Biology subjects

Zenil-Ferguson, R.

Publications and source records attributed to Zenil-Ferguson, R..

17 recordsLinked to original sources

bioRxiv2026

Morphological evolution and phylogeny are unlinked in Hawaiian Doryopteris (Cheilanthoideae: Pteridaceae)

Premise of the study: Doryopteris J.Sm. is a genus of dry-adapted ferns found widely across the southern hemisphere and the tropics. In the Hawaiian Islands, the genus is represented by four endemic species and one putative hybrid. Two of the endemic species (D. decora and D. decipiens) are widespread across all major islands, while two (D. angelica and D. takeuchii) are federally and state-listed endangered single-island endemics.We aimed to resolve the evolutionary relationships and biogeographic history of Hawaiian Doryopteris. Methods: We used a target-capture approach and the GoFlag 408 flagellate land plant probe set to sequence more than 400 nuclear loci for 40 Hawaiian and 29 non-Hawaiian individuals in Doryopteris and the related genera Lytoneuron and Ormopteris. After processing the sequences into alignments and single nucleotide polymorphism sites, we performed phylogenetic inference and population-level principal component analyses. Key results: We infer that Hawaiian Doryopteris are monophyletic and are nested within the pantropical species D. concolor. Within Hawai'i, clades and clusters of individuals correspond to geographical, geological, and climatological factors, more so than species identifications, with a few exceptions. We posit that Hawaiian Doryopteris represents an incipient radiation at the very earliest stages of divergence, and that budding speciation has led to non-monophyly of several taxa. Conclusions Our inference using genome-wide sequencing data sheds light on the complex evolutionary history of Hawaiian Doryopteris. Overall, the phylogeny of Hawaiian Doryopteris shows strong links with geographical, geological, and climatological processes and little with morphological evolution.

evolutionary biology↗

bioRxiv2026

Abiotic Factors and Competitive Exclusion Drive Assembly Patterns in Two Insular Gecko Adaptive Radiations Displaying Ecomorphological Convergence

Adaptive radiation theory posits that speciation in such lineages is largely driven by ecological opportunity in concurrent morphological expansion in response to niche availability. Here, we use a phylogenomic estimate of Australasian diplodactyloid geckos in combination with meristic and ecological data to infer patterns of ecological diversification, quantify signatures of stabilizing selection, and the factors driving speciation processes. Specifically, we focus on two relatively young but speciose and ecomorphologically diverse assemblages from the ancient islands of New Caledonia and New Zealand. Models accounting for stabilizing selection recover shifts in morphospace along many branches that also experienced shifts in ecological guild as inferred from ancestral state reconstructions. We find convergent evolution to be present between the two insular lineages as they independently transitioned to similar guilds from different ancestral ecologies. Community assembly is integral to understanding the dynamics of adaptive radiations and various studies focused on identifying if biotic or abiotic factors drive character suits and sympatry in diverse lineages. Bayesian and multiple regression analyses suggest that abiotic factors rather than interspecific competition dictates phenotypic divergence in both insular lineages. Rather, species seem to diverge phenotypically in allopatry and environmental factors, such as climate, in combination with competitive exclusion drive phenotypic overlap in sympatry. This study provides the first modern assessment of convergence for diplodactyloid geckos and provides robust evidence indicating that similar selective pressures have shaped morphological diversity in these disparate as well the factors affecting sympatry.

evolutionary biology↗

bioRxiv2026

Mutualistic microbes drive niche expansion yet constrain diversification

Mutualistic interactions are widely hypothesized to expand ecological niches and promote diversification, yet evidence for this relationship at macroevolutionary scales remains limited. Here, we investigate how fungal seed endophytes (Epichloe) influence niche breadth and diversification across over 100 species of the globally-distributed grass genus Poa. Combining global-scale climate, environmental, phylogenetic, and symbiosis data, we constructed species distribution models for suites of symbiotic and non-symbiotic plant species, then used a range of phylogenetic comparative methods to assess the influence of these symbionts on niche breadth, niche breadth evolution, and diversification. Endophyte-positive species had [~]1.4 times broader primary niche axes (most often associated with temperature tolerances), [~]2.5 times larger geographic ranges, and >30 times faster rates of niche breadth evolution than non-symbiotic species. Endophytic plants also had significantly drier climate centroids, consistent with endophyte-mediated drought tolerance, while simultaneously showing constraints along specific niche dimensions. Despite pronounced niche expansion, hidden state speciation and extinction models revealed two modes of diversification: endophytes decrease diversification rates in young lineages, and have a neutral effect in older lineages. Together, our results demonstrate that mutualists can enhance ecological flexibility while simultaneously constraining macroevolutionary outcomes, revealing a decoupling of niche expansion and diversification, and highlighting the complex role of symbiosis in shaping host evolutionary trajectories.

evolutionary biology↗

bioRxiv2024

Widespread evolution of poricidal flowers: A striking example of morphological convergence across flowering plants

The evolution of tube-like floral morphologies that control pollen release via small openings (functionally poricidal flowers) represents a taxonomically and geographically widespread instance of repeated and independent evolution of a functionally similar morphology. Poricidal flowers are also often closely associated with buzz pollination by bees. Yet we lack an updated angiosperm-wide survey of their phylogenetic distribution. We identify all known angiosperm genera containing poricidal flowers via a literature survey. We determined their phylogenetic distribution and minimum number of independent gains and losses via a species-level angiosperm-wide phylogeny. We estimated if evolution of poricidal flowers is associated with changes in speciation/extinction via diversification rate analyses. Poricidal flowers occur across 87 angiosperm families and 639 genera containing >28,000 species. At the species level, an average of 205 independent gains and 215 losses of poricidal flowers occurred. Angiosperm-wide analyses suggest an early burst in poricidal evolution, but no differences in net diversification (origination-extinction) between non-poricidal and poricidal taxa. Analyses for two focal families however indicate strong context-dependent effects of poricidal flowers on diversification. Poricidal evolution thus represents a large-scale example of convergent evolution in floral form, but effects on diversification appear to be strongly contingent on phylogenetic and ecological background.

evolutionary biology↗

bioRxiv2024

Traits related to pollination and mating result in diverse reproductive strategies in angiosperms

O_LIFlowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes are associated with floral and life-history traits that have evolved together, making it difficult to interpret correlations between traits. C_LIO_LIWe analysed variation in 21 traits related to flowers, pollination, mating, sexual systems and life history from 361 species representative of flowering plant diversity. C_LIO_LIOutcrossing was mainly found among long-lived, large-stature plants, but hermaphroditic outcrossers and dioecious species appeared as largely non-overlapping strategies in the trait space. Level of floral investment was the main difference between these strategies, with dioecious species having generally smaller, less rewarding flowers, a pattern that also occurred in biotically pollinated species. C_LIO_LIThis multi-trait study shows that pollination can be achieved in many, often contrasting, ways. Despite extensive variation in reproductive traits, dioecy stands out as being linked to floral traits primarily, while correlations with lifespan and dispersal traits appear spurious. We provide a conceptual framework based on lifespan, floral investment, and sexual separation that can be used to integrate pollination, reproduction and plant growth in future research on plant evolution and ecology. C_LI

evolutionary biology↗

bioRxiv2023

Conservation applications of ecological niche modeling: non-native ferns may compete with native ferns for limited suitable habitat in Hawaiian dryland ecosystems

PremiseCompetition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land-use change and competition from naturalized species in determining habitat availability. MethodsWe use fine-resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantify the degree to which naturalized ferns tend to occupy native species suitable area and map remaining available habitat given land-use change. ResultsOf all native species, Doryopteris angelica has the lowest percentage of occurrences of naturalized species in its suitable area while D. decora has the highest. However, all Doryopteris spp. had a higher percentage overlap--while Pellaea ternifolia had a lower percentage overlap--than expected by chance. D. decora and D. decipiens have the lowest proportions (< 20%) of suitable area covering native habitat. DiscussionAreas characterized by shared environmental preferences of native and naturalized ferns may also decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of placed-based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem.

ecology↗

bioRxiv2023

Detecting shifts in the mode of chromosomal speciation across the cosmopolitan plant lineage Carex

O_LIThe effects of single chromosome number change--dysploidy--mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one-fifth of all eukaryote lineages with holocentric chromosomes. Dysploidy effects on diversification have not been estimated because modeling chromosome numbers linked to diversification with heterogeneity along phylogenies is quantitatively challenging. C_LIO_LIWe propose a new state-dependent diversification model of chromosome evolution that links diversification rates to dysploidy rates considering heterogeneity and differentiates between anagenetic and cladogenetic changes. We apply this model to Carex (Cyperaceae), a cosmopolitan flowering plant clade with holocentric chromosomes. C_LIO_LIWe recover two distinct modes of chromosomal evolution and speciation in Carex. In one diversification mode, dysploidy occurs frequently and drives faster diversification rates. In the other mode, dysploidy is rare and diversification is driven by hidden, unmeasured factors. When we use a model that excludes hidden states, we mistakenly infer a strong, uniform positive effect of dysploidy on diversification, showing that standard models may lead to confident but incorrect conclusions about diversification. C_LIO_LIThis study demonstrates that dysploidy can have a significant role in large plant clade speciation despite the presence of other unmeasured factors that simultaneously affect diversification. C_LI

evolutionary biology↗

bioRxiv2023

Not one, but multiple radiations underlie the biodiversity of Madagascar's endangered lemurs

Lemurs are often cited as an example of adaptive radiation. Since colonizing Madagascar, more than 100 extant lemur species have evolved to fill a variety of ecological niches on the island. However, recent work suggests that lemurs do not exhibit one of the hallmarks of other adaptive radiations: explosive speciation rates that decline over time. Thus, characterizing the tempo and mode of evolution in lemurs can help us understand alternative ways that hyperdiverse clades arise over time, which might differ from traditional models. We explore the evolution of lemurs using a phylogenomic dataset with broad taxonomic sampling that includes the lemurs sister group, the lorisiforms of Asia and continental Africa. Our analyses reveal multiple bursts of diversification (without subsequent declines) that explain much of todays lemur diversity. We also find higher rates of speciation in Madagascars lemurs compared to lorisiforms, and we demonstrate that the lemur clades with exceptionally high diversification rates have higher rates of genomic introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but a driving force for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species being threatened with extinction, this phylogenomic study offers a new perspective for explaining Madagascars exceptional primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions.

evolutionary biology↗

bioRxiv2022

Over two orders of magnitude difference in rate of single chromosome loss among sundew (Drosera L., Droseraceae) lineages

Chromosome number change is a driver of speciation in eukaryotic organisms. Carnivorous sundews, the plant genus Drosera L., exhibit single chromosome number variation among and within species, especially in the Australian Drosera subg. Ergaleium D.C., potentially linked to the presence of holocentromeres. We reviewed literature, verified chromosome counts, and using an rbcL chronogram, tested alternate models where the gain, loss, and doubling rates (+1, -1, x2) were the same or different between D. subg. Ergaleium and the other subgenera. Ancestral chromosome number estimations were performed, and the distributions of self-compatibility and genome size were visualized across the genus. The best model for chromosome evolution had equal rates of polyploidy (0.014 per million years; Myr) but higher rates of single chromosome number gain (0.19 and 0.027 per Myr) and loss (0.23 and 0.00059 per Myr) in D. subg. Ergaleium compared to the other subgenera. We found no evidence for differences in single chromosome evolution to be due to differences in diploidization after polyploidy or to holocentromeres as had been proposed. This study highlights the complexity of factors influencing rates of chromosome number evolution.

evolutionary biology↗

bioRxiv2022

The rapid radiation of Bomarea (Alstroemeriaceae: Liliales), driven by the rise of the Andes

Complex geological events such as mountain uplift affect how, when, and where species originate and go extinct, but measuring those effects is a longstanding challenge. The Andes arose through a series of complex geological processes over the past c. 100 million years, impacting the evolution of regional biota by creating barriers to gene flow, opening up new habitats, and changing local climate patterns. Bomarea are tropical geophytes with ranges extending from central Mexico to central Chile. Of the roughly 120 species of Bomarea, most are found in the Andes, and previous work has suggested that Bomarea diversified rapidly and recently, corresponding with the uplift of the Andes. While many Bomarea species occur over small, isolated ranges, Bomarea edulis occurs significantly beyond the ranges of any other Bomarea species (from central Mexico to northern Argentina) and is thought to have potentially humanmediated dispersal, due to its status as a pre-Columbian food plant. To untangle the potential drivers of diversification and biogeographic history in Bomarea, we used a target-capture approach to sequence nuclear loci of 174 accessions of 124 species, including 16 outgroup species from across the family (Alstroemeriaceae). We included 43 individuals of B. edulis from across its range to assess species monophyly and identify infraspecific phylogeographic patterns. We model biogeographic range evolution in Bomarea and test if Andean orogeny has impacted its diversification. We find that Bomarea originated in the central Andes during the mid-Miocene, then spread north, following the trajectory of major mountain uplift events. Most observed speciation events occurred during the Pleistocene, while global climate cooled and oscillated and the northern Andes achieved their current form. Furthermore, we find that Andean lineages diversified faster than their non-Andean relatives. These results demonstrate a clear macroevolutionary signal of Andean orogeny on this neotropical radiation.

evolutionary biology↗

bioRxiv2022

Trait-dependent diversification in angiosperms: patterns, models and data

Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species ecology, demography and genetics.

evolutionary biology↗

bioRxiv2021

Unearthing modes of climatic adaptation in underground storage organs across Liliales

Testing adaptive hypotheses about how continuous traits evolve in association with developmentally-structured discrete traits, while accounting for the confounding influence of other, hidden, evolutionary forces, remains a challenge in evolutionary biology. For example, geophytes are herbaceous plants--with underground buds--that use underground storage organs (USOs) to survive extended periods of unfavorable conditions. Such plants have evolved multiple times independently across all major vascular plant lineages. Even within closely related lineages, however, geophytes show impressive variation in the morphological modifications and structures (i.e., "types" of USOs) that allow them to survive underground. Despite the developmental and structural complexity of USOs, the prevailing hypothesis is that they represent convergent evolutionary "solutions" to a common ecological problem, though some recent research has drawn this conclusion into question. We extend existing phylogenetic comparative methods to test for links between the hierarchical discrete morphological traits associated with USOs and adaptation to environmental variables, using a phylogeny of 621 species in Liliales. We found that plants with different USO type do not differ in climatic niche more than expected by chance, with the exception of root morphology, where modified roots are associated with lower temperature seasonality. These findings suggest that root tubers may reflect adaptations to different climatic conditions than those represented by other types of USOs. Thus, the tissue type and developmental origin of the USO structure may influence the way it mediates ecological relationships, which draws into question the appropriateness of ascribing broad ecological patterns uniformly across geophytic taxa. This work provides a new framework for testing adaptive hypotheses and for linking ecological patterns across morphologically varying taxa while accounting for developmental (non-independent) relationships in morphological data. [Macroevolution, geophytes, climatic niche evolution, imperfect correspondence]

evolutionary biology↗

bioRxiv2021

The Evolution of Nest Site Specialization and its Macroevolutionary Consequences in Passerine Birds

A long-standing hypothesis in evolutionary biology is that the evolution of resource specialization can lead to an evolutionary dead end, where specialists have low diversification rates and limited ability to evolve into generalists. In recent years, advances in comparative methods investigating trait-based differences associated with diversification have enabled more robust tests of this idea and have found mixed support. We test the evolutionary dead end hypothesis by estimating net diversification rate differences associated with nest type specialization among 3,224 species of passerine birds. In particular, we test whether the adoption of hole-nesting, a nest type specialization that decreases predation, results in reduced diversification rates relative to nesting outside of holes. Further, we examine whether evolutionary transitions to the specialist hole-nesting state have been more frequent than transitions out of hole-nesting. Using diversification models that accounted for background rate heterogeneity and different extinction rate scenarios, we found that hole-nesting specialization was not associated with diversification rate differences. Furthermore, contrary to the assumption that specialists rarely evolve into generalists, we found that transitions out of hole-nesting occur more frequently than transitions into hole-nesting. These results suggest that interspecific competition may limit adoption of hole-nesting, but that such competition does not result in limited diversification of hole-nesters. In conjunction with other recent studies using robust comparative methods, our results add to growing evidence that evolutionary dead ends are not a typical outcome of resource specialization.

evolutionary biology↗

bioRxiv2021

Pulled Diversification Rates, Lineage-Through-Time Plots and Modern Macroevolutionary Modelling

AO_SCPLOWBSTRACTC_SCPLOWEstimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has lead to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we demonstrate the characteristics of newly-proposed "pulled rates" and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

evolutionary biology↗

bioRxiv2020

Specific breeding system and ploidy interactions increase niche adaptability in potatoes

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for sustainability. Niches of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention, however, such information has not been analyzed in combination with phylogenetic histories, genomic composition and reproductive systems. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate niches inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche divergence through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate.

ecology↗

bioRxiv2019

INTERACTION BETWEEN PLOIDY, BREEDING SYSTEM, AND LINEAGE DIVERSIFICATION

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

evolutionary biology↗

bioRxiv2017

Rethinking phylogenetic comparative methods

As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but has led us to develop methods that are susceptible to the very thing we sought to build defenses against -- unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events is indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term \"phylogenetic natural history\") to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypotheses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.

evolutionary biology↗