Statistical comparison of DEC and DEC+J is identical to comparison of two ClaSSE submodels, and is therefore valid

Journal of Biogeography, Journal Year: 2022, Volume and Issue: 49(10), P. 1805 - 1824

Published: Aug. 9, 2022

Abstract Aim Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS , which implements several models a framework, allowing to be compared with standard likelihood‐based methods of statistical comparison. Ree and Sanmartín ( Journal Biogeography 45, 741–749, 2018) critiqued Dispersal–Extinction–Cladogenesis (DEC) modification it, DEC+J, adds process jump dispersal at speciation. DEC+J provides highly significant improvements fit on most (although not all) datasets. They claim that is statistically invalid for variety reasons. I analyse key claims made critique. Location Simulated data. Taxon Methods Likelihood calculations are checked between programs by‐hand calculations, summing likelihoods across all possible Model adequacy DEC versus simulation/inference experiment. Results Mistakes critique's example likelihood demonstrated. fits better datasets because inadequate situation when species have geographical ranges single areas; requires long residence times multi‐area ranges, these observed, does produce such data patterns, as prevails. More fundamentally, produces identical log‐likelihood differences two submodels ClaSSE where extinction rates fixed 0. Main Conclusions fails basic check understandable reasons, while not. As recommend valid comparison, according their own criteria.

Language: Английский

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Broad geographic dispersal is not a diversification driver for Emberizoidea

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 292(2039)

Published: Jan. 1, 2025

The movement of species to new geographical areas has been proposed be crucial for speciation. As such, dispersal regarded as a likely explanation the variation in richness among clades. Emberizoidea are highly diverse Oscine bird clade native New World that characterized their ubiquitous distribution both ecologically and geographically, making this group ideal test how biogeographical could promote To do so, we relate rates with speciation families using combination bioregionalization analysis, ancestral area reconstruction rate estimation methods. We found superfamily arose from widespread ancestor distributed over World, its range evolution being primarily driven by contraction main cladogenetic events occurring within bioregions. Moreover, demonstrate between bioregions showed no relationship rates, suggesting spaces is not driver group. Instead, individual promoted stability prove an important at broad spatial scales families.

Language: Английский

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Sixty-fourth Supplement to the American Ornithological Society’s Check-list of North American Birds

Ornithology, Journal Year: 2023, Volume and Issue: 140(3)

Published: June 6, 2023

Delichon lagopodum Siberian House-

Language: Английский

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Statistical comparison of DEC and DEC+J is identical to comparison of two ClaSSE submodels, and is therefore valid

Published: April 27, 2021

Statistical model comparison has become common in historical biogeography, enabled by the R package BioGeoBEARS, which implements several models a framework, allowing to be compared with standard likelihood-based methods of statistical comparison. Ree and Sanmartín (2018) critiqued Dispersal-Extinction-Cladogenesis (DEC) modification it, DEC+J, adds process jump dispersal at speciation. DEC+J provides highly significant improvements fit on most (although not all) datasets. They claim that is statistically invalid for variety reasons. However, analysis critique demonstrates number problems, ranging from mistakes example likelihood calculations through misunderstanding true causes advantage typical I show fits better datasets because DEC inadequate situation when species have geographic ranges single areas; requires long residence times multi-area ranges, these are observed, does produce such data patterns, as prevails. More fundamentally, demonstrate produces identical log-likelihood differences two submodels ClaSSE where extinction rates fixed 0. As recommend valid comparison, according their own criteria.

Language: Английский

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Evolutionary history of New World crakes (Aves: Rallidae) with emphasis on the tribe Laterallini

Zoologica Scripta, Journal Year: 2023, Volume and Issue: 52(4), P. 394 - 412

Published: April 7, 2023

Abstract New World crakes are intriguing, poorly known birds with cursorial cryptic habits; they belong to two unrelated tribes: Laterallini and Pardirallini. Recent genetic studies contributed the phylogenetic knowledge of these tribes, but a complete reconstruction is still missing. Here, we present most taxonomically dated gene‐based phylogeny crakes, an emphasis on Laterallini, including for first time sequences Coturnicops notatus , Laterallus levraudi L. jamaicensis tuerosi xenopterus . We used multilocus (mtDNA + nucDNA) analyses interpreted our results in light natural history group. Our novel show that: (1) sister leucopyrrhus ; (2) j. spilonota (3) C. clade that groups remaining black ( tuerosi, rogersi spilopterus ); (4) melanophaius conform recently diverged clade. Thus, indicate polyphyly this group, particularly and, time, some discrepancies previous stem from misidentified samples or Anurolimnas fasciatus. Finally, provide new preliminary insights into species limits taxa, specifically set stage integrative taxonomic assessments at generic level by incorporating (gene‐based) data.

Language: Английский

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Historical biogeography of North American killifishes (Cyprinodontiformes) recapitulates geographical history in the Gulf of México watershed

Zoological Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 202(2)

Published: Oct. 1, 2024

Abstract We analysed phylogenetic relationships within a major clade of Cyprinodontiformes (Teleostei) that includes five families North American killifishes. used DNA sequences from genes for 130 species, with four fossil calibrations and three secondary calibrations, to generate time-calibrated phylogeny. estimated diversification rates, ancestral areas, habitats each node. Findings were interpreted detailed biogeographical synthesis. The results indicate the arose in Eocene along Gulf México coast. speciation rate was uniform through time, except acceleration Cyprinodontidae after ~10.9 Mya. In other families, neither viviparity nor marine-to-freshwater transition associated accelerated speciation. Sea-level fluctuations might have created pump by stimulating cycles dispersal vicariance Diversification also included many cases inland immigration coastal ancestors. For upland lineages, ancient river drainages accord lineage distributions, including enigmatic disjunctions Goodeidae Fundulus. uplands occurred via barrier displacement alluvial or tectonically active landscapes. Killifishes display high environmental tolerance persist harsh, peripheral environments unsuitable most fishes. Hence, combination antiquity, adaptability, dynamic geography, persistence can explain living diversity New World

Language: Английский

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Phylogeny based on ultra-conserved elements clarifies the evolution of rails and allies (Ralloidea) and is the basis for a revised classification

Ornithology, Journal Year: 2021, Volume and Issue: 138(4)

Published: July 16, 2021

Abstract The rails (Family Rallidae) are the most diverse and widespread group in Gruiformes. Their extensive fossil history, global geographic distribution, tendency to rapidly evolve flightless species on islands make them an attractive subject of evolutionary studies, but rarity modern museum specimens so many rail has, until recently, limited scope molecular phylogenetics studies. As a result, classification remains one unsettled among major bird radiations. We extracted DNA from 82 species, including 27 study skins collected as long ago 1875, generated nucleotide sequences thousands homologous ultra-conserved elements (UCEs). Our phylogenetic analyses, using both concatenation multispecies coalescent approaches, resulted well-supported highly congruent phylogenies that resolve lineages reveal several currently recognized genera be polyphyletic. A fossil-calibrated time tree is well-resolved supports hypothesis split into 2 (subfamilies Himantornithinae Rallinae) ~34 mya, clade age estimates have wide confidence intervals. results, combined with results other recently published phylogenomics studies Gruiformes, form basis for proposed Rallidae recognizes 40 9 tribes.

Language: Английский

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Evolutionary and Biogeographical History of Penguins (Sphenisciformes): Review of the Dispersal Patterns and Adaptations in a Geologic and Paleoecological Context

Diversity, Journal Year: 2022, Volume and Issue: 14(4), P. 255 - 255

Published: March 30, 2022

Despite its current low diversity, the penguin clade (Sphenisciformes) is one of groups birds with most complete fossil record. Likewise, from evolutionary point view, it an interesting group given adaptations developed for marine life and extreme climatic occupation capacity that some species have shown. In present contribution, we reviewed integrated all geographical phylogenetic information available, together exhaustive updated review record, to establish propose a biogeographic scenario allows spatial-temporal reconstruction history Sphenisciformes, discussing our results those obtained by other authors. This allowed us understand how abiotic processes are responsible patterns diversity evidenced both in modern past lineages. Thus, using BioGeoBEARS methodology estimation, were able reconstruct biogeographical entire based on Bayesian phylogeny total evidence. As result, New Zealand origin Sphenisciformes during late Cretaceous early Paleocene indicated, subsequent dispersal expansion across Antarctica southern South America. During Eocene, there was remarkable diversification ecological niches Antarctica, probably associated more temperate conditions Southern Hemisphere. A wide morphological variability might at beginning Paleogene diversification. Oligocene, trends towards freezing generalized cooling Neogene, turnover led survival (in Zealand) ancestors crown Sphenisciform Later these expanded diversified Hemisphere, strongly linked oceanographic Miocene. Finally, should be noted Antarctic recolonization hostile occurred lineages Pleistocene, possibly due exaptations made possible repeated dispersion through cold waters Cenozoic, also allowing necessary live tundra glaciations.

Language: Английский

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Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases

Zoological Journal of the Linnean Society, Journal Year: 2022, Volume and Issue: 198(1), P. 47 - 71

Published: Oct. 20, 2022

Abstract Biomes are climatically and biotically distinctive macroecological units that formed over geological time scales. Their features consolidate them as ‘evolutionary scenarios’, with their own diversification dynamics. Under the concept of phylogenetic niche conservatism, we assessed, for first time, evolution biome occupation in birds. We aimed to analyse patterns adaptation different climatic regimes determinant factors colonization emerging biomes by clades from ancestral biomes. In this work, reconstructed history two birds (Galliformes Falconiformes) under an integrative perspective through a comprehensive review ecological, phylogenetic, palaeontological biogeographical evidence. Our findings both groups consistent scenario conservatism highlight importance changes climate during Miocene niches. particular, our results indicate high associated situated some extremes global gradient (evergreen tropical rainforest, steppe tundra) bird taxa. Finally, historical dynamics seasonal biomes, such deciduous woodlands savannas, appear have played preponderant role processes these lineages.

Language: Английский

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Whole-genome analysis reveals the diversification of Galapagos rail (Aves: Rallidae) and confirms the success of goat eradication programs

Journal of Heredity, Journal Year: 2024, Volume and Issue: 115(4), P. 444 - 457

Published: March 15, 2024

Similar to other insular birds around the world, Galapagos rail (Laterallus spilonota Gould, 1841) exhibits reduced flight capacity following its colonization of archipelago ~1.2 mya. Despite their short evolutionary history, rails have colonized seven different islands spanning entire width archipelago. were once common on with sufficiently high altitudes support shrubs in humid habitats. After humans introduced goats, this habitat was severely due overgrazing. Habitat loss devastated some populations, less than 50 individuals surviving, rendering genetic diversity a pressing conservation concern. Additionally, one enigma is reappearance island Pinta after they considered extirpated. Our approach investigate history and geographic distribution as well examine genome-wide effects historical population bottlenecks using 39 whole genomes across populations. We recovered an early divergence ancestors leading isolated populations second clade comprising rest islands, historically forming single landmass. Subsequently, separation landmass ~900 kya may led isolation Isabela more panmictic found Santa Cruz Santiago islands. that contain long runs homozygosity (>2 Mb) could be related introduction goats. Finally, our findings show modern eradication goats critical avoiding episodes inbreeding most

Language: Английский

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