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Natalie Cooper @nhcooper123.bsky.social · 23/06/2026

🧵 Excited to share my final PhD paper in Ecology Letters! A classic question in ecology is why some clades contain more species in local assemblages than others. We argue that part of the answer lies in the timing of speciation itself. doi.org/10.1111/ele....

Species richness patterns of exemplary clades. (a, c, e) Assemblage species richness (as a proportion of clade richness) of three exemplar avian families (Passerellidae, Dendrocolaptidae & Onychorhynchidae) showing low, intermediate and high levels of co-occurrence across the Americas. Pie charts show clade richness (decreasing in size in order) and the black lines point toward the grid cell of highest richness all in different locations in the Americas. (b) The relationship between clade richness and maximum local species richness (n = 40 families). An ordinary least squares regression estimates an intercept of −0.257 and slope of 0.761. (d) Distribution of maximum (proportional) local species richness across clades, showing large variation between clades.

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Reposted by Bouwe Reijenga

Anyone at #Evol2026 got any proposals?

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Speciation History Shapes Patterns of Assemblage Species Richness in Birds

Speciation creates biodiversity. But because species originate in isolation, the legacy of when speciation occurred can remain visible in local assemblages for millions of years. doi.org/10.1111/ele.... with Rampal Etienne, David Murrell & @alexpigot.bsky.social

doi.org

Speciation is the ultimate source of biodiversity. However, because most species arise in spatial isolation, how speciation shapes patterns of co-occurring species richness remains unclear. Here we e...

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More broadly, we suggest that patterns of assemblage richness should be evaluated against models that explicitly incorporate the geographic context of speciation. Ignoring these historical dynamics risks attributing historical signals to contemporary processes.

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This has implications for how we interpret patterns of biodiversity. Variation in local richness is often discussed in terms of contemporary ecological regulation. Our results (also focusing on lineage through time plots) show that speciation history can also leave a persistent signature.

Importantly, these mechanisms are not alternatives to history. They are ways in which ecological and evolutionary processes preserve the imprint of speciation through time (i.e. this is how "time-for-colonisation" differs from "time-for-speciation").

What generates such long delays? The answer is probably a combination of processes. Geographic barriers can persist long after speciation. Reproductive isolation may remain incomplete. And ecological differences may accumulate slowly.

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And, phylogenetic assemblage correlates of proportional richness are well predicted by the historical model, but not by non-historical alternatives.

Relationship between phylogenetic metrics and assemblage species richness for real bird clades and model simulations. Colours and rows denote the empirical relationships for all clades (orange) and relationships simulated under the ‘historical variable rate’ (yellow), ‘historical global rate’ (blue) colonisation rate and ‘non-historical’ (dark blue) model. For the simulation scenarios the mean proportion of co-occurring species across 2500 replicated simulations are plotted. Columns represent the five phylogenetic metrics capturing different aspects of clade evolutionary history: The crown age of the clade, phylogenetic imbalance (Colless' index), mean branch length of the extant species, ρ a measure of temporal change in diversification rates through time where positive (negative) values indicate an increase (decrease) and log-transformed clade species richness. Shaded areas represent 95% confidence intervals of fitted generalised linear models with quasibinomial error distribution and logit link function weighted for clade richness.

The proportion of co-occurring species correlates positively with clade age, shows no correlation with phylogenetic imbalance, a positive correlation with the mean age of species, no correlation with changes in diversification rate, and a slight negative relationship with clade species richness. The two historical models predict these patterns well, but the non-historical model predicts none.

Remarkably, much of the observed variation among bird families can be predicted from speciation history alone. A model with a single colonisation rate across clades reproduced broad patterns in assemblage richness.

Observed variation in assemblage richness of passerine clades compared to model predictions is shown between three model predictions: A historical model with variable colonisation rates between clades, a historical model with a global rate across clades, and a non-historical model in which colonisation is assumed to be near instantaneous after speciation. The three plots follow a standard structure where the proportion of co-occuring species across the clades is plotted between the model prediction and the empriical values, i.e. as per the figure legend: Assemblage richness is plotted as a % of the total number of species in each clade. Model predictions are shown for (a) the ‘historical variable rate’, (b) ‘historical global rate’, and (c) the ‘non-historical’ model. A 1:1 line shows where the empirical the predicted richness matches. Bars represent the 95% confidence intervals of predicted assemblage richness from 2500 replicate simulations of each model. Colours indicate if empirical assemblages fall within (blue) or outside (red) of model expectations. The results show that the historical variable rate model captures all clades, the historical global model predicts 21/25 and the non-historical model predicts 16/25 clades but shows very little variation between predicted proportional richness.

Older clades tend to contain a higher proportion of species in sympatry because their lineages have had longer to overcome the barriers separating them. Conversely, rapidly diversifying clades are often dominated by younger species that remain geographically separated.

As a consequence, assemblage richness thus depends not only on how many species a clade contains, but also on when those species originated.

We estimate that on average, species require ~8 million years to colonise the focal assemblage after speciation. This means that the transition to sympatry occurs at macroevolutionary time scales and roughly the same pace that new species are produced.

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We asked a simple question: How long does that transition take? To answer it, we combined phylogenetic data, species distributions and modify and apply DAMOCLES, a model of community assembly, across passerine bird families.

Visualisation of how speciation history influence assemblage richness. (a) Conceptualisation of the link between allopatric speciation, range expansion and assemblage richness. Upward-pointing arrows show timing of events (speciation, colonisation, and local extinction) on a hypothetical phylogentic tree that shows two speciation events. When speciation occurs the ancestral geographic range (red rectangle) is divided into two (yellow and green) and at most one species will be present (λ1) in the local assemblage (circle). Upon the second speciation event, the ancestor has gone locally extinct. Neither of the descendants (blue and purple) will therefore be present (λ0) in the local assemblage (open circles). The build-up of local assemblage thus depends on the colonisation of species (γ), as well as local extinction (μ), as species undergo expansion (green) or contractions (yellow) of their geographic range. (b) Two hypothetical clades, each with four species (similar design as above), with the top clade having older species on average than the bottom clade. Filled circles highlight the presence of a lineage in the local assemblage and arrows indicate colonisation events. For both clade the ancestor was present in the assemblage, but the dynamics of allopatric speciation and colonisation result in a higher assemblage richness at present in the clade with older species.

Most species originate in geographic isolation. As a result, speciation does not immediately add species to local assemblages. Before species can co-occur, they first have to make the transition from allopatry (or parapatry) to sympatry.