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opencc-zeroNov 2023View details →

Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

opencc-zeroSep 2022View details →

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

Fig. 6 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 6. Percent similarity among bins averaged to 1 degree bins. A. om7 interval. B. om8 interval. C. om9 interval. The thicker the line, the greater the similarity between the two cells connected by the line.

Fig. 4 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 4. Correlations between richness per map and number of localities. A. om7 interval. B. om8 interval. C. om9 interval. The gap in the distribution of points for the om8 interval highlights the discontinuity between a group of maps with few taxa at a few localities and other maps with a large number of localities and high richness.

Fig. 5 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 5. Rarefaction curves for each interval, based on number of occurrences. The confidence envelope of the species richness for om9 departs significantly from those of om7 and om8 above 50 occurrences, but the significantly higher species−richness of om8 only becomes apparent at sample sizes of around 250 specimens, indicating that a few, rare taxa are boosting richness in the om8 interval.

Fig. 2 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 2. Distribution of Muschelkalk ammonoid localities used in this study plotted on a map of modern Germany. The overall geographic spread of localities does not change greatly over time.

Fig. 3 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 3. Correlations between richness per map and number of occurrences. A. om7 interval. B. om8 interval. C. om9 interval.

Fig. 1 in Using abundance data to assess the relative role of sampling biases and evolutionary radiations in Upper Muschelkalk ammonoids

Fig. 1. Chart of stratigraphic interval names and durations for the Muschelkalk of the Germanic Basin with ammonoid immigration events marked (simplified from Klug et al. 2005: fig. 1).

Figure 7 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 7. Cartoon to depict consensus relationships among Charadriiformes ('shorebirds') along with the holotype specimen of Morsoravis sedile, a new and exceptionally well-preserved fossil from Palaeocene–Lower Eocene deposits in Jutland, Denmark (1–2; G. J. Dyke, M. van Tuinen & D. M. Waterhouse, unpubl. data). The tree is based on various sources; see text for details. Scale bar = 10 mm.

Figure 6 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 6. Cartoon to depict consensus relationships among Galliformes ('landfowl') along with some selected fossil material (based on Dyke, 2003b and Dyke et al., 2003): A, hypothesis for the phylogenetic positions of the Lower Eocene (c. 55 Mya) taxa Gallinuloides and Paraortygoides; B, fossil elements of Paraortygoides from the Lower Eocene London Clay Formation of England (see Dyke & Gulas, 2002); C, holotype specimen of Gallinuloides wyomingensis from the Lower Eocene Green River Formation of Wyoming (North America) (Dyke, 2003b). Scale bar = 10 mm.

Figure 5 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 5. Cartoon depicting consensus phylogenetic relationships among Anseriformes ('waterfowl') (based on Livezey, 1997) (Presbyornithidae includes the taxa Presbyornis and Teviornis; see text for details) along with a selection of wellpreserved fossil taxa: A, holotype skull of Anatalavis oxfordi in lateral view from the Lower Eocene London Clay Formation (The Natural History Museum, London, Palaeontology Department Collections, BMNH PAL 5922) (see Dyke, 2001b); B, holotype coracoid of BMNH PAL 5922 in dorsal and medial views) (scale bars = 10 mm); C, holotype carpometacarpus of Teviornis gobiensis from the Late Cretaceous Nemegt Formation of Mongolia (Palaeontological Institute of the Russian Academy of Sciences, PIN 4499–1) in dorsal and ventral views (see Kurochkin et al., 2002). Scale bar = 10 mm.

Figure 4 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 4. Phylogenetic relationships within Palaeognathae including the well-represented fossil taxa Palaeotis and Lithornis (see text for details): A, new specimen of Lithornis from the Palaeocene-Lower Eocene Fur Formation of Denmark (Dankrae Collections of the Geologisk Museum, Copenhagen, DK 330) encased in cement stone nodule; B, skull of DK 330 acid prepared in oblique lateral view; C, palate of Lithornis in ventral view (ba, basitemporal plate; de, dentary; pa, palatine; pt, pterygoid; vo, vomer); D, the phylogenetic placement of Lithornis and Palaeotis inferred from cladistic analysis of osteological characters (see G. J. Dyke & M. van Tuinen, unpubl. data for details of analysis and matrices).

Figure 3 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 3. Seven possible definitions for the 'radiation of birds'. The true radiation of morphology observed in today's birds may have taken place as recently as points 6 or 7. Archaic ornithurines have not been found after the K–T boundary (black arrow). Although predicted from molecular clock analyses (dotted line; see text), little convincing evidence exists for neornithine fossils preceding the K–T boundary. The variation in number of species among traditional neornithine orders indicates that the 'radiation' was not equal across every major clade. Numbers refer to the following major evolutionary bird divergences: 1, diversification of Aves; 2, origin of Neornithes; 3, diversification of Neornithes; 4, origin of Neoaves; 5, origin of most orders (including 'Neoavian comb'); 6, diversification of most orders; 7, diversification of most families.

Figure 1 in The evolutionary radiation of modern birds (Neornithes): reconciling molecules, morphology and the fossil record

Figure 1. Summary cladogram to show the phylogenetic relationships at the base of Neornithes (based on Cracraft et al., 2004). Despite advances in the use of genetic data to resolve the phylogenetic relationships of birds, differences between data sets remain and have led to conflict with regard to the interrelationships of clades within Neoaves. The part of this tree to the right-hand side (relationships within Neoaves) has often been referred to as the 'neoavian comb' (Cracraft et al., 2004).

publicSep 2022View details →

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

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publicFeb 2025View details →

Data from: No support for solar radiation as a major evolutionary driver of malar stripes in falcons

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