the systematics, biogeography, and character evolution in the tribe based on plastid and nuclear DNA sequences. Results: Phylogenetic analyses including c. 70% of the species in the tribe show that the genera Vicia and Lathyrus in their current circumscription are not monophyletic: Pisum and Vavilovia are nested in Lathyrus, the genus Lens is nested in Vicia. A small, well-supported clade including Vicia hirsuta, V. sylvatica, and some Mediterranean endemics, is the sister group to all remaining species in the tribe. Fabeae originated in the East Mediterranean region in the Miocene (23–16 million years ago (Ma)) and spread at least 39 times into Eurasia, seven times to the Americas, twice to tropical Africa and four times to Macaronesia. Broad bean (V. faba) and its sister V. paucijuga originated in Asia and might be sister to V. oroboides. Lentil (Lens culinaris ssp. culinaris) is of Mediterranean origin and together with eight very close relatives forms a clade that is nested in the core Vicia, where it evolved c. 14 Ma. The Pisum clade is nested in Lathyrus in a grade with the Mediterranean L. gloeosperma, L. neurolobus, and L. nissolia. The extinct Azorean endemic V. dennesiana belongs in section Cracca and is nested among Mediterranean species. According to our ancestral character state reconstruction results, ancestors of Fabeae had a basic chromosome number of 2n=14, an annual life form, and evenly hairy, dorsiventrally compressed styles. Conclusions: Fabeae evolved in the Eastern Mediterranean in the middle Miocene and spread from there across Eurasia, into Tropical Africa, and at least seven times to the Americas. The middle-Atlantic islands were colonized four times but apparently did not serve as stepping-stones for Atlantic crossings. Long-distance dispersal events are relatively common in Fabeae (seven per ten million years). Current generic and infrageneric circumscriptions in Fabeae do not reflect monophyletic groups and should be revised. Suggestions for generic level delimitation are offered.info:eu-repo/semantics/publishedVersio

Ficus insipida subsp. insipida (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species

Aim: To examine the phylogeography of Ficus insipida subsp. insipida in order to investigate patterns of spatial genetic structure across the Neotropics and within Amazonia. Location: Neotropics. Methods: Plastid DNA (trnH-psbA; 410 individuals from 54 populations) and nuclear ribosomal internal transcribed spacer (ITS; 85 individuals from 27 populations) sequences were sampled from Mexico to Bolivia, representing the full extent of the taxon's distribution. Divergence of plastid lineages was dated using a Bayesian coalescent approach. Genetic diversity was assessed with indices of haplotype and nucleotide diversities, and genetic structure was examined using spatial analysis of molecular variance (SAMOVA) and haplotype networks. Population expansion within Amazonia was tested using neutrality and mismatch distribution tests. Results: trnH-psbA sequences yielded 19 haplotypes restricted to either Mesoamerica or Amazonia; six haplotypes were found among ITS sequences. Diversification of the plastid DNA haplotypes began c. 14.6 Ma. Haplotype diversity for trnH-psbA was higher in Amazonia. Seven genetically differentiated SAMOVA groups were described for trnH-psbA, of which two were also supported by the presence of unique ITS sequences. Population expansion was suggested for both markers for the SAMOVA group that contains most Amazonian populations. Main conclusions: Our results show marked population genetic structure in F. insipida between Mesoamerica and Amazonia, implying that the Andes and seasonally dry areas of northern South America are eco-climatic barriers to its migration. This pattern is shared with other widespread pioneer species affiliated to wet habitats, indicating that the ecological characteristics of species may impact upon large-scale phylogeography. Ficus insipida also shows genetic structure in north-western Amazonia potentially related to pre-Pleistocene historical events. In contrast, evident population expansion elsewhere in Amazonia, in particular the presence of genetically uniform populations across the south-west, indicate recent colonization. Our findings are consistent with palaeoecological data that suggest recent post-glacial expansion of Amazonian forests in the south

Phylogeny and biogeography of Ceiba Mill. (Malvaceae, Bombacoideae)

The Neotropics is the most species-rich area in the world, and the mechanisms that generated and maintain its biodiversity are still debated. This paper contributes to the debate by investigating the evolutionary and biogeographic history of the genus Ceiba Mill. (Malvaceae, Bombacoideae). Ceiba comprises 18 mostly Neotropical species, largely endemic to two major biomes, seasonally dry tropical forests (SDTFs) and rain forests. Its species are among the most characteristic elements of Neotropical SDTF, one of the most threatened biomes in the tropics. Phylogenetic analyses of DNA sequence data (from the nuclear ribosomal internal transcribed spacers [nrITS] for 30 accessions representing 14 species of Ceiba) recovered the genus as monophyletic. The phylogeny showed geographic and ecological structure in three main clades: (i) a rain forest lineage of nine accessions of C. pentandra sister to the remaining species; (ii) a highly supported clade composed of C. schottii and C. aesculifolia from Central American and Mexican SDTF, plus two accessions of C. samauma from semi-humid, inter Andean valleys in Peru; and (iii) a highly supported South American SDTF clade including 10 species showing little sequence variation. Within this South American SDTF clade, no species represented by multiple accessions were resolved as monophyletic. We demonstrate that the patterns of species age, monophyly, and geographic structure previously reported for SDTF species within the Leguminosae family are not shared by Ceiba, suggesting that further phylogenetic studies of unrelated groups are required to understand general patterns