Biology subjects

Zapata, F.

Publications and source records attributed to Zapata, F..

13 recordsLinked to original sources

bioRxiv2025

The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands

Islands are natural laboratories for studying dispersal, speciation, and extinction, yet the historical dynamics of many insular radiations remain poorly understood because of the difficulty aligning the tempo and mode of diversification with paleogeography during phylogenetic inference. We introduce a phylogenetic modeling framework, named TimeFIG, that combines data about species ranges and genetic variation with paleogeographic information to simultaneously infer divergence times, ancestral ranges, and historical diversification rates, without relying on fossils to time-calibrate the phylogeny. Applying TimeFIG to the spectacular radiation of Hawaiian Kadua (Rubiaceae) points to colonization of either modern Kaua'i or ancient now-eroded islands, with island isolation as the strongest correlate of dispersal, and with a tendency for net diversification to be highest on "middle-aged" islands. Modeling diversification within an explicit spatiotemporal context, while accounting for historical uncertainty regarding the timing and placement of phylogenetic and biogeographic events, enables the rigorous testing of foundational hypotheses in island biology and evolutionary theory for clades beyond Kadua.

evolutionary biology↗

bioRxiv2024

Phylogenomics of the North American Desert Radiation Linanthus (Polemoniaceae) Reveals Mixed Trait Lability and No Single Geographic Mode of Speciation

PremiseUnderstanding how arid-adapted plants have diversified in harsh environments is a central question in evolutionary biology. Linanthus (Polemoniaceae) occurs in biodiverse dry areas of Western North America and exhibits extensive floral trait variation, multiple color polymorphisms, differences in blooming time, and variation in life history strategies. Here, we reconstruct the evolutionary history of this group. MethodsWe generated restriction-site associated (ddRAD) sequences for 180 individuals and target capture (TC) sequences for 63 individuals, with complete species sampling. Using maximum likelihood and pseudo-coalescent approaches, we inferred phylogenies of Linanthus and used these phylogenies to model the evolution of phenotypic traits and investigate the geographic speciation history of this genus. Key resultsShallow relationships are consistent and well supported with both ddRAD and TC data. Most species are monophyletic despite rampant local sympatry and range overlap, suggesting strong isolating barriers. The non-monophyly of some species is possibly due to rapid speciation or issues with current species delimitation. Perenniality likely evolved from annuality, a rare shift in angiosperms. Night blooming evolved three times independently. Flower color polymorphism is an evolutionarily labile trait and is likely ancestral. No single geographic mode of speciation characterizes the radiation but most species overlap in range, suggesting they evolved in parapatry. ConclusionsOur results illustrate the complexity of phylogenetic inference for recent radiations, even with multiple sources of genomic data and extensive sampling. This analysis provides a foundation to understand aridity adaptations, such as evolution of flower color polymorphisms, night blooming, and perenniality, as well as speciation mechanisms.

evolutionary biology↗

bioRxiv2024

Caldas meets Janzen: Thermal regimes of montane plants and implications for global patterns of speciation

The seasonality hypothesis posits that limited seasonal temperature variability in tropical mountains leads to greater climatic zonation along elevation gradients compared to temperate regions. This is predicted to result in narrow thermal tolerances and restricted dispersal for organisms, which may reduce gene flow and increase opportunities for climate-associated parapatric or allopatric speciation in tropical mountains relative to temperate-zone mountains. This hypothesis has been tested in various animal groups but not in plants. We examine the elevational and thermal ranges of pairs of sister species of angiosperms from mountains worldwide. Our findings indicate no significant difference in the breadth and overlap of elevational ranges between tropical and temperate species. However, tropical species have narrower thermal ranges and show greater similarity in these ranges between sister species compared to temperate ones. Such narrow thermal specialization in tropical plants facilitates population divergence and allopatric speciation within thermal zones more than in temperate species.

evolutionary biology↗

bioRxiv2024

Toward Sustainable Biocultural Tourism: An Integrated Spatial Analysis of Cultural and Biodiversity Richness in Colombia

O_LITourism plays a vital role in both economic development and depending on the scale, it can also aid environmental conservation. Tourism planning often considers culture-based and nature-based tourism separately, failing to recognize the synergies between them, with the potential to market locations as biocultural destinations. C_LIO_LIUsing Colombia as a case study, we created metrics of taxonomic biological diversity as measured by vertebrate species richness (including birds, mammals, freshwater fishes, reptiles, and amphibians) and institutionalized cultural richness (by counting the number of UNESCO world heritage sites, intangible cultural heritage sites, museums, endemic music festivals, Afro-Colombian territories, and Indigenous reserves), and evaluated the spatial correlations between them. C_LIO_LITo determine biocultural tourism potential, we evaluated whether biocultural richness was accessible, and mapped potential biocultural tourism supply. By mapping areas of sports fisheries, birdwatching destinations, and airport arrivals we also estimated spatial demand. We also analyzed the difference between demand and supply to assess the realized and untapped potential for biocultural destinations. C_LIO_LIWhile biocultural richness is high in the Amazon, Pacific, and Caribbean regions, we found that there are no win-win-win locations where culture, species richness, and accessibility are all high. Areas with great potential for biocultural tourism development largely coincide with designated Indigenous reserves and Afro-Colombian territories. C_LIO_LIThis study underscores the power of integrating cultural and biological variables to reshape the tourism sector. Our paper offers practical recommendations for policymakers, conservation organizations, and local communities seeking to create transformative and inclusive tourism experiences. C_LI

ecology↗

bioRxiv2024

Can't carve air, can't weave names: Plant species used in Colombian artisan crafts are not equally assessed for vulnerability at the international and national level

Humanity has maintained cultural connections with our environments for time immemorial. Plants and artisan crafts are a prime example, as craft purpose, skill, design, and species used can vary greatly between communities and the loss of a critical plant species can result in a loss of access to cultural craft practices. To mitigate global biodiversity loss, conservationists are faced with the challenge of assessing species vulnerability to extinction and prioritizing species for conservation funding using information instruments, like the IUCN red list. This process does not necessarily consider a species cultural importance. In this paper we sought to address this gap for plant species used in artisan crafts in Colombia. We aim to answer the following: (1) how represented are endemic species in artisan crafts; (2) how threatened are artisan craft species according to (a) international and (b) national vulnerability status? We used the number of species-associated common names as a proxy for cultural awareness. We found that continentally regional species were far more represented in Colombian artisan crafts than national endemics. We also found a strong positive relationship between number of common names and national vulnerability assessment status, but no statistically significant relationship for international vulnerability status. Based on our results, well-known plants used in Colombian artisan crafts are more likely to be assessed nationally than internationally. While the IUCN is thorough in their recommendations, more can be done to prioritize the inclusion of conservation assessments for species based on their contributions to cultural diversity. Positionality statementWe are 14 scientists and practitioners who are deeply committed to the conservation of nature and culture in a changing world. We are trained in diverse fields including ecology, evolutionary biology, botany, music, anthropology, law, and public health. We all have postgraduate academic education (Masters or PhDs underway) but most of us are early career scholars. Six of us grew up in Colombia and we represent many places including Mexico, the United States, Ireland, Chile, Brazil, Germany, and Viet Nam. None of us self-identify as Indigenous.

ecology↗

bioRxiv2023

Darwin's Overlooked Radiation: genomic evidence points to the early stages of a radiation in the Galapagos prickly pear cactus (Opuntia, Cactaceae)

The Galapagos Islands are a prime example of a natural laboratory for the study of evolutionary radiations. While much attention has been devoted to iconic species like Darwins finches 1-4, the islands offer an equally unique but often overlooked opportunity for plant radiations 5. Yet, compared to their animal counterparts, our understanding of the patterns and processes underpinning Galapagos plant radiations remains relatively limited 6,7. We present evidence of the early stages of a radiation in prickly-pear cactus (Opuntia, Cactaceae), a plant lineage widespread across the archipelago. Phylogenomic and population genomic analyses show that notwithstanding overall low genetic differentiation across populations, there is marked geographic structure that is broadly consistent with current taxonomy and the dynamic paleogeography of the Galapagos. Because such low genetic differentiation stands in stark contrast to the exceptional eco-phenotypic diversity displayed by cacti across islands, it is plausible that phenotypic plasticity precedes genetic divergence and is the source of adaptive evolution, or that introgression between populations facilitates local adaptation. Models of population relationships including admixture indicate that gene flow is common between certain islands, likely facilitated by dispersal via animals known to feed on Opuntia flowers, fruits, and seeds across the archipelago. Scans of genetic differentiation between populations reveal candidate loci associated with seed traits and environmental stressors, suggesting that a combination of biotic interactions and abiotic pressures due to the harsh conditions characterizing island life in a volcanic, equatorial archipelago may underlie the diversification of prickly-pear cacti. Considered in concert, these results are relevant to both the mechanisms of plant eco-phenotypic differentiation and the evolutionary history and conservation of the Galapagos biota.

evolutionary biology↗

bioRxiv2021

Evolution of gene expression across species and specialized zooids in Siphonophora

BackgroundSiphonophores are complex colonial animals, consisting of asexually-produced bodies (called zooids) that are functionally specialized for specific tasks, including feeding, swimming, and sexual reproduction. Though this extreme functional specialization has captivated biologists for generations, its genomic underpinnings remain unknown. We use RNA-seq to investigate gene expression patterns in five zooids and one specialized tissue (pneumatophore) across seven siphonophore species. Analyses of gene expression across species present several challenges, including identification of comparable expression changes on gene trees with complex histories of speciation, duplication, and loss. Here, we conduct three analyses of expression. First, we examine gene expression within species. Then, we conduct classical analyses examining expression patterns between species. Lastly, we introduce Speciation Branch Filtering, which allows us to examine the evolution of expression in a phylogenetic framework. ResultsWithin and across species, we identified hundreds of zooid-specific and species-specific genes, as well as a number of putative transcription factors showing differential expression in particular zooids and developmental stages. We found that gene expression patterns tended to be largely consistent in zooids with the same function across species, but also some large lineage-specific shifts in gene expression. ConclusionsOur findings show that patterns of gene expression have the potential to define zooids in colonial organisms. We also show that traditional analyses of the evolution of gene expression focus on the tips of gene phylogenies, identifying large-scale expression patterns that are zooid or species variable. The new explicit phylogenetic approach we propose here focuses on branches (not tips) offering a deeper evolutionary perspective into specific changes in gene expression within zooids along all branches of the gene (and species) trees.

evolutionary biology↗

bioRxiv2020

Diversification, disparification, and hybridization in the desert shrubs Encelia

O_LIThere are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. C_LIO_LIUsing a nearly complete species-level phylogeny along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity, and assess phenotypic divergence across environmental gradients. C_LIO_LIWe show that Encelia originated and diversified recently (mid-Pleistocene) and rapidly, with rates comparable to notable adaptive radiations in plants. Encelia probably originated in the hot deserts of North America, with subsequent diversification across steep environmental gradients. We uncover multiple instances of gene flow between species. The radiation of Encelia is characterized by fast rates of phenotypic evolution, trait lability, and extreme disparity across environments and between species-pairs with overlapping geographic ranges. C_LIO_LIEncelia exemplifies how interspecific gene flow in combination with high trait lability can enable exceptionally fast diversification and disparification across steep environmental gradients. C_LI

evolutionary biology↗

bioRxiv2020

Natural selection maintains species despite widespread hybridization in the desert shrub Encelia

Natural selection is an important driver of genetic and phenotypic differentiation between species. A powerful way to test the role of natural selection in the formation and maintenance of species is to study species complexes in which potential gene flow is high but realized gene flow is low. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of species hybridize at ecologically divergent parapatric boundaries in the adaptive radiation of Encelia, such mechanisms may maintain species boundaries throughout this group. SIGNIFICANCE STATEMENTIn Baja California, the deserts meet the coastal dunes in a narrow transition visible even from satellite images. We study two species pairs of desert shrubs (Encelia) that occur across this transition. Although these species can interbreed, they remain distinct. Using a combination of genetics, field experiments, 3D-imaging, and physiological measurements, we show that natural selection counteracts the homogenizing effects of gene exchange. The different habitats of these species create multiple mechanisms of selection - drought, salinity, herbivory, and burial, which together maintain these species in their native habitats and their hybrids in intermediate habitats. This study illustrates how environmental factors influence traits and fitness and how this in turn maintain species, highlighting the importance of natural selection in speciation.

evolutionary biology↗

bioRxiv2018

Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups, however there was little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 30 siphonophore species analyzed in combination with 13 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose twice.

evolutionary biology↗

bioRxiv2017

Revising transcriptome assemblies with phylogenetic information in Agalma1.0

MotivationOne of the most common transcriptome assembly errors is to mistake different transcripts of the same gene as transcripts from multiple closely related genes. It is difficult to identify these errors during assembly, but in a phylogenetic analysis these errors can be diagnosed from gene trees containing clades of tips from the same species with improbably short branch lengths.\n\nResultstreeinform is a module implemented in Agalma1.0 that uses phylogenetic analyses across species to refine transcriptome assemblies. It identifies transcripts of the same gene that were incorrectly assigned to multiple genes and reassign them as transcripts of the same gene.\n\nAvailability and Implementationtreeinform is implemented in Agalma1.0, available at https://bitbucket.org/caseywdunn/agalma.\n\nContactaugust_guang@brown.edu\n\nSupplementary informationSupplementary information is available at bioRxiv.

bioinformatics↗

bioRxiv2017

Atlantean Evolution in Darwin’s Finches—Issues and Perspectives in Species Delimitation using Phenotypic Data

Progress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: (1) reliance on graphical analyses of phenotypic space that do not consider the frequency of phenotypes; (2)exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and (3) use of measures of central tendencies to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwins ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of \"Sisyphean\" evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. Approaches allowing one to fit normal mixture models without a priori information about species limits offer new perspectives in the kind of inferences available to systematists, with significant repercusions on ideas about the structure of biological biodiversity. [morphology; normal mixture model; phenotype; principal components analysis; species limits; variable selection.]

evolutionary biology↗

bioRxiv2017

Pairwise comparisons are problematic when analyzing functional genomic data across species

AbstractThere is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions, and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to be more similar than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead we find they reflect species relationships. These reanalyses concretely demonstrate the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.\n\nSignificanceComparisons of genome function between species are providing important insight into the evolutionary origins of diversity. Here we demonstrate that comparative functional genomics studies can come to the wrong conclusions if they do not take the relationships of species into account and instead rely on pairwise comparisons between species, as is common practice. We re-examined two previously published studies and found problems with pairwise comparisons that draw both their original conclusions into question. One study had found support for the ortholog conjecture and the other had concluded that the evolution of gene expression was different between animal phyla than within them. Our results demonstrate that to answer evolutionary questions about genome function, it is critical to consider evolutionary relationships.

genomics↗