Biology subjects

Donoghue, M. J.

Publications and source records attributed to Donoghue, M. J..

6 recordsLinked to original sources

bioRxiv2026

Phylogeny and Species Delimitation in Isoxylosteum, a Lonicera Clade Endemic to the Himalayan-Tibetan-Hengduan Region

The Himalayan-Tibetan-Hengduan (HTH) region is the richest biodiversity hotspot for high-elevation plants. However, owing to its remote and physically challenging topography as well as the trans-national nature of the region, many taxonomic problems in the area remain unresolved, particularly in the Himalaya. This, in turn, has impeded our understanding of the assembly of its extraordinary high-elevation flora. Here, we resolve phylogenetic relationships and delimit species in a distinctive clade of honeysuckles that is endemic to the HTH, the Isoxylosteum clade of Lonicera, using restriction-site associated DNA sequencing (RADseq) and morphological data. Five species complexes of Isoxylosteum have standardly been recognized. Three of these complexes are highly variable and have been divided into several varieties or species each. Phylogenetic, population structure, and morphological analyses of leaf and floral traits from samples collected across the range of the clade support the recognition of five species, including a species that has most often been recognized as a variety of L. rupicola (L. rupicola var. minuta). Instead, we find that it is sister to L. spinosa. This is surprising because the geographic range of L. minuta is contiguous with the other varieties of L. rupicola in the northern Hengduan region but widely separated from L. spinosa whose range lies mainly to the west of the Tibetan plateau. On close examination we find that several morphological and ecological traits also support a closer relation of L. minuta to L. spinosa. None of the other eight previously recognized varieties and species were supported. Floral traits showed high discriminatory power, correctly classifying 89% of samples to species. By comparison, leaf dimensions classified species with 59% accuracy. Our results identify diagnostic morphological apomorphies for each recognized species and major clade and provide a revised taxonomic framework for Isoxylosteum.

evolutionary biology↗

bioRxiv2025

Seventy-five Years of Systematic Biology: Looking Back, Moving Forward

AbstractWhat does "systematic biology" mean today, where has it been in the past, and where is it going? We explore these questions by considering five elements - collaboration, integration, discourse, infrastructure, and society - that we think have allowed systematic biology to adapt to change and sustain growth without losing its unique identity. In the spirit of celebrating the 75th anniversary of our flagship journal, we generated a comprehensive dataset for all Systematic Biology and Systematic Zoology articles that we could locate (N = 5,150) and used bibliometric and textual analyses to illustrate ways in which our field has transformed over time. We offer our humble opinions on how our community can ensure that systematic biologists inherit an enlightening, dynamic, and enduring future.

evolutionary biology↗

bioRxiv2020

EphA7 Isoforms Differentially Regulate Cortical Dendrite Development

The shape of a neuron reflects its cellular function and ultimately, how it operates in neural circuits. Dendrites receive and integrate incoming signals, including excitatory input onto dendritic spines, so understanding how dendritic development proceeds is fundamental for discerning neural function. Using loss- and gain-of-function paradigms, we previously demonstrated that EphA7 receptor signaling during cortical development impacts dendrites in two ways: restricting growth early and promoting spine formation later. Here, the molecular basis for this shift in EphA7 function is defined. Expression analyses reveal that both full-length (EphA7-FL) and truncated (EphA7-T1; lacking kinase domain) isoforms of EphA7 are expressed in the developing cortex, with peak expression of EphA7-FL overlapping with dendritic elaboration and highest levels of EphA7-T1 coinciding with spine formation. Overexpression studies in cultured neurons demonstrate that EphA7-FL inhibits both dendritic growth and spine formation, while EphA7-T1 increases spine density. Furthermore, signaling downstream of EphA7 varies during development; in vivo inhibition of kinase-dependent mTOR by rapamycin in EphA7 mutant neurons rescues the dendritic branching, but not the dendritic spine phenotypes. Finally, interaction and signaling modulation was examined. In cells in culture, direct interaction between EphA7-FL and EphA7-T1 is demonstrated which results in EphA7- T1-based modulation of EphA7-FL phosphorylation. In vivo, both isoforms are colocalized to cortical synapses and levels of phosphorylated EphA7-FL decrease as EphA7-T1 levels rise. Thus, the phenotypes of EphA7 during cortical dendrite development are explained by divergent functions of two variants of the receptor.

neuroscience↗

bioRxiv2019

Modeling phylogenetic biome shifts on a planet with a past

The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineages biome affinity and location relative to the spatiotemporal distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.

evolutionary biology↗

bioRxiv2019

Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum

Phylogeny, fossils, biogeography, and biome occupancy provide evidence that reflects the singular evolutionary history of a clade. Despite the connections that bind them together, these lines of evidence are most often studied separately, by first inferring a fossil-dated molecular phylogeny, then mapping on ancestral ranges and biomes inferred from extant species. Here we jointly model the evolution of biogeographic ranges, biome affinities, and molecular sequences, incorporating fossils to estimate a dated phylogeny for all of the 163 extant species of the woody plant clade Viburnum (Adoxaceae) that we currently recognize. Our analyses indicate that while the major Viburnum lineages evolved in the Eocene, the majority of extant species originated since the Miocene. Viburnum radiated first in Asia, in warm, broad-leaved evergreen (lucidophyllous) forests. Within Asia we infer several early shifts into more tropical forests, and multiple shifts into forests that experience prolonged freezing. From Asia we infer two early movements into the New World. These two lineages probably first occupied warm temperate forests and adapted later to spreading cold climates. One of these lineages (Porphyrotinus) occupied cloud forests and moved south through the mountains of the Neotropics. Several other movements into North America took place more recently, facilitated by prior adaptations to freezing in the Old World. We also infer four disjunctions between Asia and Europe: the Tinus lineage is the oldest and probably occupied warm forests when it spread, while the other three were more recent and in cold-adapted lineages. These results variously contradict published accounts, especially the view that Viburnum radiated initially in cold forests and, accordingly, maintained vessel elements with scalariform perforations. We explored how the location and biome assignments of fossils affected our inference of ancestral areas and biome states. Our results are sensitive to, but not entirely dependent upon, the inclusion of fossil biome data. We argue that it will be critical to take advantage of all available lines of evidence to decipher events in the distant past, and the joint estimation approach developed here provides cautious hope even when fossil evidence is limited.

evolutionary biology↗

bioRxiv2019

Diversification in evolutionary arenas -- assessment and synthesis

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography, and the metaphorical concepts of adaptive radiation and evolutionary stasis describe two opposing aspects causing variation in diversification rates. Here we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions and across spatial and temporal scales. Our framework describes the diversification rate (d) as a function of the abiotic environment (a), the biotic environment (b) and clade-specific phenotypes or traits (c); thus d[~]a,b,c. We refer to the four components (a-d) and their interactions collectively as the Evolutionary Arena. We outline analytical approaches to this framework and present a case study on conifers, for which we parameterise the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys. The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge.

evolutionary biology↗