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Figure 2 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 2. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI sequence. OUTs with isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 4 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 4. Number of base changes of transition and tansversion vs corrected pairwide distance diagram for whole mitochondrial gene.

Figure 1 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 1. Simplified cicada timetree built by BEAST v1.X, applying a 1,534 bp in maximum COI sequence. Inserted figure: Base substitution rate (= ratemedian shown at each node; substitutions per siteper millionyear; s/s/ myr) vsage (= posterior age shown at each node) diagram. Red approximate curve with its formula was drawn by an Excel function, with the intersection for the curve = 0.0128 s/s/myr, the rate median shown on Tracer.

Figure 3 in Cicada minimum age tree: Cryptic speciation and exponentially increasing base substitution rates in recent geologic time

Figure 3. Cicada timetree built by BEAST v1.X, applying 1,534 bp COI and 874 bp 18S rRNA sequences. OUTswith isolate number: our own analyzed specimens shown in Table 1, and others: from GenBank/DDJB. In outgroup Hemiptera; #: analyzed family by Johnson et al. (2018); % analyzed family by Misof et al. (2014). Inserted figure: Base substitution rate (= rate median shown at each node; substitutions per site per million year; s/s/myr) vs age (= posterior age shown at each node) diagram. Red approximatecurve with its formulawas drawn by Excel function, with the intersection for the curve = 0.0114 s/s/myr, the rate median shown on Tracer. Note that this rate is a little slower than thatsolely of COI in Figures 1 and 2, reflecting slowerrate of 18S rRNAthan COI (see Osozawa et al. 2017a).

opencc-zeroDec 2021View details →

Data for: Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds

Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by conducting 2,339 field experiments to measure song discrimination for 175 taxon pairs of allopatric or parapatric New World passerine birds, and estimated recent speciation rates from a global molecular phylogeny of birds. Taxon pairs with high song discrimination in allopatry failed to regularly interbreed in parapatry, evidence that song discrimination is indeed an important reproductive barrier. However, evolutionary rates of song discrimination were not associated with recent speciation rates, and song discrimination evolves faster in suboscine passerines than their more species-rich sister clade, the oscines. Our findings support the long-held idea that song is a key premating reproductive barrier in birds, but show that faster evolution of this reproductive barrier between populations does not result in faster diversification betweeen species.

opencc-zeroOct 2022View details →

Speciation rates are unrelated to the formation of population structure in Malagasy Gemsnakes

Speciation rates vary substantially over the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary processes exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have shown both correlation and no correlation. No study has examined the relationship between speciation rates and population structure in a young group endemic to an island. We examine this correlation in 109 Gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar originating in the early Miocene, thus controlling for extinction associated with time and area. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of Gemsnakes. Rates of speciation show low variation, and population structure varying widely across species indicates that speciation rates and population structure disconnection are largely due to persistence of lineages not susceptible to extinction. Extinction can be due to many factors all of which can prevent long-term persistence of species. We discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.

publicJan 2023View details →

Data for: Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds

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publicJun 2023View details →

Speciation rates are unrelated to the formation of population structure in Malagasy Gemsnakes

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opencc-zeroFeb 2021View details →

Speciation rate and the diversity of fishes in freshwaters and the oceans

Aim: The number of fish taxa that occur exclusively in marine biomes is approximately equal to the number that occur in freshwater biomes. Both the geographic area and habitable volume of the marine realm are vastly greater than for Earth's freshwater ecosystems, suggesting that the density of marine species is proportionately much lower in the oceans. Because freshwater lineages are relatively recently derived from older marine lineages, this difference in species density suggests that speciation rates might be elevated in freshwater systems. I tested whether speciation rates differ systematically between freshwater and marine habitats. Location: Aquatic ecosystems worldwide Taxon: Ray-finned fishes (Actinopterygii) Methods: Marine-freshwater transitions were tabulated from literature survey and from ancestral state reconstruction. I tested for repeated effects of salinity transitions on speciation rate using formal state-dependent diversification methods (STRAPP, FiSSE). Using maximum likelihood, I then tested for absolute (unreplicated) differences in speciation rate between marine and freshwater lineages. Results: Ray-finned fishes have undergone numerous transitions from marine to freshwater systems, but the vast majority of freshwater species richness has resulted from a handful of freshwater colonization events. Speciation rates in freshwater lineages are substantially faster on average than those of marine lineages, but transitions to freshwaters do not lead to elevated rates of speciation in general. This paradox of state-dependent diversification arises because of the disproportionate effect of several freshwater clades with high species richness and fast rates of speciation. Main Conclusions: Transitions to freshwater do not cause faster rates of speciation, but freshwater ecosystems worldwide are dominated by several clades with relatively fast rates of speciation. There is no evidence that invasion of a novel habitat (freshwater) is generally sufficient to trigger a burst of speciation in colonizing lineages. These results raise an important conceptual problem for the interpretation of state-dependent diversification analyses.

opencc-byNov 2023View details →

An elevational phylogeographic diversity gradient in Neotropical birds is decoupled from speciation rates

A key question about macroevolutionary speciation rates is whether they are controlled by microevolutionary processes operating at the population level. For example, does spatial variation in population genetic differentiation underlie geographical gradients in speciation rates? Previous work suggests speciation rates increase with elevation in Neotropical birds, but underlying population-level gradients remain unexplored. Here, we characterize elevational phylogeographic diversity between montane and lowland birds in the megadiverse Andes-Amazonian system and assess its relationship to speciation rates to evaluate the link between population-level differentiation and species-level diversification. We aggregated and georeferenced nearly 7000 mitochondrial DNA sequences across 103 species or species complexes in the Andes and Amazonia and used these sequences to describe phylogeographic differentiation across both regions. Our results show increased levels of both discrete and continuous metrics of population structure in the Andean mountains compared to the Amazonian lowlands. However, higher levels of population differentiation do not predict higher rates of speciation in our dataset. Multiple potential factors may lead to our observed decoupling of initial population divergence and speciation rates, including the ephemerality of incipient species and the multifaceted nature of the speciation process, as well as methodological challenges associated with estimating rates of population differentiation and speciation.

publicOct 2024View details →

Data from: The metapopulation bridge to macroevolutionary speciation rates: a conceptual framework and empirical test

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publicSep 2020View details →

Speciation rate and the diversity of fishes in freshwaters and the oceans

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publicNov 2023View details →

An elevational phylogeographic diversity gradient in Neotropical birds is decoupled from speciation rates

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publicMar 2025View details →

Species richness and speciation rates for all terrestrial animals emerge from a synthesis of ecological theories

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publicJun 2021View details →

Differential speciation rates, colonization time, and niche conservatism affect community assembly across adjacent biogeographical regions

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opencc-zeroNov 2020View details →

Data from: Historical climatic instability predicts the inverse latitudinal pattern in speciation rate of modern mammalian biota

Evolutionary rate explanations for latitudinal diversity gradients predict faster speciation and diversification rates in richer, older, and more stable tropical regions (climatic stability hypothesis). Numerous modern lineages have emerged in high latitudes, however, suggesting that climatic oscillations can drive population divergence, at least among extratropical species (glacial refugia hypothesis). This conflicting evidence suggests that geographical patterns of evolutionary rates are more complicated than previously thought. Here, we reconstructed the complex evolutionary dynamics of a comprehensive dataset of modern mammals, both terrestrial and marine. We performed global and regional regression analyses to investigate how climatic instability could have indirectly influenced contemporary diversity gradients through its effects on evolutionary rates. In particular, we explored global and regional patterns of the relationships between species richness and assemblage-level evolutionary rates and between evolutionary rates and climatic instability. We found an inverse relationship between evolutionary rates and species richness, especially in the terrestrial domain. Additionally, climatic instability was strongly associated with the highest evolutionary rates at high terrestrial latitudes, supporting the glacial refugia hypothesis there. At low latitudes, evolutionary rates were unrelated to climatic stability. The inverse relationship between evolutionary rates and the modern latitudinal diversity gradient casts doubt on the idea that higher evolutionary rates in the tropics underlie the current diversity patterns of modern mammals. Alternatively, the longer time spans for diversity to accumulate in the older and more stable tropics (and not high diversification rates) may explain the latitudinal diversity gradient.

opencc-zeroDec 2012View details →

Data from: Evolution of a hotspot genus: geographic variation in speciation and extinction rates in Banksia (Proteaceae)

Background: Hotspots of angiosperm species richness and endemism in Mediterranean-climate regions are among the most striking, but least well-understood, geographic patterns of biodiversity. Recent studies have emphasized the importance of rapid diversification within hotspots, compared to non-hotspot regions, as a major contributor to these patterns. We constructed the first near-complete phylogeny of Banksia (Proteaceae) to test whether diversification rates have differed between lineages confined to the southwest Australian hotspot and those found throughout southern, eastern and northern Australia. We then tested for variation in diversification rates among the bioclimatic zones within the southwest hotspot itself. Results: Although Banksia species richness in the southwest is ten times that of the rest of the continent, we find little evidence for more rapid diversification in the southwest, although this result is inconclusive. However, we find firmer support for substantial rate variation within the southwest hotspot, with more rapid diversification in the semi-arid heaths and shrublands, compared to the high-rainfall forests. Most of the Banksia diversity of the southwest appears to be generated in the heaths and shrublands, with a high migration rate out of this zone boosting diversity of the adjacent forest zone. Conclusions: The geographic pattern of diversification in Banksia appears more complex than can be characterized by a simple hotspot vs. non-hotspot comparison, but in general, these findings contrast with the view that the high diversity of Mediterranean hotspots is underpinned by rapid radiations. Steady accumulation of species at unexceptional rates, but over long periods of time, may also have contributed substantially to the great botanical richness of these regions.

opencc-zeroDec 2017View details →

Data from: Rates of population differentiation and speciation are decoupled in sea snakes

Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographic population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16 species from two closely related clades that show contrasting diversification dynamics across northern Australia. Contrary to expectations from theory and several empirical studies, our results show that, at the geographic scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographic structure. In contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have three-fold slower speciation rates. Alternative factors, such as ecological specialisation, species duration, and geographic range size, may underlie rapid speciation in sea snakes.

opencc-zeroDec 2014View details →

Data from: Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae)

Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results:To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions:Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change.