Lake expansion elevates equilibrium diversity via increasing colonization

Hauffe, Torsten; Delicado, Diana; Etienne, Rampal S.; Valente, Luís

doi:10.1111/jbi.13914

Cited by 13 publications

(23 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Stronger competition and predation pressure in rivers may also inhibit speciation (Briggs 1966; Lowe-McConnell 1969; Seehausen 2015), such that fishes experience ecological release when they colonize lakes (Yoder et al 2010; Burress and Tan 2017). The observation that the present-day richness of many lakes appears to be below the lake’s carrying capacity (Barbour and Brown 1974; Doenz et al 2018; Hauffe et al 2020) supports the idea of high ecological opportunity in lakes.…”

Section: Discussionmentioning

confidence: 70%

Comparing diversification rates in lakes, rivers, and the sea

Miller

2020

Preprint

View full text Add to dashboard Cite

19The diversity of species inhabiting freshwater relative to marine habitats is striking, given that 20 freshwater habitats make up less than 1% of Earth's water. The most commonly proposed 21 mechanism for this pattern is that freshwater habitats are more fragmented than marine habitats, 22 resulting in increased opportunities for allopatric speciation in freshwater and thus increased 23 speciation rates relative to marine habitats. However, some authors suggest that speciation is 24 faster in sympatry than allopatry, as illustrated by lacustrine radiations such as African cichlids. 25 Sympatric speciation may be common in lakes, while allopatric speciation may be dominant in 26 rivers. If allopatric speciation is inherently slower than sympatric speciation, we might expect 27 differences in rates of speciation between lineages primarily confined to riverine versus 28 lacustrine habitats. These differences within freshwater habitats may be important to consider 29 when comparing diversification rates between freshwater and marine lineages. Here I compared 30 rates of speciation associated with ray-finned fishes in marine, riverine and lacustrine habitats. I 31 also used geographic range data to compare rates of speciation associated with allopatric and 32 sympatric speciation modes in freshwater fishes. I found that lakes had faster rates of speciation 33 than other aquatic habitats. However, most freshwater fish diversity arose through allopatric 34 speciation in rivers, despite their slower speciation rate. Speciation rates were more strongly 35 correlated with habitat (riverine or lacustrine) than present-day range overlap (allopatry or 36 sympatry). Surprisingly, riverine and marine habitats had similar rates of speciation. Models of 37 evolution suggest that lacustrine habitats are evolutionary unstable, and biased transition rates 38 explain the dearth of lacustrine species. Collectively, these results suggest that while allopatric 39 speciation is important for generating freshwater diversity, this mechanism may not be the cause 40 of faster speciation rates between freshwater and marine habitats. 41 3 KEY WORDS 42 43 Fishes, allopatric speciation, sympatric speciation, speciation rates, lacustrine radiations, 44 diversification 45 46 47 48 49 50

show abstract

Section: Discussionmentioning

confidence: 70%

Comparing diversification rates in lakes, rivers, and the sea

Miller

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…We identified instances where bug 2 was present: cases where there are re-colonisations of the same mainland species present on the island at the end of a simulation. The datasets with the highest proportion of islands with at least one re-colonisation were the Lake Biwa fishes (Hauffe et al 2020), Canary Island birds (part of the Macaronesian bird dataset from Valente et al 2017b) and Greater Antillean bats (Valente et al 2017a). This was to be expected, as these insular systems have high colonisation rates, and thus are likely to have more recolonisations.…”

Section: Re-analysis Of Previous Publications Using Daisiementioning

confidence: 84%

“…In a later version of DAISIE (Valente et al 2017b(Valente et al , 2018, the branching times of cladogenetic species resulting from recolonisations were passed on to the likelihood (in addition to the colonisation and any branching times of the initial colonist), but no information on re-colonisations whose descendant lineages had no branching times (those that have not speciated and those that were endemic singletons) was added. In the most recent version of DAISIE (Valente et al 2019(Valente et al , 2020Hauffe et al 2020), instead of passing the branching times of re-colonisations to the likelihood functions, the code instead considered any endemic species resulting from re-colonisations as missing unsampled species descending from that mainland species. These missing species were used in likelihood optimization as information on the diversity descending from that mainland species.…”

Section: Bug 2: Re-colonisation By the Same Mainland Species In Simulationsmentioning

confidence: 99%

“…Points a) and b) are not affected by the bugs because these analyses use the number of species (endemic and non-endemic) from the simulations, and the number of species is not affected by the bugs, as they only influence branching times (bug 1) and the way the likelihood function interprets the simulated data (bug 2). Therefore, here we assess only the error that could have occurred in c), the bootstrap analyses, which were carried out in Valente et al 2015Valente et al , 2017bValente et al , 2017aValente et al , 2018Valente et al , 2020Hauffe et al 2020. We re-ran analyses which could have been affected by the bugs, for selected publications. We first compiled the datasets simulated with DAISIE used in the main analyses of all previous published studies.…”

Section: Re-analysis Of Previous Publications Using Daisiementioning

confidence: 99%

“…Among other aims, DAISIE has been used to test for equilibrium dynamics in island birds (Valente et al 2015(Valente et al , 2017b, estimate time to recover from anthropogenic extinction in island bats and birds (Valente et al 2017a(Valente et al , 2019 and to test MacArthur & Wilson's theory of island biogeography on a global evolutionary scale in birds (Valente et al 2020). Bootstrap analyses of simulated datasets have shown that parameters can be estimated with high precision and little bias (Valente et al 2015(Valente et al , 2017a(Valente et al , 2017b(Valente et al , 2018(Valente et al , 2020Hauffe et al 2020).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Report of programming bugs in the DAISIE R package: consequences and correction

Valente¹,

Kristensen²,

Phillimore³

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

DAISIE (Dynamic Assembly of Islands through Speciation, Immigration and Extinction) is a framework for a dynamic stochastic model of island biogeography that can be used to estimate the rates of colonisation, speciation and extinction (CES rates) from phylogenetic trees of insular communities by maximum likelihood, and to simulate such data sets given a set of rates. The framework is available in an R package, and has been used in various studies to estimate CES rates for different insular systems based on molecular phylogenetic data. Simulations with estimated parameters have been used to explore the goodness-of-fit of the model and uncertainty in parameter estimates via bootstrap. We report two minor bugs in the simulation code that was used in the manuscripts published to date that have used DAISIE. One affects the branching times for some species that evolve via cladogenesis, the other affects cases when a single mainland species colonises an island multiple times. While these bugs do not have any effect on maximum likelihood estimation or model selection from empirical (non-simulated) data, they do have the potential to affect analyses based on simulated data. Here, we describe and fix the two bugs. To assess the magnitude of the error that they introduced, we re-run simulations and bootstrap analyses for the published cases that are most likely to be affected. We find that the differences between results generated with the new code and the original code are very minor, equivalent in magnitude to differences that would be obtained when using a different set of random numbers to generate the simulations. We conclude that the qualitative and to a large extent also the quantitative results of previous publications using DAISIE are robust to these bugs, and we provide a new version of the R package (v 3.2.0) with the corrected code.

show abstract

The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar

et al. 2023

Self Cite

View full text Add to dashboard Cite

Many of Madagascar’s unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar’s mammalian biodiversity under these rates, the “evolutionary return time” (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.

show abstract

Lake expansion elevates equilibrium diversity via increasing colonization

Cited by 13 publications

References 42 publications

Comparing diversification rates in lakes, rivers, and the sea

Comparing diversification rates in lakes, rivers, and the sea

Report of programming bugs in the DAISIE R package: consequences and correction

The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar

Contact Info

Product

Resources

About