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opencc-zeroSep 2021View details →

Testing for adaptive radiation: a new approach applied to Madagascar frogs

<div class="WordSection1"> Adaptive radiation is a key topic at the intersection of ecology and evolutionary biology. Yet the definition and identification of adaptive radiation both remain contentious. Here, we introduce a new approach for identifying adaptive radiations which combines key aspects of two widely used definitions. Our approach compares evolutionary rates in morphology, performance, and diversification between the candidate radiation and other clades. We then apply this approach to a putative adaptive radiation of frogs from Madagascar (Mantellidae). We collect new data on morphology and performance from mantellid frogs and compare rates of diversification and multivariate evolution of size, shape, and performance between mantellids and other frogs. We find that mantellids potentially pass our test for accelerated rates of evolution for shape, but not for size, performance, or diversification. Our results demonstrate that clades can have accelerated phenotypic evolution without rapid diversification (dubbed "adaptive non-radiation"). We also highlight general issues in testing for adaptive radiation, including taxon sampling and the problem of including another adaptive radiation in the comparison clades. Finally, we suggest that similar tests should be conducted on other putative adaptive radiations on Madagascar, comparing their evolutionary rates to those of related clades outside Madagascar. Based on our results, we speculate that older Madagascar clades may show evolutionary patterns more similar to those on a continent than an island. </div>

opencc-zeroMar 2022View details →

Genomic changes underlying repeated niche shifts in an adaptive radiation

In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.

opencc-zeroApr 2022View details →

Genetic architecture of adaptive radiation across two trophic levels

Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20,000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology, and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed Quantitative Trait Locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.

opencc-zeroMay 2022View details →

Data from: Periodic environmental disturbance drives repeated ecomorphological diversification in an adaptive radiation of Antarctic fishes

The ecological theory of adaptive radiation has profoundly shaped our conceptualization of the rules that govern diversification. However, while many radiations follow classic early burst patterns of diversification as they fill ecological space, the longer-term fates of these radiations depend on many factors, such as climatic stability. In systems with periodic disturbances, species-rich clades can contain nested adaptive radiations of subclades with their own distinct diversification histories, and how adaptive radiation theory applies in these cases is less clear. Here, we investigated patterns of ecological and phenotypic diversification within two iterative adaptive radiations of cryonotothenioid fishes in Antarctica's Southern Ocean: crocodile icefishes and notoperches. For both clades, we observe evidence of repeated diversification into disparate regions of trait space between closely related taxa and into overlapping regions of trait space between distantly related taxa. We additionally find little evidence that patterns of ecological divergence are correlated with evolution of morphological disparity, suggesting that these axes of divergence may not be tightly linked. Finally, we reveal evidence of repeated convergence in sympatry that suggests niche complementarity. These findings reflect the dynamic history of Antarctic marine habitats, and may guide hypotheses of diversification dynamics in environments characterized by periodic disturbance.

opencc-zeroJul 2022View details →

Topographically distinct adaptive landscapes for teeth, skeletons, and size explain the adaptive radiation of Carnivora (Mammalia)

Models of adaptive radiation were originally developed to explain the early, rapid appearance of distinct modes of life within diversifying clades. Phylogenetic tests of this hypothesis have yielded limited support for temporally declining rates of phenotypic evolution across diverse clades, but the concept of an adaptive landscape that links form to fitness, while also crucial to these models, has received more limited attention. Using methods that assess the temporal accumulation of morphological variation and estimate the topography of the underlying adaptive landscape, I found evidence of an early partitioning of craniodental morphological variation in Carnivora (Mammalia) that occurs on an adaptive landscape with multiple peaks, consistent with classic ideas about adaptive radiation. Although strong support for this mode of adaptive radiation is present in traits related to diet, its signal is not present in body mass data or for traits related to locomotor behavior and substrate use. These findings suggest that adaptive radiations may occur along some axes of ecomorphological variation without leaving a signal in others and that their dynamics are more complex than simple univariate tests might suggest.

opencc-zeroApr 2024View details →

Replicated functional evolution in cichlid adaptive radiations

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Victoria, Malawi and Tanganyika) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than in Lake Tanganyika, despite being much older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting extremely rapid trait evolution at early stages, particularly in lake radiations. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.

Figs. 21–35 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Figs. 21–35 Shell aspects; left and center columns = frontal and apical view of female holotype; right column = frontal view of male paratype. (21–23) L. incycloseris sp. nov.; (24–26) L. inpleuractis sp.

Fig. 4 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Fig. 4 Transversional (solid circles) and transitional (open circles) rates in pairwise comparisons between ITS2 sequences (Table 1) plotted against rates of all substitutions; rates calculated using Paup 4.0b10 (Swofford 2002)

Fig. 48 Partial Cytochrome Oxidase I sequences for 14 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Fig. 48 Partial Cytochrome Oxidase I sequences for 14 species of Leptoconchus; for each species, the respective combination of underlined nucleotides is considered diagnostic

Fig. 5 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Fig. 5 Transversional (solid circles) and transitional (open circles) rates in pairwise comparisons between COI sequences plotted against rates of all substitutions; rates calculated using Paup 4.0b10 (Swofford 2002)

Fig. 2 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Fig. 2 Map of Indo-Pacific region from Red Sea to Papua New Guinea, with research localities 1–10 (1= Egypt, Red Sea, Marsa Nakari c. 350 km S of Hurghada; 2 =Oman; 3=Maldives, Ari Atoll, Vilamendhoo Island; 4=Thailand, Krabi, PhiPhi Islands; 5=Palau; 6 =

Fig. 1 in Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals

Fig. 1 Leptoconchus snails inside of mushroom corals. a Coral broken to reveal gastropod endoparasites; arrow indicates snail about 2 cm in diameter. b Detail of upper surface of coral; arrow indicates snail's only opening to the outside world, a siphon extended through a 2–3 mm hole. c Detail of underside of coral; arrows indicate male left

FIGURE 16 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 16. Eutherian morphotype EuE (UCMP specimen 218901, from locality V91065; right) in anterior (1) and posterior (2) stereopair views, and in lateral (3), medial (4), and distal (5) views.

FIGURE 19 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 19. Summary of humerus morphotypes and relative sizes in our study area in the Hell Creek and Tullock formations of eastern Montana. Multituberculate morphotypes are shown as black bars, metatherians as gray bars, and eutherians as white bars. Numbers within the bars indicate the sample size for each temporal bin. Morphotypes are arranged left to right according to increasing size (see text for specimen numbers, localities, and details; Appendices 7–8 for morphotype mean sizes). Gradients for MuF, EuC, and EuD indicate morphotypes were present in the timeaveraged Bug Creek Anthills assemblages, and the morphotype range may extend into the Pu1 and/or the Lancian. Pu2 assemblages are not known from our study area (hashmarks indicate resultant uncertainty of range-through morphotypes; Clemens 2015). The age model is based on previous geochronological work in this study area (Swisher et al., 1993; Renne et al., 2011, 2013; Wilson, 2014; Sprain et al. 2014); note the temporal axis is not to scale. Modified from Sprain et al. (2014). Abbreviations: Fm, Formation; NALMA, North American Land Mammal "age"; Pu1, early Puercan; Pu3, middle/late Puercan; queries (?) indicate specimens that are only tentatively attributed to that morphotype, see Methods.

FIGURE 9 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 9. Multituberculate morphotype MuF (UCMP specimen 127384, from locality V87001; left), in ventral (1) and dorsal (2) stereopair views, and in lateral (3), medial (4), and distal (5) views.

FIGURE 11 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 11. Metatherian morphotype MeA (UCMP specimen 152394, from locality V93169; left) in anterior (1) and posterior (2) stereopair views, and in lateral (3), medial (4), and distal (5) views.

FIGURE 6 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 6. Multituberculate morphotype MuC (UCMP specimen 153039, from locality V84193; left), in ventral (1) and dorsal (2) stereopair views, and in lateral (3), medial (4), and distal (5) views.

FIGURE 12 in Mammalian distal humerus fossils from eastern Montana, USA with implications for the Cretaceous-Paleogene mass extinction and the adaptive radiation of placentals

FIGURE 12. Eutherian morphotype EuA (UCMP specimen 153100, from locality V99438; left) in anterior (1) and posterior (2) stereopair views, and in lateral (3), medial (4), and distal (5) views. Specimen images are CT scan views, not photographs; see Methods for details. Rough patches inside the shaft and within the entepicondylar foramen are the result of sediment infilling, whereas other rough areas (i.e., supinator crest, medial entepicondyle, posterior articular surfaces) indicate specimen breakage.