Biology subjects

Ramirez-Barahona, S.

Publications and source records attributed to Ramirez-Barahona, S..

8 recordsLinked to original sources

bioRxiv2025

CactEcoDB: Trait, spatial, environmental, phylogenetic and diversification data for the cactus family

Integrated datasets linking traits, spatial distributions, environmental variables and phylogenies are essential for comparative research, but remain limited for many plant taxa, including those which are most threatened. Cactaceae are a morphologically and ecologically diverse succulent family that are iconic components of ecosystems across the Americas, and face high extinction risk. To support future comparative research, we present CactEcoDB (The Cactus Ecological Database), an Open Access dataset of curated spatial, ecological, trait, phylogenetic, and diversification data for over 1,000 cactus species. CactEcoDB includes species-level trait data, geographic occurrence records, environmental variables, range size estimates, speciation rates, and the largest time-calibrated phylogeny of cacti to date. By integrating these diverse data in a single platform, CactEcoDB enables analyses of trait evolution, trait-environment interactions, biogeography, climatic niche evolution, and macroevolutionary dynamics in one of the most celebrated and threatened plant families.

evolutionary biology↗

bioRxiv2023

Did succulents diversify in response to aridity? Evolutionary analyses of major succulent lineages around the world

The succulent syndrome is one of the most iconic life strategies in angiosperms, maximising water storage through a suite of adaptations to water-scarcity. Though succulence is considered a classic case of convergent evolution driven by shared environmental drivers, we lack a full understanding of whether the timing and drivers of the diversification of succulent lineages are, in fact, concordant. Here we analyse time-calibrated phylogenetic reconstructions of the seven richest lineages of succulents, and study diversification dynamics in relation to abiotic variables. Our analyses reveal different levels of synchronicity and relation with aridity. The impact of atmospheric CO2 on succulent macroevolution is varied. While transitions and radiations are especially concentrated in recent time, following a collapse of atmospheric CO2 [~]15 million years ago, CO2-dependent diversification is not supported in most lineages. With the exception of Euphorbia, we find that succulence elevates net diversification, though the effects on underlying speciation and extinction disagree. The phylogenetic distribution of transitions to succulence and rate shift increases suggest these phenomena are decoupled, indicating that succulence might not adhere to a classic key innovation model. We discuss that these evolutionary patterns reveal the ecological complexity of the succulent strategy, beyond simplistic interpretations as adaptations towards aridity.

plant biology↗

bioRxiv2023

No evidence for angiosperm mass extinction at the Cretaceous-Paleogene (K-Pg) boundary

The Cretaceous-Paleogene mass extinction event (K-Pg) witnessed up to 75% of animal species going extinct, most notably among these are the non-avian dinosaurs. A major question in macroevolution is whether this extinction event influenced the rise of flowering plants (angiosperms). The fossil record suggests that the K-Pg event had a minor impact on the extinction rates of angiosperm lineages, yet the diversification of extant angiosperms was delayed and started after the K-Pg boundary. However, phylogenetic evidence for angiosperm extinction dynamics remains unexplored. Through the analyses of two angiosperm mega-phylogenies containing ~32,000-74,000 extant species, here we show relatively constant extinction rates throughout geological time and no evidence for a mass extinction at the K-Pg boundary. Despite uncertainty of earliest angiosperm branching times, their staggering diversity, and complex evolutionary dynamics, our preliminary analyses provide congruent results with the fossil record and support the macroevolutionary resilience of angiosperms to the K-Pg mass extinction.

evolutionary biology↗

bioRxiv2023

Laurasian legacies in the Gondwanan tree fern order Cyatheales

AO_SCPLOWBSTRACTC_SCPLOWPresent-day geographic and phylogentic patterns often reflect the Gondwana-Laurasia separation and subsequent history of continental drift. However, some lineages show non-overlapping fossil distributions relative to extant species and in some cases extant Gondwanan lineages have Laurasian extinct relatives. Here, I combined distribution data for 101 fossils and 442 extant species of tree ferns (Cyatheales) to reconstruct their biogeographic history over the last 220 million years. The time calibrated tree showed most tree ferns families originating during the Jurassic and the onset of crown group diversification beginning during the Cretaceous; a major shift in diversification rates occurred in the largest tree fern family (Cyatheaceae) that comprises ~90% of extant diversity in the group. Biogeographical reconstructions based on extant distributions alone supported a Gondwanan origin for the group; the most probable ancestral range encompassed Australasia and South America. Alternatively, incorporating fossil distribution data into reconstructions showed a Laurasian origin and a most probable ancestral range in Eurasia. These results evince the Laurasian legacies of the Cyatheales spanning the Triassic-Cretaceous, which otherwise remain hidden from biogeographic inferences. These results show that extant-only biogeographic analyses are limited when fossils distribution are more wide spread than in the present-day, highlighting the need to directly incorporate fossils into biogeographical analyses and improve the reliability of ancestral geographic range estimation.

evolutionary biology↗

bioRxiv2022

Integrating Fossil Flowers into the Angiosperm Phylogeny using a Total Evidence Approach

Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were sampled to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits.

paleontology↗

bioRxiv2021

Greenland's thaw pushes the biodiversity crisis

Anthropogenic greenhouse gas emissions have led to sustained global warming over the last decades1. This is already reshaping the distribution of biodiversity across the world and can lead to the occurrence of large-scale singular events, such as the melting of polar ice sheets2,3. The potential impacts of such a melting event on species persistence across taxonomic groups - in terms of magnitude and geographic extent - remain unexplored. Here we assess impacts on biodiversity of global warming and melting of Greenlands ice sheet on the distribution of 21,146 species of vascular plants and tetrapods across twelve megadiverse countries. We show that high global warming would lead to widespread reductions in species geographic ranges (median range loss, 35-78%), which are magnified (median range loss, 95-99%) with the added contribution of Greenlands melting and its potentially large impact on oceanic circulation and regional climate changes. Our models project a decline in the geographical extent of species hotspots across countries (median reduction, 48-95%) and a substantial alteration of species composition in the near future (mean temporal dissimilarity, 0.26-0.89). These results imply that, in addition to global warming, the influence of Greenlands melting can lead to the collapse of biodiversity across the globe, providing an added domino in its cascading effects.

ecology↗

bioRxiv2020

Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host dietary guild in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders. We found that gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity among gut microbiotas increased with host phylogenetic relatedness (r=0.73), yet this relationship was not consistent among seven closely related Bovid host species (r=0.21 NS). Within bovids, host dietary guild explained more of the variation in the gut microbiota than did host species. Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota, but these gut microbial communities could be furthered modified by host ecology, especially among closely related host species.

ecology↗

bioRxiv2019

Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize

Climate change is one of the most important threats to biodiversity and crop sustainability. The impact of climate change is often evaluated on the basis of expected changes in species geographical distributions. Genomic diversity, local adaptation, and migration are seldom integrated into projections of species responses to climate change. Here we predict that climate change will impact populations of two wild relatives of maize, the teosintes Zea mays ssp. mexicana and Z. mays ssp. parviglumis, by altering patterns of local adaptation and decreasing migration probabilities. These alterations appear to be geographically heterogeneous across populations, suggesting that the possible impacts of climate change will vary considerably among populations. This in spite that most populations exhibit high levels of genetic diversity and are predicted to lie within future suitable areas. The heterogeneous patterns of local adaptation uncovered in teosintes are also evident across maize landraces, which suggests that climate change may give way to future maladaptation of several landraces within currently cultivated areas, possibly leading to increased chances of production shocks under increased temperatures. The predicted alterations to habitat distribution, migration potential, and patterns of local adaptation in wild and cultivated maize, raises a red flag for the future of populations. This underscores the need for continued integration of agronomical practices, genomic data, and climate models to better understand the impacts of a rapidly changing climate on cultivated and wild species.

evolutionary biology↗