Evolution in the South American ‘Lost World’: insights from multilocus phylogeography of stefanias (Anura, Hemiphractidae, <i>Stefania</i>)

Kok, Philippe J. R.; Russo, Valerio Giovanni; Ratz, Sebastian; Means, D. Bruce; MacCulloch, Ross D.; Lathrop, Amy; Aubret, Fabien; Bossuyt, Franky

doi:10.1111/jbi.12860

Cited by 37 publications

(65 citation statements)

References 43 publications

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“…Based on a rate of mitochondrial sequence divergence of approximately 1% per million years, this would provide an age estimate of 1.5 Myr for the divergence of upland G. carapo from nearby lowland populations. This suggests that G. carapo is a more recent addition to the fauna of upland Guiana, in line with ages of some amphibians found on tepui summits (Kok et al, 2012(Kok et al, , 2016. Based on these results, we suggest that upland Guianas ichthyofauna consist of a mosaic of relatively ancient endemics combined with more recent arrivals like G. carapo.…”

Section: Biogeographical Relationships Between Upland and Lowland Gsupporting

confidence: 74%

Fish biogeography in the “Lost World” of the Guiana Shield: Phylogeography of the weakly electric knifefish Gymnotus carapo (Teleostei: Gymnotidae)

Lehmberg

Elbassiouny

Bloom

et al. 2018

Journal of Biogeography

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Aim The Guiana Shield region exhibits extraordinary topography that includes sheer, flat‐topped mountains (tepuis) atop an upland platform. Rivers of the eastern Pakaraima Mountains descend to Atlantic coastal lowlands, often traversing spectacular rapids and waterfalls. For fish species distributed in both uplands and lowlands, it is unclear whether these rapids and waterfalls present population or biogeographical boundaries. We sought to test this using the geographically widespread banded‐electric knifefish (Gymnotus carapo) as a model. Location The Guiana Shield region of South America. Methods We sampled 60 Gymnotus carapo specimens from the Guiana Shield region, and 75 G. carapo and closely related species from other parts of South America. We sequenced the mitochondrial cytochrome b gene and an intron from the nuclear S7 ribosomal protein gene, and used maximum likelihood and Bayesian tree‐building approaches to generate phylogenetic trees of haplotypes. Results Haplotype sharing is minimal between populations separated by elevational barriers. We found evidence for two main haplotype clades in the Guiana Shield: one distributed in Atlantic coastal regions that includes most lowland samples, and one inland that includes most upland samples. Inland Guiana samples are more closely related to samples from the Amazon basin than to those of Atlantic coastal regions. A single sample from Tafelberg tepui in Suriname was most closely related to the Atlantic coastal lineages. Main conclusions Riverine barriers that result from steep elevational gradients in the Guiana Shield inhibit gene flow between uplands and lowlands, even for a widely distributed species. Biogeographical relationships of Guiana Shield G. carapo are complex, with most upland lineages showing affinities to the Amazon basin, rather than to nearby lowland drainages of the Atlantic coast.

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Section: Biogeographical Relationships Between Upland and Lowland Gsupporting

confidence: 74%

Fish biogeography in the “Lost World” of the Guiana Shield: Phylogeography of the weakly electric knifefish Gymnotus carapo (Teleostei: Gymnotidae)

Lehmberg

Elbassiouny

Bloom

et al. 2018

Journal of Biogeography

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“…(), Skeels and Cardillo () and Kok et al. (). The application of model selection in these cases appears to be motivated by the same reasons one selects among models of nucleotide evolution for phylogeny reconstruction: that the best‐fit model is necessary for accurate inferences.…”

Section: Introductionmentioning

confidence: 99%

“…For simple inference of ancestral ranges on a fixed phylogeny, a DEC-based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models. et al (2016), Givnish et al (2016), Skeels and Cardillo (2017) and Kok et al (2017). The application of model selection in these cases appears to be motivated by the same reasons one selects among models of nucleotide evolution for phylogeny reconstruction: that the best-fit model is necessary for accurate inferences.This trend is unfortunate for two reasons: first, DEC+J is a poor model of founder event speciation, and second, unlike nucleotide models, DEC and DEC+J cannot be compared using standard…”

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confidence: 99%

Conceptual and statistical problems with the DEC+J model of founder‐event speciation and its comparison with DEC via model selection

Ree

Sanmartín

2018

Journal of Biogeography

552

364

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Phylogenetic studies of geographic range evolution are increasingly using statistical model selection methods to choose among variants of the dispersal‐extinction‐cladogenesis (DEC) model, especially between DEC and DEC+J, a variant that emphasizes “jump dispersal,” or founder‐event speciation, as a type of cladogenetic range inheritance scenario. Unfortunately, DEC+J is a poor model of founder‐event speciation, and statistical comparisons of its likelihood with DEC are inappropriate. DEC and DEC+J share a conceptual flaw: cladogenetic events of range inheritance at ancestral nodes, unlike anagenetic events of dispersal and local extinction along branches, are not modelled as being probabilistic with respect to time. Ignoring this probability factor artificially inflates the contribution of cladogenetic events to the likelihood, and leads to underestimates of anagenetic, time‐dependent range evolution. The flaw is exacerbated in DEC+J because not only is jump dispersal allowed, expanding the set of cladogenetic events, its probability relative to non‐jump events is assigned a free parameter, j, that when maximized precludes the possibility of non‐jump events at ancestral nodes. DEC+J thus parameterizes the mode of speciation, but like DEC, it does not parameterize the rate of speciation. This inconsistency has undesirable consequences, such as a greater tendency towards degenerate inferences in which the data are explained entirely by cladogenetic events (at which point branch lengths become irrelevant, with estimated anagenetic rates of 0). Inferences with DEC+J can in some cases depart dramatically from intuition, e.g. when highly unparsimonious numbers of jump dispersal events are required solely because j is maximized. Statistical comparison with DEC is inappropriate because a higher DEC+J likelihood does not reflect a more close approximation of the “true” model of range evolution, which surely must include time‐dependent processes; instead, it is simply due to more weight being allocated (via j) to jump dispersal events whose time‐dependent probabilities are ignored. In testing hypotheses about the geographic mode of speciation, jump dispersal can and should instead be modelled using existing frameworks for state‐dependent lineage diversification in continuous time, taking appropriate cautions against Type I errors associated with such methods. For simple inference of ancestral ranges on a fixed phylogeny, a DEC‐based model may be defensible if statistical model selection is not used to justify the choice, and it is understood that inferences about cladogenetic range inheritance lack any relation to time, normally a fundamental axis of evolutionary models.

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“…The application of molecular genetics and its integration into taxonomic research on anurans has revealed a tremendous amount of hidden diversity, particularly in the most species-rich tropical regions (e.g., Köhler et al 2005a;Stuart et al 2006;Fouquet et al 2007;Crawford et al 2010Crawford et al , 2013Funk et al 2012;Barej et al 2015;Kok et al 2017). A great part of this uncovered diversity is considered to represent different species (Fouquet et al 2007;Vieites et al 2009).…”

Section: Dna Barcodingmentioning

confidence: 99%

The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

Köhler

Jansen

Rodríguez³

et al. 2017

Zootaxa

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479

410

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Vocalizations of anuran amphibians have received much attention in studies of behavioral ecology and physiology, but also provide informative characters for identifying and delimiting species. We here review the terminology and variation of frog calls from a perspective of integrative taxonomy, and provide hands-on protocols for recording, analyzing, comparing, interpreting and describing these sounds. Our focus is on advertisement calls, which serve as premating isolation mechanisms and, therefore, convey important taxonomic information. We provide recommendations for terminology of frog vocalizations, with call, note and pulse being the fundamental subunits to be used in descriptions and comparisons. However, due to the complexity and diversity of these signals, an unequivocal application of the terms call and note can be challenging. We therefore provide two coherent concepts that either follow a note-centered approach (defining uninterrupted units of sound as notes, and their entirety as call) or a call-centered approach (defining uninterrupted units as call whenever they are separated by long silent intervals) in terminology. Based on surveys of literature, we show that numerous call traits can be highly variable within and between individuals of one species. Despite idiosyncrasies of species and higher taxa, the duration of calls or notes, pulse rate within notes, and number of pulses per note appear to be more static within individuals and somewhat less affected by temperature. Therefore, these variables might often be preferable as taxonomic characters over call rate or note rate, which are heavily influenced by various factors. Dominant frequency is also comparatively static and only weakly affected by temperature, but depends strongly on body size. As with other taxonomic characters, strong call divergence is typically indicative of species-level differences, whereas call similarities of two populations are no evidence for them being conspecific. Taxonomic conclusions can especially be drawn when the general advertisement call structure of two candidate species is radically different and qualitative call differences are thus observed. On the other hand, quantitative differences in call traits might substantially vary within and among conspecific populations, and require careful evaluation and analysis. We provide guidelines for the taxonomic interpretation of advertisement call differences in sympatric and allopatric situations, and emphasize the need for an integrative use of multiple datasets (bio-acoustics, morphology, genetics), particularly for allopatric scenarios. We show that small-sized frogs often emit calls with frequency components in the ultrasound spectrum, although it is unlikely that these high frequencies are of biological relevance for the majority of them, and we illustrate that detection of upper harmonics depends also on recording distance because higher frequencies are attenuated more strongly. Bioacoustics remains a prime approach in integrative taxonomy of anurans if uncertainty due to possible intraspecific variation and technical artifacts is adequately considered and acknowledged.

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Evolution in the South American ‘Lost World’: insights from multilocus phylogeography of stefanias (Anura, Hemiphractidae, Stefania)

Cited by 37 publications

References 43 publications

Fish biogeography in the “Lost World” of the Guiana Shield: Phylogeography of the weakly electric knifefish Gymnotus carapo (Teleostei: Gymnotidae)

Fish biogeography in the “Lost World” of the Guiana Shield: Phylogeography of the weakly electric knifefish Gymnotus carapo (Teleostei: Gymnotidae)

Conceptual and statistical problems with the DEC+J model of founder‐event speciation and its comparison with DEC via model selection

The use of bioacoustics in anuran taxonomy: theory, terminology, methods and recommendations for best practice

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